Re: [ccp4bb] Determining space group

[Eleanor Dodson]

Yes - I wondered how much data can be extracted from each crystal..
Eleanor

On Fri, 22 Jul 2022 at 19:23, Kay Diederichs 
wrote:

> Hi Eleanor,
>
> yes, for sufficiently complete datasets a reference dataset is enough.
> But in serial crystallography, there is typically little overlap between
> individual data sets. And the data quality is often low.
>
> In my posting I forgot to say that CrystFEL also has a facility to
> overcome indexing ambiguity.
>
> Best wishes,
> Kay
>
> On Fri, 22 Jul 2022 19:02:19 +0100, Eleanor Dodson <
> eleanor.dod...@york.ac.uk> wrote:
>
> >Surely once you have indexed one crystal, you can use the facility to
> check
> >the next ones indexing against the reference - aka pointless?
> >
> >On Fri, 22 Jul 2022 at 16:20, Kay Diederichs <
> kay.diederi...@uni-konstanz.de>
> >wrote:
> >
> >> Hi Monika,
> >>
> >> in June we had a summer school at MaxIV, and one of the topics was
> serial
> >> crystallography - with lectures and tutorials. Maybe you can talk to the
> >> people who attended the course, and the organizers, Ana Gonzalez and
> Thomas
> >> Ursby, and ask them for help.
> >>
> >> It is more difficult to determine the spacegroup in serial
> >> crystallography, compared to conventional crystallography. This is
> because
> >> there are several spacegroups that have an indexing ambiguity
> >> (non-equivalent ways to index a given diffraction pattern), e.g. P3, P4,
> >> P6, P321, ..., altogether 38 out of the 65 Sohncke groups . So just
> merging
> >> the data blindly may give you "computationally twinned" data. Take a
> look
> >> at doi:10.1107/S1399004713025431 .
> >>
> >> If you use XDS/XSCALE, you can analyze the scaled but unmerged data with
> >> xscale_isocluster .
> >> If you use DIALS, you could use dials.cosym for this purpose.
> >>
> >> Best wishes,
> >> Kay
> >>
> >> On Fri, 22 Jul 2022 09:51:14 +, Monika Bjelcic <
> >> monika.bjel...@maxiv.lu.se> wrote:
> >>
> >> >Hi,
> >> >
> >> >I’m hoping someone can help me how to determine a space group from my
> >> collection.
> >> >I did serial crystallography on a crystal that doesn’t have a cryo
> >> structure. I was able to determine the Point group but for the next step
> >> I’m stuck.
> >> >
> >> >Kind regards,
> >> >Monika Bjelcic
> >> >PhD student at BioMAX
> >> >[cid:image001.jpg@01D3B796.B7E175A0]
> >> >MAX IV Laboratory
> >> >Lund University
> >> >Postal address: P.O. Box 118, SE-221 00 Lund, Sweden
> >> >Visiting address: Fotongatan 2, 224 84 Lund, Sweden
> >> >Mobile:  +46-761357994
> >> >
> >> >
> >>
> >
> >> >
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> >> >
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Re: [ccp4bb] Determining space group

[Kay Diederichs]

Hi Eleanor,

yes, for sufficiently complete datasets a reference dataset is enough.
But in serial crystallography, there is typically little overlap between 
individual data sets. And the data quality is often low.

In my posting I forgot to say that CrystFEL also has a facility to overcome 
indexing ambiguity.

Best wishes,
Kay

On Fri, 22 Jul 2022 19:02:19 +0100, Eleanor Dodson  
wrote:

>Surely once you have indexed one crystal, you can use the facility to check
>the next ones indexing against the reference - aka pointless?
>
>On Fri, 22 Jul 2022 at 16:20, Kay Diederichs 
>wrote:
>
>> Hi Monika,
>>
>> in June we had a summer school at MaxIV, and one of the topics was serial
>> crystallography - with lectures and tutorials. Maybe you can talk to the
>> people who attended the course, and the organizers, Ana Gonzalez and Thomas
>> Ursby, and ask them for help.
>>
>> It is more difficult to determine the spacegroup in serial
>> crystallography, compared to conventional crystallography. This is because
>> there are several spacegroups that have an indexing ambiguity
>> (non-equivalent ways to index a given diffraction pattern), e.g. P3, P4,
>> P6, P321, ..., altogether 38 out of the 65 Sohncke groups . So just merging
>> the data blindly may give you "computationally twinned" data. Take a look
>> at doi:10.1107/S1399004713025431 .
>>
>> If you use XDS/XSCALE, you can analyze the scaled but unmerged data with
>> xscale_isocluster .
>> If you use DIALS, you could use dials.cosym for this purpose.
>>
>> Best wishes,
>> Kay
>>
>> On Fri, 22 Jul 2022 09:51:14 +, Monika Bjelcic <
>> monika.bjel...@maxiv.lu.se> wrote:
>>
>> >Hi,
>> >
>> >I’m hoping someone can help me how to determine a space group from my
>> collection.
>> >I did serial crystallography on a crystal that doesn’t have a cryo
>> structure. I was able to determine the Point group but for the next step
>> I’m stuck.
>> >
>> >Kind regards,
>> >Monika Bjelcic
>> >PhD student at BioMAX
>> >[cid:image001.jpg@01D3B796.B7E175A0]
>> >MAX IV Laboratory
>> >Lund University
>> >Postal address: P.O. Box 118, SE-221 00 Lund, Sweden
>> >Visiting address: Fotongatan 2, 224 84 Lund, Sweden
>> >Mobile:  +46-761357994
>> >
>> >
>> >
>> >
>> >To unsubscribe from the CCP4BB list, click the following link:
>> >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> >
>> >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
>> available at https://www.jiscmail.ac.uk/policyandsecurity/
>>
>> 
>>
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>
>
>
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Re: [ccp4bb] Determining space group

[Eleanor Dodson]

Surely once you have indexed one crystal, you can use the facility to check
the next ones indexing against the reference - aka pointless?

On Fri, 22 Jul 2022 at 16:20, Kay Diederichs 
wrote:

> Hi Monika,
>
> in June we had a summer school at MaxIV, and one of the topics was serial
> crystallography - with lectures and tutorials. Maybe you can talk to the
> people who attended the course, and the organizers, Ana Gonzalez and Thomas
> Ursby, and ask them for help.
>
> It is more difficult to determine the spacegroup in serial
> crystallography, compared to conventional crystallography. This is because
> there are several spacegroups that have an indexing ambiguity
> (non-equivalent ways to index a given diffraction pattern), e.g. P3, P4,
> P6, P321, ..., altogether 38 out of the 65 Sohncke groups . So just merging
> the data blindly may give you "computationally twinned" data. Take a look
> at doi:10.1107/S1399004713025431 .
>
> If you use XDS/XSCALE, you can analyze the scaled but unmerged data with
> xscale_isocluster .
> If you use DIALS, you could use dials.cosym for this purpose.
>
> Best wishes,
> Kay
>
> On Fri, 22 Jul 2022 09:51:14 +, Monika Bjelcic <
> monika.bjel...@maxiv.lu.se> wrote:
>
> >Hi,
> >
> >I’m hoping someone can help me how to determine a space group from my
> collection.
> >I did serial crystallography on a crystal that doesn’t have a cryo
> structure. I was able to determine the Point group but for the next step
> I’m stuck.
> >
> >Kind regards,
> >Monika Bjelcic
> >PhD student at BioMAX
> >[cid:image001.jpg@01D3B796.B7E175A0]
> >MAX IV Laboratory
> >Lund University
> >Postal address: P.O. Box 118, SE-221 00 Lund, Sweden
> >Visiting address: Fotongatan 2, 224 84 Lund, Sweden
> >Mobile:  +46-761357994
> >
> >
> >
> >
> >To unsubscribe from the CCP4BB list, click the following link:
> >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
> >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>
> 
>
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Re: [ccp4bb] Determining space group

[Kay Diederichs]

Hi Monika,

in June we had a summer school at MaxIV, and one of the topics was serial 
crystallography - with lectures and tutorials. Maybe you can talk to the people 
who attended the course, and the organizers, Ana Gonzalez and Thomas Ursby, and 
ask them for help.

It is more difficult to determine the spacegroup in serial crystallography, 
compared to conventional crystallography. This is because there are several 
spacegroups that have an indexing ambiguity (non-equivalent ways to index a 
given diffraction pattern), e.g. P3, P4, P6, P321, ..., altogether 38 out of 
the 65 Sohncke groups . So just merging the data blindly may give you 
"computationally twinned" data. Take a look at doi:10.1107/S1399004713025431 .

If you use XDS/XSCALE, you can analyze the scaled but unmerged data with 
xscale_isocluster .
If you use DIALS, you could use dials.cosym for this purpose.

Best wishes,
Kay

On Fri, 22 Jul 2022 09:51:14 +, Monika Bjelcic  
wrote:

>Hi,
>
>I’m hoping someone can help me how to determine a space group from my 
>collection.
>I did serial crystallography on a crystal that doesn’t have a cryo structure. 
>I was able to determine the Point group but for the next step I’m stuck.
>
>Kind regards,
>Monika Bjelcic
>PhD student at BioMAX
>[cid:image001.jpg@01D3B796.B7E175A0]
>MAX IV Laboratory
>Lund University
>Postal address: P.O. Box 118, SE-221 00 Lund, Sweden
>Visiting address: Fotongatan 2, 224 84 Lund, Sweden
>Mobile:  +46-761357994
>
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
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[ccp4bb] Determining space group

[Monika Bjelcic]

Hi,

I’m hoping someone can help me how to determine a space group from my 
collection.
I did serial crystallography on a crystal that doesn’t have a cryo structure. I 
was able to determine the Point group but for the next step I’m stuck.

Kind regards,
Monika Bjelcic
PhD student at BioMAX
[cid:image001.jpg@01D3B796.B7E175A0]
MAX IV Laboratory
Lund University
Postal address: P.O. Box 118, SE-221 00 Lund, Sweden
Visiting address: Fotongatan 2, 224 84 Lund, Sweden
Mobile:  +46-761357994




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Re: [ccp4bb] on space group P 3 2 1

[Jon Cooper]

Hello, all you ever need is:

https://www.ebi.ac.uk/pdbe/pisa/

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

 Original Message 
On 25 Sep 2020, 14:35, Smith Lee wrote:

> Dear All,
>
> For pdb ID 1g4a, it is of space group P 3 2 1. In the paper for this pdb 
> (Crystal Structures of the HslVU Peptidase–ATPase Complex Reveal an 
> ATP-Dependent Proteolysis Mechanism), it has been configured to compact 
> hexamer from the pdb 1g4a, with the pdb 1g4a can be regarded from a dimer.
>
> For the sapce group P 3 2 1,
> the listing of symmetry operators was as following,
> X, Y, Z
> -Y, X -Y, Z
> -X +Y, -X, Z
> Y, X, -Z
> X -Y, -Y, -Z
> -X, -X +Y, -Z
>
> which indicates the 6 molecules are far away from each other.
>
> Then by which method, we can get the pdb for the compact hexamer as shown in 
> the figure 3 in the paper, from the pdb 1g4a?
>
> I am looking forward to getting your advice.
>
> Smith
>
> ---
>
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Re: [ccp4bb] on space group P 3 2 1

[Oliver Smart]

Dear Lee,

I would recommend that you visit: 
https://www.ebi.ac.uk/pdbe/entry/pdb/1g4a/analysis there you can download the 
assembly indicated by the REMARK 350 Octadecamer that describes the "AUTHOR 
DETERMINED BIOLOGICAL UNIT". The download will be in mmcif format that many 
programs can support. If you need the coordinates in PDB format then there are 
a number of ways to convert. I would recommend using CCP4 coot to load and save.

Hope this helps,

Oliver



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Re: [ccp4bb] on space group P 3 2 1

[Philip D. Jeffrey]

:: which indicates the 6 molecules are far away from each other.
Those are just the symmetry operators for space group P321.  It tells you 
nothing about how far apart the molecules are, although the cell dimensions do 
in fact impose some constraints.

However look at REMARK 350 in the PDB format file, which describes the 
orthogonal space operator to (probably) generate what you had in mind.

Phil Jeffrey
Princeton


From: CCP4 bulletin board  on behalf of Smith Lee 
<0459ef8548d5-dmarc-requ...@jiscmail.ac.uk>
Sent: Friday, September 25, 2020 9:35 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] on space group P 3 2 1

Dear All,

For pdb ID 1g4a, it is of space group P 3 2 1. In the paper for this pdb 
(Crystal Structures of the HslVU Peptidase–ATPase Complex Reveal an 
ATP-Dependent Proteolysis Mechanism), it has been configured to compact hexamer 
from the pdb 1g4a, with the pdb 1g4a can be regarded from a dimer.

For the sapce group P 3 2 1,
the listing of symmetry operators was as following,
  X, Y, Z
 -Y,  X -Y, Z
  -X +Y,-X, Z
  Y, X,-Z
   X -Y,-Y,-Z
 -X, -X +Y,-Z

which indicates the 6 molecules are far away from each other.

Then by which method, we can get the pdb for the compact hexamer as shown in 
the figure 3 in the paper, from the pdb 1g4a?

I am looking forward to getting your advice.

Smith



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[ccp4bb] on space group P 3 2 1

[Smith Lee]

Dear All,
For pdb ID 1g4a, it is of space group P 3 2 1. In the paper for this pdb 
(Crystal Structures of the HslVU Peptidase–ATPase Complex Reveal an 
ATP-Dependent Proteolysis Mechanism), it has been configured to compact hexamer 
from the pdb 1g4a, with the pdb 1g4a can be regarded from a dimer.
For the sapce group P 3 2 1, the listing of symmetry operators was as following,
  X, Y, Z   
 
 -Y,  X -Y, Z   
 
  -X +Y,    -X, Z   
 
  Y, X,    -Z   
 
   X -Y,    -Y,    -Z   
 
 -X, -X +Y,    -Z 

which indicates the 6 molecules are far away from each other.
Then by which method, we can get the pdb for the compact hexamer as shown in 
the figure 3 in the paper, from the pdb 1g4a?
I am looking forward to getting your advice.
Smith




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[ccp4bb] AW: [ccp4bb] on space group

[Herman . Schreuder]

Dear Smith,

I think your question was clear, and the answer you got was clear as well.

However, I think the question you asked was not the right question. You want to 
use a particular phrase to describe your crystal packing and you want the 
CCP4BB to endorse this. When the answer was negative, you asked again the same 
question.

The real question, in my eyes, is “What is the best way to describe my P65 
crystal packing” since I guess you want to use this in your paper. Here I would 
use something like “in the crystal, the subunits are related by a 6-fold screw 
axis”. To be more precise, you could even mention a 65-screw axis. Other board 
members may even have better descriptions.

By the way, 61, 62, 63, 64 and 65 axes are all 6-fold screw axes, but of 
different types.

Best,
Herman


Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Smith Lee
Gesendet: Donnerstag, 19. Januar 2017 06:22
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] on space group

Dear All,

Here may I make my question much clear? For the space group P 65 crystal, it 
seems we can call it "6-fold packing of subunits around a screw axis in the 
crystal". Then for the space group P 64 crystal, can it also be called "6-fold 
packing of subunits around a screw axis in the crystal"?

Smith

On Thursday, January 19, 2017 11:50 AM, Ethan Merritt 
<merr...@u.washington.edu<mailto:merr...@u.washington.edu>> wrote:

On Thursday, 19 January 2017 02:33:14 AM you wrote:

>
> Dear All,
> In the literature, somebody call space group P65 crystal as  "six fold screw 
> axis crystal packing", then I would not make any mistake if I call P64 space 
> group crystal also as  "six fold screw axis crystal packing",am I right?
> I am looking forward to getting a reply from you.
> Smith


"six-fold screw axis" refers to the symmetry.

"crystal packing" refers to the molecule-to-molecule contacts regardless of 
symmetry.

So no, I don't think "six fold screw axis crystal packing" makes any sense.

--
Ethan A Merritt, Dept of Biochemistry
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,  University of Washington, Seattle 98195-7742

Re: [ccp4bb] on space group

[Smith Lee]

Dear All,
Here may I make my question much clear? For the space group P 65 crystal, it 
seems we can call it "6-fold packing of subunits around a screw axis in the 
crystal". Then for the space group P 64 crystal, can it also be called "6-fold 
packing of subunits around a screw axis in the crystal"?
Smith 

On Thursday, January 19, 2017 11:50 AM, Ethan Merritt 
 wrote:
 

 On Thursday, 19 January 2017 02:33:14 AM you wrote:
> 
> Dear All,
> In the literature, somebody call space group P65 crystal as  "six fold screw 
> axis crystal packing", then I would not make any mistake if I call P64 space 
> group crystal also as  "six fold screw axis crystal packing",am I right?
> I am looking forward to getting a reply from you.
> Smith

"six-fold screw axis" refers to the symmetry.

"crystal packing" refers to the molecule-to-molecule contacts regardless of 
symmetry.

So no, I don't think "six fold screw axis crystal packing" makes any sense.

-- 
Ethan A Merritt, Dept of Biochemistry
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,  University of Washington, Seattle 98195-7742


   

[ccp4bb] on space group

[Smith Lee]

Dear All,
In the literature, somebody call space group P65 crystal as  "six fold screw 
axis crystal packing", then I would not make any mistake if I call P64 space 
group crystal also as  "six fold screw axis crystal packing",am I right?
I am looking forward to getting a reply from you.
Smith

Re: [ccp4bb] on space group

[Harry Powell]

Hi

A great way to learn about crystallographic things (including how to  
run the programs and how to interpret the output) is to attend one of  
the short courses that are held around the world on a regular basis,  
and talk to the experts that develop the programs - CCP4 has one (I  
understand, though I might be wrong because it hasn't been announced  
yet) due to take place in Nanjing in September. I don't know how  
local to Nanjing Smith might be, but it would be worth considering.




Dear All,

Alhough there are on-line explainations on the space group, I found  
it was difficult to fully understand. Here we take P 1 21 1 as an  
exmaple, will you please explain to me with easy language what each  
number indicates？Or do we have a on-line server which can  
demonstrate the meaning of each number? How can we get out crystal  
arrangement with repeating the unit cell in the format of space group?


Smith



Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick  
Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH


Chairman of International Union of Crystallography Commission on  
Crystallographic Computing
Chairman of European Crystallographic Association SIG9  
(Crystallographic Computing)

Re: [ccp4bb] on space group

[Jurgen Bosch]

Shameless self-promotion aka advertisement:

http://lupo.jhsph.edu/boschlab/Xray_Workshop.html

Jürgen
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry  Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742tel:%2B1-410-614-4742
Lab:  +1-410-614-4894tel:%2B1-410-614-4894
Fax:  +1-410-955-2926tel:%2B1-410-955-2926
http://lupo.jhsph.edu

On May 13, 2015, at 4:46 AM, Harry Powell 
ha...@mrc-lmb.cam.ac.ukmailto:ha...@mrc-lmb.cam.ac.uk wrote:

Hi

A great way to learn about crystallographic things (including how to run the 
programs and how to interpret the output) is to attend one of the short courses 
that are held around the world on a regular basis, and talk to the experts that 
develop the programs - CCP4 has one (I understand, though I might be wrong 
because it hasn't been announced yet) due to take place in Nanjing in 
September. I don't know how local to Nanjing Smith might be, but it would be 
worth considering.


Dear All,

Alhough there are on-line explainations on the space group, I found it was 
difficult to fully understand. Here we take P 1 21 1 as an exmaple, will you 
please explain to me with easy language what each number indicates？Or do we 
have a on-line server which can demonstrate the meaning of each number? How can 
we get out crystal arrangement with repeating the unit cell in the format of 
space group?

Smith


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge, CB2 0QH

Chairman of International Union of Crystallography Commission on 
Crystallographic Computing
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing)

[ccp4bb] on space group

[Smith Liu]

Dear All,
 
Alhough there are on-line explainations on the space group, I found it was 
difficult to fully understand. Here we take P 1 21 1 as an exmaple, will you 
please explain to me with easy language what each number indicates？Or do we 
have a on-line server which can demonstrate the meaning of each number? How can 
we get out crystal arrangement with repeating the unit cell in the format of 
space group?
 
Smith
 
 

Re: [ccp4bb] on space group

[Sean Seaver]

Dear Smith,

Here are some resources, I would then google around any topics or terms that 
are unclear.

http://mcl1.ncifcrf.gov/dauter_pubs/284.pdf

http://www.ruppweb.org/Xray/comp/space_instr.htm

See page 3 for an example using P 1 21 1:
http://xray.tamu.edu/pdf/notes/guidetospacegroups.pdf

Take Care,

Sean Seaver, PhD

P212121
http://store.p212121.com/





--

Dear All,
 
Alhough there are on-line explainations on the space group, I found it was 
difficult to fully understand. Here we take P 1 21 1 as an exmaple, will you 
please explain to me with easy language what each number indicates？Or do we 
have a on-line server which can demonstrate the meaning of each number? How can 
we get out crystal arrangement with repeating the unit cell in the format of 
space group?
 
Smith

Re: [ccp4bb] on space group

[Mayer, Mark (NIH/NICHD) [E]]

As other people have advised in response to some of your previous posts: Invest 
in a copy of Bernard Rupp's fantastic text book. Judging from the number of 
posts you make, you seem interested in learning the art of crystallography. 
This book will answer most if not all of your questions

http://www.ruppweb.org/default.htm

From: Smith Liu [smith_liu...@163.com]
Sent: Tuesday, May 12, 2015 9:47 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] on space group

Dear All,

Alhough there are on-line explainations on the space group, I found it was 
difficult to fully understand. Here we take P 1 21 1 as an exmaple, will you 
please explain to me with easy language what each number indicates？Or do we 
have a on-line server which can demonstrate the meaning of each number? How can 
we get out crystal arrangement with repeating the unit cell in the format of 
space group?

Smith

Re: [ccp4bb] P321 space group problem

[Megha Shah]

Thank you everyone for your suggestions. I will try and work on all the 
suggestions and get back to you all in case it doesn't work.

Megha

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Megha Shah 
[megha.s...@utoronto.ca]
Sent: Monday, February 16, 2015 10:29 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] P321 space group problem

Dear all,

I am trying to crystallize a small soluble protein. I have collected few 
diffraction data sets for the same. Every time I collect a data set I find that 
the crystal is diffracting at different angles only in one particular 
direction, the z direction. These are few examples for the native data sets I 
have collected.

Native crystal: space group P 31 2 148.52   48.52161.90   90   90  120
 P 31 2 148.94   48.94169.89   
90   90  120
 P 3 2 1  48.40   48.40154.48   
90   90  120

We see similar pattern in SeMet crystals too. Thus, it becomes difficult to 
merge the native and SeMet data sets. Is there a way to get around this 
problem? I am looking forward to suggestions.

Megha

[ccp4bb] P321 space group problem

[Megha Shah]

Dear all,

I am trying to crystallize a small soluble protein. I have collected few 
diffraction data sets for the same. Every time I collect a data set I find that 
the crystal is diffracting at different angles only in one particular 
direction, the z direction. These are few examples for the native data sets I 
have collected.

Native crystal: space group P 31 2 148.52   48.52161.90   90   90  120
 P 31 2 148.94   48.94169.89   
90   90  120
 P 3 2 1  48.40   48.40154.48   
90   90  120

We see similar pattern in SeMet crystals too. Thus, it becomes difficult to 
merge the native and SeMet data sets. Is there a way to get around this 
problem? I am looking forward to suggestions.

Megha

[ccp4bb] MR: space group and cell units

[Uma Ratu]

Dear All:

I try to solve a structure by using Phaser.

The data set was collected at 3.9 A with 98.1% (95%) completeness. Based on
pointless, the best space group for the data set is P21212. And the data
can be processed with P21, P212121 as well. The I/sigma value for the data
is 13.3 (1.9).

There are some structure models available from PDB with space groups at
P21, P212121 or P21212. I used these structures as templates to get initial
models. I then use Refmac5 to refine the models. But the R-factors/R-free
are around 0.5 /0.5. When I exam the .pdb and .mtz in coot, the models are
not aligned with density.

I then use the templates (PDB entries) against the processed .mtz files
using Refmac5. Again, the R-factors are higher than 0.5.

I notice that my data set has different cell units with templates. When the
space group match to one template, the cell dimensions is differ from the
template. When the cell dimension matches to one template, the space group
is different. Is this the problem for modeling?

Sequence identity between my protein and templates is 99%. Two residues
were mutated in my protein.

I use Phaser for molecular replacement, and Refmac5 for refinement. Data
was processed using xds or mosfilm.

Thank you for advice

Uma




On Wed, Aug 1, 2012 at 2:27 PM, Uma Ratu rosiso2...@gmail.com wrote:

 Dear All:

 I try to use Phaser to solve the structure by Molecular Replacement.

 The data set is collected @180 degree. I process the data using HKL, and
 have resonable good score: rejection (0.05), Linear R-factor (0.038),
 completeness (98.3), resolution (50-1.5).

 I then use Phaser to do MR. The parameter setting are:
 automated search
 components in asymmetric unit;number of residue 1332; number in
 asymmetric unit 1
 perform search search using ensemble1 number of copies to search for 4

 The protein is in tetramer form. I define this by using the residue number
 (1332) which is 4 x monomer.

 After run, Phaser only gave 9 partial solutions, and no solution with all
 components. The resulted PDB contains only dimer form of the protein, not
 the tetramer. And the first TFZ score is around 2.5, which is too low for
 MR.

 I have the report file of data processing and the summary of Phaser
 attached.

 Could you please advice which part is wrong, why can I get the tetramer
 form of the protein?

 Thank you

 Uma

Re: [ccp4bb] MR: space group and cell units

[Uma Ratu]

HI, Mark:

Thank you for your suggestions.

try all possible spacegroups with PHASER
Yes, this is done with all the modeling.

make sure you are using a monomer as search model
I also tried with monomer as search model. When run with refmac5, the
R-value is above 0.5.

I exam the model in coot. Some parts of model match with density. But some
parts of model do not matched to the density.

At what resolution are the templates in the PDB?
3.0 - 3.9 A

At this stage, I would like to compare the structure at backbone level, not
the side chain.

May have to adjust model piece by piece to fit into the map.

Thanks

Uma





On Wed, Jul 30, 2014 at 12:43 PM, Mark J van Raaij mjvanra...@cnb.csic.es
wrote:

 try all possible spacegroups with PHASER, make sure you are using a
 monomer as search model, not a crystallographic multimer.
 In any case 3.9 A is not going to give you much information and you will
 be hard-pressed to see the mutation differences - so perhaps forget about
 this data and improve the crystals first to get higher-resolution data to
 2.5A or preferably even better. At what resolution are the templates in the
 PDB? You should be able to get similar resolution to those.


 Mark J van Raaij
 Lab 20B
 Dpto de Estructura de Macromoleculas
 Centro Nacional de Biotecnologia - CSIC
 c/Darwin 3
 E-28049 Madrid, Spain
 tel. (+34) 91 585 4616
 http://www.cnb.csic.es/~mjvanraaij
 Associate Editor of Virology Journal
 Academic Editor of PLoS One






 On 30 Jul 2014, at 18:38, Uma Ratu wrote:

  Dear All:
 
  I try to solve a structure by using Phaser.
 
  The data set was collected at 3.9 A with 98.1% (95%) completeness. Based
 on pointless, the best space group for the data set is P21212. And the data
 can be processed with P21, P212121 as well. The I/sigma value for the data
 is 13.3 (1.9).
 
  There are some structure models available from PDB with space groups at
 P21, P212121 or P21212. I used these structures as templates to get initial
 models. I then use Refmac5 to refine the models. But the R-factors/R-free
 are around 0.5 /0.5. When I exam the .pdb and .mtz in coot, the models are
 not aligned with density.
 
  I then use the templates (PDB entries) against the processed .mtz files
 using Refmac5. Again, the R-factors are higher than 0.5.
 
  I notice that my data set has different cell units with templates. When
 the space group match to one template, the cell dimensions is differ from
 the template. When the cell dimension matches to one template, the space
 group is different. Is this the problem for modeling?
 
  Sequence identity between my protein and templates is 99%. Two residues
 were mutated in my protein.
 
  I use Phaser for molecular replacement, and Refmac5 for refinement. Data
 was processed using xds or mosfilm.
 
  Thank you for advice
 
  Uma
 
 
 
 
  On Wed, Aug 1, 2012 at 2:27 PM, Uma Ratu rosiso2...@gmail.com wrote:
  Dear All:
 
  I try to use Phaser to solve the structure by Molecular Replacement.
 
  The data set is collected @180 degree. I process the data using HKL, and
 have resonable good score: rejection (0.05), Linear R-factor (0.038),
 completeness (98.3), resolution (50-1.5).
 
  I then use Phaser to do MR. The parameter setting are:
  automated search
  components in asymmetric unit;number of residue 1332; number in
 asymmetric unit 1
  perform search search using ensemble1 number of copies to search for 4
 
  The protein is in tetramer form. I define this by using the residue
 number (1332) which is 4 x monomer.
 
  After run, Phaser only gave 9 partial solutions, and no solution with
 all components. The resulted PDB contains only dimer form of the protein,
 not the tetramer. And the first TFZ score is around 2.5, which is too low
 for MR.
 
  I have the report file of data processing and the summary of Phaser
 attached.
 
  Could you please advice which part is wrong, why can I get the tetramer
 form of the protein?
 
  Thank you
 
  Uma
 

[ccp4bb] AW: Space group ambiguity in Zanuda

[Herman . Schreuder]

Dear Alastair,

Since there does not seem to be a compelling reason to use P 32 to describe the 
contents of your unit cell, I would use P 32 1 2. Refining a structure in a 
lower symmetry space group often gives slightly lower Rfactors since the 
refinement program has more parameters to play with . Also selection of the 
free reflections plays a role. If you have free and working reflections related 
by the twofold, the free reflections are not really free in P 32, which may 
cause artificially lower Rfrees.

A different story would be if your missing residues would be close to the 
twofold and would adopt alternative conformations. However, even in this case, 
it would be very unlikely that all molecules say in the upper part of the 
asymmetric unit would adopt conformation A and in the lower part conformation 
B. Much more likely would be a random distribution, which brings you back to P 
32 1 2.

Best,
Herman


Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Alastair 
MC EWEN
Gesendet: Dienstag, 7. Januar 2014 17:38
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Space group ambiguity in Zanuda


Dear All,



I have a question regarding the output of Zanuda. We are working on a structure 
solved in P 32 1 2 with one molecule in the asymmetric unit. The structure was 
solved by molecular replacement and refines well to R = 20.6%, Rfree = 25.2% 
with data to 1.8Å and 90% of the model built. Most of the missing residues are 
15 residue long section that is predicted to form a helix and although there is 
some ambiguous density it is not possible to construct anything.



To check the solution I submitted the structure to Zanuda which suggested that 
the symmetry was too high and the correct space group should be P 32. I have 
refined the structure in P 32 and although the stats are better (R = 19.9%, 
Rfree = 23.1%) there is no improvement in the density and the two copies remain 
largely identical. However when I resubmitted this structure to Zanuda it 
suggests that the symmetry is too low and the correct space group is P 32 1 2. 
But looking at the log file I am not sure why this should be so. The program 
does pick P 32 in step 2 but then selects P 32 1 2 at the end of step 3 even 
though the R free is better in P 32 (R is slightly worse).



I'm not sure what I am missing here. I have tried molecular replacement in P 1 
followed by refinement and still get P 32 1 2 picked over P 32 which has the 
best R and Rfree. I have attached an extract from the log files at the end of 
this email. Does anyone have any suggestions?



Thanks in advance,



Alastair McEwen







P 32 logfile



   Step 1.
   R-factors for the starting model.
   Transformation into a supergroup.

   current time:Nov 27 14:19 CET
   expected end of job (rough estimate):Nov 27 14:30 CET

   -
   | Subgroup | Spacegroup | R.m.s.d. |   Refinement in tested group   |
   |  || from the ||
   |   Ref|| starting |  Rigid   | Restrained  |
   |  || model, A |--|-|
   |  ||  |R |R |  R-free  |
   |--||--|--|--|--|
   |2   | P 32   |  0.0006  |--|  0.2716  |  0.3084  |
   |  6   | P 32 1 2   |  0.1035  |--|--|--|
   ^

   Step 2.
   Refinements in subgroups.
   There are 4 subgroups to test.

   current time:Nov 27 14:19 CET
   expected end of job: Nov 27 14:32 CET

   ^
   |2   | P 32   |  0.0006  |--|  0.2716  |  0.3084  |
   -
   |  1   | P 1|  0.1728  |  0.2777  |  0.2521  |  0.3288  |
   |  2   | P 32   |  0.1738  |  0.2779  |  0.2509  |  0.3279  |
   |  3   | C 1 2 1|  0.2080  |  0.2872  |  0.2519  |  0.3315  |
   |  6   | P 32 1 2   |  0.2040  |  0.2899  |  0.2526  |  0.3434  |
   -
   |2   | P 32   |  0.1738  |  0.2779  |  0.2509  |  0.3279  |
   ^

   Step 3.
   Refinement of the best model.
   Candidate symmetry elements are added one by one.

   current time:Nov 27 14:25 CET
   expected end of job: Nov 27 14:32 CET

   ^
   |2   | P 32   |  0.1738  |  0.2779  |  0.2509  |  0.3279

[ccp4bb] AW: [ccp4bb] Wrong Space Group?

[Herman . Schreuder]

Dear Bonsor,

I fully second James suggestions but have a few additional comments:
If you get a solution in P6522 with one molecule, you should get the same 
solution in P65 with 2 molecules. One of the crystallographic symmetry 
operators would then be non-crystallographic.
The current version of Refmac will test all possible twinning operations, so 
there is no need to do it yourself (provided of course that you get a molecular 
replacement solution). 
I would also try your rebuilt model with extended helix as a model for MR. 
I suspect that the dimer which has formed is asymmetric and that it may be 
randomly packed in your crystal. If the helix is a small compared to the 
complete protein, it may not show up in twinning tests.

Good luck!
Herman 



-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von James 
Holton
Gesendet: Sonntag, 15. Dezember 2013 23:29
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Wrong Space Group?

Its possible you are in a lower space group, perhaps with some twinning, but 
your search model is different enough to only find a solution when things are 
over-merged.

Try refining your P6522 model against data merged in P65. If the other copy 
(symmetry mate in P6522) does not show up, you may be in trouble (wrong MR 
solution). I'd also try refinement/building in the other triogonal/hexagonal 
space groups, but again, start with the PDB file that you got for P6522.  Just 
change the space group in the header, and switch out the MTZ file. You will 
need to merge your data in each space group and also check the a-b flip 
re-indexing for most of them. Have a look at the CCP4 reindexing list for the 
h,k,l operators to try:
http://www.ccp4.ac.uk/html/reindexing.html
note how similar they are to the twinning operators:
http://www.ccp4.ac.uk/html/twinning.html
If I have counted right, that means you have 36 jobs to run.
  
  I'd also recommend turning the TWIN option in refmac off and on for each of 
these cases. This will always give you a lower R factor, because of the dynamic 
range compression you get with twinning, but if one particular combination of 
twinning with a particular space group and axis reindexing is markedly better 
than all the others, then you have just found your right space group.  So, now 
we are up to 72 jobs, but hardly a lot of work compared to growing the crystals 
in the first place.

You might also want to try being clever and generating the symmetry mates of 
your P6522 model and refine these partners as separate molecules as you reduce 
the symmetry of the data.  It's tricky, but think of it as an exercise.  Which 
real-space operator becomes what reciprocal-space operator?  You can check your 
answer by loading it up in coot and seeing if symmetry mates clash with the 
input coordinates.

Yes, its a lot of work to try all these combinations, but that's the annoying 
thing about twinning, it opens up a lot of ambiguities.

Good luck!

-James Holton
MAD Scientist

On 12/14/2013 6:44 AM, D Bonsor wrote:
 Dear all,

 I have collected ~160 degrees of data on a new crystal form of a protein 
 which has already been solved. Data was processed with XDS and reindex, 
 scaled and truncated with Aimless. Both XDS and Pointless suggested a Laue 
 group of  P6/mmm with a possible space group of P6122 or P6522. Stats showed 
 an overall Rmerge of 0.131 but an Rpim of 0.041 (multiplicity/redundancy of 
 19.1), a completeness of 99.1% and resolution of 2.8Ang.

 With cell dimensions of 63.1 63.1 243, only one protein chain can be found in 
 the asymmetric unit (two copies would leave a solvent content of 8%). I ran 
 phaser with all alternative space groups and a single solution in P6522 with 
 a TFZ of 10.0.

 I then performed 20 Refmac cycles ending up with an R/Rfree of 35.5/45.5. I 
 open the structure and map in Coot and could see that there was a large 
 conformational change of helix-turn-helix actually becoming just a long helix 
 (https://www.dropbox.com/s/4s6g8apatsi5xcg/Before_Building.png) and then 
 dimerizing through the long helix with one of the symmetry mates.

 This section was rebuilt 
 (https://www.dropbox.com/s/5j7tv0i5yq3mxxx/After_Building.png) and ran 
 through Refmac again resulting in an R/Rfree of 35.5/44.3. Looking through 
 the rest of the structure I see nothing else really to be modeled. Nothing 
 that could bring the Rfactors down to a reasonable range.

 I have therefore tried several things. I ran the structure through Zanuda 
 server to look at other space group possibilities. The server suggested I was 
 in the correct space group. However I did reprocess the data to P6, P3, P312, 
 P321, C2221, P2 and C2, and reran phaser in search all alternative space 
 groups using the original search model but found no solutions. I did 
 reprocess the data in P1, though I did not collect enough data.

 Twinning tests show no twinning. Although that does not mean there is no 
 twinning, I can

Re: [ccp4bb] Wrong Space Group?

[James Holton]

Its possible you are in a lower space group, perhaps with some twinning, but your search 
model is different enough to only find a solution when things are over-merged.

Try refining your P6522 model against data merged in P65. If the other copy (symmetry mate in 
P6522) does not show up, you may be in trouble (wrong MR solution). I'd also try 
refinement/building in the other triogonal/hexagonal space groups, but again, start with the PDB 
file that you got for P6522.  Just change the space group in the header, and switch out the MTZ 
file. You will need to merge your data in each space group and also check the a-b flip 
re-indexing for most of them. Have a look at the CCP4 reindexing list for the h,k,l 
operators to try:
http://www.ccp4.ac.uk/html/reindexing.html
note how similar they are to the twinning operators:
http://www.ccp4.ac.uk/html/twinning.html
If I have counted right, that means you have 36 jobs to run.
 
 I'd also recommend turning the TWIN option in refmac off and on for each of these cases. This will always give you a lower R factor, because of the dynamic range compression you get with twinning, but if one particular combination of twinning with a particular space group and axis reindexing is markedly better than all the others, then you have just found your right space group.  So, now we are up to 72 jobs, but hardly a lot of work compared to growing the crystals in the first place.


You might also want to try being clever and generating the symmetry mates of 
your P6522 model and refine these partners as separate molecules as you reduce the 
symmetry of the data.  It's tricky, but think of it as an exercise.  Which real-space 
operator becomes what reciprocal-space operator?  You can check your answer by loading it 
up in coot and seeing if symmetry mates clash with the input coordinates.

Yes, its a lot of work to try all these combinations, but that's the annoying 
thing about twinning, it opens up a lot of ambiguities.

Good luck!

-James Holton
MAD Scientist

On 12/14/2013 6:44 AM, D Bonsor wrote:

Dear all,

I have collected ~160 degrees of data on a new crystal form of a protein which 
has already been solved. Data was processed with XDS and reindex, scaled and 
truncated with Aimless. Both XDS and Pointless suggested a Laue group of  
P6/mmm with a possible space group of P6122 or P6522. Stats showed an overall 
Rmerge of 0.131 but an Rpim of 0.041 (multiplicity/redundancy of 19.1), a 
completeness of 99.1% and resolution of 2.8Ang.

With cell dimensions of 63.1 63.1 243, only one protein chain can be found in 
the asymmetric unit (two copies would leave a solvent content of 8%). I ran 
phaser with all alternative space groups and a single solution in P6522 with a 
TFZ of 10.0.

I then performed 20 Refmac cycles ending up with an R/Rfree of 35.5/45.5. I 
open the structure and map in Coot and could see that there was a large 
conformational change of helix-turn-helix actually becoming just a long helix 
(https://www.dropbox.com/s/4s6g8apatsi5xcg/Before_Building.png) and then 
dimerizing through the long helix with one of the symmetry mates.

This section was rebuilt 
(https://www.dropbox.com/s/5j7tv0i5yq3mxxx/After_Building.png) and ran through 
Refmac again resulting in an R/Rfree of 35.5/44.3. Looking through the rest of 
the structure I see nothing else really to be modeled. Nothing that could bring 
the Rfactors down to a reasonable range.

I have therefore tried several things. I ran the structure through Zanuda server to look 
at other space group possibilities. The server suggested I was in the correct space 
group. However I did reprocess the data to P6, P3, P312, P321, C2221, P2 and C2, and 
reran phaser in search all alternative space groups using the original search 
model but found no solutions. I did reprocess the data in P1, though I did not collect 
enough data.

Twinning tests show no twinning. Although that does not mean there is no 
twinning, I can see that P6522 has no twin laws. Does that mean no twinning can 
occur in P6522 or that it can occur but there is no law to be able to separate 
the amplitudes?

I also collected data on a single point mutation of the protein. Although this 
diffracted to a slightly weaker resolution (3.2Ang), I also observe the same 
problem of good maps in P6522 but no solution in the groups described above, a 
clear indication that this helix has elongated but terrible Rfactors.

Based upon that the maps look good in P6522 do you believe that I have solved 
the structure in the correct space group but my data collection is at fault or 
in fact that I have some form of pseudosymmetry or something else going on and 
that the space group has lower symmetry but not in the space groups I have 
checked. Or is it something else.

Any suggestions, criticisms or you need further information please contact me 
and enjoy your weekend.

Re: [ccp4bb] Wrong Space Group?

[Kay Diederichs]

On Fri, 13 Dec 2013 19:44:44 +, D Bonsor dbon...@ihv.umaryland.edu wrote:

Dear D,

I agree with Tim and Jürgen that
a) the map after Phaser, and before refinement is the most unbiased and should 
be used for sequence assignment. 
b) there may be a sequence register shift error that is responsible for the 
high R-values, and is masked by overfitting

So I would try
a) To stay on the safe side, you could chop the Phaser model into secondary 
structure elements and do rigid-body refinement. This yields maps that are 
largely unbiased.
b) sharpening (very easy in coot) and inspection of these unbiased maps, to 
confirm the sequence register
c) submit the Phaser model to Arp/wArp re-building, and also try the 
buccaneer/refmac iterative re-building, and maybe phenix.autobuild

But the problem may also be your data. 
a) Maybe every second reflection is not integrated because it is weak? That is 
easy to check with XDSGUI using Tools/show frame with predicted spots
b) other pathologies like spot overlap or experimental instability (what is the 
value of ISa in CORRECT.LP ?) - you could post FRAME.cbf and IDXREF.LP, 
INTEGRATE.LP and CORRECT.LP and pointless/xtriage statistics

If the true space group is P6x22, then the data cannot be twinned. But if the 
true space group has lower symmetry the data may appear to be P6x22 .

HTH,

Kay

P.S. XDSGUI latest version can be obtained from 
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSGUI


Dear all,

I have collected ~160 degrees of data on a new crystal form of a protein which 
has already been solved. Data was processed with XDS and reindex, scaled and 
truncated with Aimless. Both XDS and Pointless suggested a Laue group of  
P6/mmm with a possible space group of P6122 or P6522. Stats showed an overall 
Rmerge of 0.131 but an Rpim of 0.041 (multiplicity/redundancy of 19.1), a 
completeness of 99.1% and resolution of 2.8Ang.

With cell dimensions of 63.1 63.1 243, only one protein chain can be found in 
the asymmetric unit (two copies would leave a solvent content of 8%). I ran 
phaser with all alternative space groups and a single solution in P6522 with a 
TFZ of 10.0. 

I then performed 20 Refmac cycles ending up with an R/Rfree of 35.5/45.5. I 
open the structure and map in Coot and could see that there was a large 
conformational change of helix-turn-helix actually becoming just a long helix 
(https://www.dropbox.com/s/4s6g8apatsi5xcg/Before_Building.png) and then 
dimerizing through the long helix with one of the symmetry mates.

This section was rebuilt 
(https://www.dropbox.com/s/5j7tv0i5yq3mxxx/After_Building.png) and ran through 
Refmac again resulting in an R/Rfree of 35.5/44.3. Looking through the rest of 
the structure I see nothing else really to be modeled. Nothing that could 
bring the Rfactors down to a reasonable range. 

I have therefore tried several things. I ran the structure through Zanuda 
server to look at other space group possibilities. The server suggested I was 
in the correct space group. However I did reprocess the data to P6, P3, P312, 
P321, C2221, P2 and C2, and reran phaser in search all alternative space 
groups using the original search model but found no solutions. I did 
reprocess the data in P1, though I did not collect enough data. 

Twinning tests show no twinning. Although that does not mean there is no 
twinning, I can see that P6522 has no twin laws. Does that mean no twinning 
can occur in P6522 or that it can occur but there is no law to be able to 
separate the amplitudes? 

I also collected data on a single point mutation of the protein. Although this 
diffracted to a slightly weaker resolution (3.2Ang), I also observe the same 
problem of good maps in P6522 but no solution in the groups described above, a 
clear indication that this helix has elongated but terrible Rfactors.

Based upon that the maps look good in P6522 do you believe that I have solved 
the structure in the correct space group but my data collection is at fault or 
in fact that I have some form of pseudosymmetry or something else going on and 
that the space group has lower symmetry but not in the space groups I have 
checked. Or is it something else.

Any suggestions, criticisms or you need further information please contact me 
and enjoy your weekend.

[ccp4bb] Wrong Space Group?

[D Bonsor]

Dear all,

I have collected ~160 degrees of data on a new crystal form of a protein which 
has already been solved. Data was processed with XDS and reindex, scaled and 
truncated with Aimless. Both XDS and Pointless suggested a Laue group of  
P6/mmm with a possible space group of P6122 or P6522. Stats showed an overall 
Rmerge of 0.131 but an Rpim of 0.041 (multiplicity/redundancy of 19.1), a 
completeness of 99.1% and resolution of 2.8Ang.

With cell dimensions of 63.1 63.1 243, only one protein chain can be found in 
the asymmetric unit (two copies would leave a solvent content of 8%). I ran 
phaser with all alternative space groups and a single solution in P6522 with a 
TFZ of 10.0. 

I then performed 20 Refmac cycles ending up with an R/Rfree of 35.5/45.5. I 
open the structure and map in Coot and could see that there was a large 
conformational change of helix-turn-helix actually becoming just a long helix 
(https://www.dropbox.com/s/4s6g8apatsi5xcg/Before_Building.png) and then 
dimerizing through the long helix with one of the symmetry mates.

This section was rebuilt 
(https://www.dropbox.com/s/5j7tv0i5yq3mxxx/After_Building.png) and ran through 
Refmac again resulting in an R/Rfree of 35.5/44.3. Looking through the rest of 
the structure I see nothing else really to be modeled. Nothing that could bring 
the Rfactors down to a reasonable range. 

I have therefore tried several things. I ran the structure through Zanuda 
server to look at other space group possibilities. The server suggested I was 
in the correct space group. However I did reprocess the data to P6, P3, P312, 
P321, C2221, P2 and C2, and reran phaser in search all alternative space 
groups using the original search model but found no solutions. I did reprocess 
the data in P1, though I did not collect enough data. 

Twinning tests show no twinning. Although that does not mean there is no 
twinning, I can see that P6522 has no twin laws. Does that mean no twinning can 
occur in P6522 or that it can occur but there is no law to be able to separate 
the amplitudes? 

I also collected data on a single point mutation of the protein. Although this 
diffracted to a slightly weaker resolution (3.2Ang), I also observe the same 
problem of good maps in P6522 but no solution in the groups described above, a 
clear indication that this helix has elongated but terrible Rfactors.

Based upon that the maps look good in P6522 do you believe that I have solved 
the structure in the correct space group but my data collection is at fault or 
in fact that I have some form of pseudosymmetry or something else going on and 
that the space group has lower symmetry but not in the space groups I have 
checked. Or is it something else.

Any suggestions, criticisms or you need further information please contact me 
and enjoy your weekend.

Re: [ccp4bb] Wrong Space Group?

[Bosch, Juergen]

2.8 is not a terrible resolution to try out Buccaneer or Parrot. Your terrible 
R-factor might be due to a shift in residues perhaps ? Your After-building map 
does not show much of a side chain density to judge if you are in frame or off.
But the elongated helix is in my eyes convincing enough.

One thing you might want to try is to use composite omit maps to reduce your 
bias from MR and verify that what you built is indeed correct.

Jürgen

On Dec 13, 2013, at 2:44 PM, D Bonsor 
dbon...@ihv.umaryland.edumailto:dbon...@ihv.umaryland.edu wrote:

Dear all,

I have collected ~160 degrees of data on a new crystal form of a protein which 
has already been solved. Data was processed with XDS and reindex, scaled and 
truncated with Aimless. Both XDS and Pointless suggested a Laue group of  
P6/mmm with a possible space group of P6122 or P6522. Stats showed an overall 
Rmerge of 0.131 but an Rpim of 0.041 (multiplicity/redundancy of 19.1), a 
completeness of 99.1% and resolution of 2.8Ang.

With cell dimensions of 63.1 63.1 243, only one protein chain can be found in 
the asymmetric unit (two copies would leave a solvent content of 8%). I ran 
phaser with all alternative space groups and a single solution in P6522 with a 
TFZ of 10.0.

I then performed 20 Refmac cycles ending up with an R/Rfree of 35.5/45.5. I 
open the structure and map in Coot and could see that there was a large 
conformational change of helix-turn-helix actually becoming just a long helix 
(https://www.dropbox.com/s/4s6g8apatsi5xcg/Before_Building.png) and then 
dimerizing through the long helix with one of the symmetry mates.

This section was rebuilt 
(https://www.dropbox.com/s/5j7tv0i5yq3mxxx/After_Building.png) and ran through 
Refmac again resulting in an R/Rfree of 35.5/44.3. Looking through the rest of 
the structure I see nothing else really to be modeled. Nothing that could bring 
the Rfactors down to a reasonable range.

I have therefore tried several things. I ran the structure through Zanuda 
server to look at other space group possibilities. The server suggested I was 
in the correct space group. However I did reprocess the data to P6, P3, P312, 
P321, C2221, P2 and C2, and reran phaser in search all alternative space 
groups using the original search model but found no solutions. I did reprocess 
the data in P1, though I did not collect enough data.

Twinning tests show no twinning. Although that does not mean there is no 
twinning, I can see that P6522 has no twin laws. Does that mean no twinning can 
occur in P6522 or that it can occur but there is no law to be able to separate 
the amplitudes?

I also collected data on a single point mutation of the protein. Although this 
diffracted to a slightly weaker resolution (3.2Ang), I also observe the same 
problem of good maps in P6522 but no solution in the groups described above, a 
clear indication that this helix has elongated but terrible Rfactors.

Based upon that the maps look good in P6522 do you believe that I have solved 
the structure in the correct space group but my data collection is at fault or 
in fact that I have some form of pseudosymmetry or something else going on and 
that the space group has lower symmetry but not in the space groups I have 
checked. Or is it something else.

Any suggestions, criticisms or you need further information please contact me 
and enjoy your weekend.

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry  Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://lupo.jhsph.edu

[ccp4bb] switching space group

[MAGGIE]

Hi,

I have a structure which should have space group P212121, but it has been
processed to P21212.  It can not be solved and refined.  Right now I do not
have HKL2000, but I need change the space group to P212121.  Is there a way
for me to do this using CCP4?

Thank you,

Maggie

Re: [ccp4bb] switching space group

[Ian Tickle]

Hi Maggie

echo  symm  P212121 | mtzutils  HKLIN  in.mtz  HKLOUT  out.mtz

should do the trick.

Cheers

-- Ian


On 6 November 2013 18:13, MAGGIE dongmeij...@gmail.com wrote:

 Hi,

 I have a structure which should have space group P212121, but it has been
 processed to P21212.  It can not be solved and refined.  Right now I do not
 have HKL2000, but I need change the space group to P212121.  Is there a way
 for me to do this using CCP4?

 Thank you,

 Maggie

Re: [ccp4bb] switching space group

[Vikrant Upadhyay]

Hi Maggie, 

you can re-process your data using XDS and can provide the desired space group 
in the XDS.INP file. It won't take much time.

Vikrant

Vikrant Upadhyay
Postdoctoral associate
Dr. Crina Nimigean's lab, A-1050
Department of Anesthesiology
Weill Cornell Medical College
525 East 68th Street
New York, NY 10065

On Nov 6, 2013, at 1:13 PM, MAGGIE dongmeij...@gmail.com wrote:

 Hi,
  
 I have a structure which should have space group P212121, but it has been 
 processed to P21212.  It can not be solved and refined.  Right now I do not 
 have HKL2000, but I need change the space group to P212121.  Is there a way 
 for me to do this using CCP4? 
  
 Thank you,
  
 Maggie

Re: [ccp4bb] switching space group

[Phoebe A. Rice]

If you're only changing the 2-fold axis along c to a 2-fold screw axis, you 
don't need to go back to the raw image files and reprocess them!   Just tweak 
the header of the .sca file and carry on (and take notes on what you did).


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Vikrant Upadhyay 
[vikrant192...@gmail.com]
Sent: Wednesday, November 06, 2013 5:13 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] switching space group

Hi Maggie,

you can re-process your data using XDS and can provide the desired space group 
in the XDS.INP file. It won't take much time.

Vikrant

Vikrant Upadhyay
Postdoctoral associate
Dr. Crina Nimigean's lab, A-1050
Department of Anesthesiology
Weill Cornell Medical College
525 East 68th Street
New York, NY 10065

On Nov 6, 2013, at 1:13 PM, MAGGIE 
dongmeij...@gmail.commailto:dongmeij...@gmail.com wrote:

Hi,

I have a structure which should have space group P212121, but it has been 
processed to P21212.  It can not be solved and refined.  Right now I do not 
have HKL2000, but I need change the space group to P212121.  Is there a way for 
me to do this using CCP4?

Thank you,

Maggie

Re: [ccp4bb] switching space group

[Edward A. Berry]

I liked Ian Tickle's 1-line ccp4 script for changing the space group with 
mtzutils.
I believe CAD can do this also. In any case, there's no need to reprocess.
Some reflections present in the current data will be systematically absent in
the new space group, but presumably they will be eliminated in the process.

Phoebe A. Rice wrote:

If you're only changing the 2-fold axis along c to a 2-fold screw axis, you 
don't need to
go back to the raw image files and reprocess them!   Just tweak the header of 
the .sca
file and carry on (and take notes on what you did).

--
*From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Vikrant 
Upadhyay
[vikrant192...@gmail.com]
*Sent:* Wednesday, November 06, 2013 5:13 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] switching space group

Hi Maggie,

you can re-process your data using XDS and can provide the desired space group 
in the
XDS.INP file. It won't take much time.

Vikrant

Vikrant Upadhyay
Postdoctoral associate
Dr. Crina Nimigean's lab, A-1050
Department of Anesthesiology
Weill Cornell Medical College
525 East 68th Street
New York, NY 10065

On Nov 6, 2013, at 1:13 PM, MAGGIE dongmeij...@gmail.com 
mailto:dongmeij...@gmail.com
wrote:


Hi,

I have a structure which should have space group P212121, but it has been 
processed to
P21212.  It can not be solved and refined.  Right now I do not have HKL2000, 
but I need
change the space group to P212121.  Is there a way for me to do this using CCP4?

Thank you,
Maggie

Re: [ccp4bb] switching space group

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Maggie,

in addition to what others explained, data integration does not depend
on the space group. It only depends on the Laue group, and P21212 and
P212121 belong to the same Laue group. You would see no difference at
all in reprocessing, and in this case Ian's suggestion is sufficient.

When I am not sure whether or not changing the space group make any
real difference to the data I like using pointless to set it right, or
even run phaser if I do have a PDB-file.

Cheers,
Tim

On 11/06/2013 07:13 PM, MAGGIE wrote:
 Hi,
 
 I have a structure which should have space group P212121, but it
 has been processed to P21212.  It can not be solved and refined.
 Right now I do not have HKL2000, but I need change the space group
 to P212121.  Is there a way for me to do this using CCP4?
 
 Thank you,
 
 Maggie

- -- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A
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Version: GnuPG v1.4.15 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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6gYf1SJYB3SwS5QerUcVaIo=
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Re: [ccp4bb] which space group?!?

[Alexandre OURJOUMTSEV]

Dear Jürgen, dear Katherine,

Sorry for a late reaction.

In our article in Acta Cryst., 2009, D65, 1283-1291 (Section 4) we show an 
accurate distribution of the most frequent R, Rfree, Rfree-R  as a practically 
linear function of the Log(resolution) , and not that of the resolution itself, 
and give the corresponding equations. Also we look for the min/max and the 
dispersion of R/ Rfree values around these most frequent values.

Best regards,

Sacha

From: Bosch, Juergen [jubo...@jhsph.edu]
Sent: Tuesday, July 23, 2013 2:23 PM
To: Katherine Donovan
Subject: Re: [ccp4bb] post to ccp4bb
Hi Katherine,

As a rule of thumb you should expect R values around your resolution/10 so in 
the low to mid 20 - 18/23 sound reasonable for that resolution.

How many molecules in the asu do you have in each case ?

Jürgen

[ccp4bb] FW: [ccp4bb] which space group?!?

[Katherine Donovan]

Hi,

The density in both space groups looks very similar, with no obvious 
differences.
The data was processed in XDS followed by refinement in REFMAC and then PHENIX.

Yes, the statistics of the orthorhombic structure is probably more realistic. 
But when both are refined in REFMAC these statistics are much higher (probably 
more at a reasonable level).

I have 2 molecules in the ASU in the C2221 structure and 4 in the P21 structure.

Cheers,

Katherine

From: Bosch, Juergen [jubo...@jhsph.edu]
Sent: Tuesday, July 23, 2013 2:23 PM
To: Katherine Donovan
Subject: Re: [ccp4bb] post to ccp4bb

Hi Katherine,

I would say a twin fraction of 0.5 is suspicious of a higher symmetry.
In the end the density should give it away, do the side chains look as well 
defined in both cases ?
How did you process your images Mosflm,iMosflm, HKL2000 or XDS ?
As a rule of thumb you should expect R values around your resolution/10 so in 
the low to mid 20 - 18/23 sound reasonable for that resolution.

How many molecules in the asu do you have in each case ?

Jürgen

On Jul 22, 2013, at 9:11 PM, Katherine Donovan wrote:

Hi All,

I have a data set that was collected to about 2.2A, which I have processed in 
either P21 (to 2.4 A) or C2221 (2.25A).

I am unsure which space group is more correct.

I have a higher symmetry space group with higher resolution and average 
statistics or a lower symmetry space group with lower resolution and great 
statistics.

The statistics provided by aimless below.


Any help would be hugely appreciated.

Thanks,

Katherine




P21
AIMLESS
P21 and cut the data to 2.4A for a Mn I/sd  2.

Average unit cell:   74.68130  129.290  106.8 90
   Overall  InnerShell  OuterShell
Low resolution limit   48.09 48.09  2.44
High resolution limit   2.40 13.15  2.40
Rmerge  (within I+/I-) 0.085 0.038 0.581
Rmerge  (all I+ and I-)0.099 0.042 0.687
Rmeas (within I+/I-)   0.117 0.053 0.792
Rmeas (all I+  I-)0.116 0.050 0.798
Rpim (within I+/I-)0.080 0.037 0.534
Rpim (all I+  I-) 0.059 0.026 0.405
Rmerge in top intensity bin0.045- -
Total number of observations  352569  2057 17425
Total number unique92184   569  4538
Mean((I)/sd(I))  9.6  23.6   2.0
Mn(I) half-set correlation CC(1/2) 0.995 0.995 0.648
Completeness   100.0  97.2 100.0
Multiplicity 3.8   3.6   3.8

PHENIX – XTRIAGE
One possible pseudo merohedral twin operator
2-fold axis
h, -k, -h-l

I**2/I**2 = 2.032
F**2/F**2 = 0.787
|E**2-1| = 0.734
|L|, L**2 = 0.490, 0.321
Multivariate Z score L-test = 0.616

NZ test = Maximum deviation acentric = 0.007
Maximum deviation centric = 0.051
L test =   Mean L = 0.490

Estimated twin fraction:
0.450 (Britton analyses)
0.477 (H-test)
0.478 (Maximum likelihood method)

Likely point group of the data is C 2 2 2

Analysis of the systematic absences indicates a number of likely space group 
candidates:
C 2 2 21

Patterson analysis of peak with length larger than 15 Angstrom:
Frac. Cood = 0.00, 0.166, 0.00
Distance to origin = 21.530
Height (origin = 100) = 3.787
p-value (height) = 9.991e-01

Final REFMAC refinement in P21
Rfactor = 0.2391
Rfree = 0.2674
After multiple rounds of refinement the twinning information is:
Twin domains = 2
Twin fractions = 0.5201, 0.4799

FINAL refinement PHENIX – P21
Rwork = 0.1637
Rfree = 0.1938
Twin fraction = 0.5 for twin operator h, -k, -h-l
Ramachandran outliers = 0.1%
Rotamer outliers = 3.6%
C-beta outliers = 0


C2221
AIMLESS
Cut the data back to 2.25 for a Mn I/sd 2.

Average unit cell:   74.68  247.413090 90 90
   Overall  InnerShell  OuterShell
Low resolution limit   48.09 48.09  2.31
High resolution limit   2.25  9.81  2.25

Rmerge  (within I+/I-) 0.117 0.044 0.984
Rmerge  (all I+ and I-)0.126 0.046 1.068
Rmeas (within I+/I-)   0.136 0.051 1.145
Rmeas (all I+  I-)0.135 0.050 1.147
Rpim (within I+/I-)0.069 0.026 0.577
Rpim (all I+  I-) 0.050 0.019 0.417
Rmerge in top intensity bin0.050- -
Total number of observations  427886  5201 7
Total number unique57553   788  4433
Mean((I)/sd(I)) 11.4  32.6   2.0
Mn(I) 

Re: [ccp4bb] wrong space group or wrong refinement strategy

[Randy Read]

If that solution applies to the original model you used (and not to re-solving 
the structure with the molecular replacement solution before or after 
refinement), then your tetramer model is just being rotated by 90 degrees 
around the 4-fold and placed on a different origin, i.e. the solution is 
equivalent to the starting model, except for applying symmetry and a change of 
origin.

If that's true, then it implies that this is an isomorphous crystal to the one 
giving the model you're using for molecular replacement.  Is that crystal in 
P41 with similar cell dimensions?  Rigid-body refinement would be a sensible 
option in such a case, with the advantage that your new model is guaranteed to 
be on the same origin and thus easier to compare with the old model.

Getting to the main question, you really have to look at the result of twinning 
tests.  If they suggest that your crystal is twinned, then it's probably P41 
with the twinning increasing the apparent symmetry of the data.  But it's 
important to look at all the evidence, not just the Rfree after refinement, 
especially as the application of a twin target always lowers Rfree.

Best wishes,

Randy Read

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills RoadE-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   
www-structmed.cimr.cam.ac.uk

On 1 Dec 2012, at 00:59, ruisher hu wrote:

 Hi, Dear CCP4 group,
 
 I recently collect one dataset and indexed as P4 space group. When I try to 
 do MR with a tetramer as input, I found the solution file suggested P41. 
 
 SOLU SET RFZ=5.2 TFZ=10.3 PAK=0 LLG=239 LLG=366 TFZ==20.9
 SOLU SPAC P 41
 SOLU 6DIM ENSE ensemble1 EULER 50.265 0.217 219.800 FRAC 0.50029 0.49916 
 -0.00408 BFAC -0.04000
 SOLU ENSE ensemble1 VRMS 0.639
 SOLU SET RFZ=5.2 TFZ=10.0 PAK=0 LLG=239 TFZ==11.2 LLG=365
 SOLU SPAC P 41
 SOLU 6DIM ENSE ensemble1 EULER 128.607 179.813 38.677 FRAC 0.49991 0.49905 
 -0.00208 BFAC -0.06264
 SOLU ENSE ensemble1 VRMS 0.642
 
 However when I did refinement in phenix, I have some trouble getting the 
 R/Rfree down. It complains about some twinning or maybe higher symmetry like 
 P422. When I apply twin law, h,-k,-l, I'm able to refine to 0.34/0.37 but 
 still, hard to continue the refinement. The strategy I used for refinement is 
 xyz coordinates, real-space, individual B-factors, occupancies, with NCS 
 restraints and twin law. 
 
 So I tried to rescaled into P41212 space group, and run MR again, with two 
 chains as an input and found one solution
SOLU SET  RFZ=4.5 TFZ=9.5 PAK=0 LLG=115 TFZ==10.0 LLG=118 TFZ==10.4
SOLU SPAC P 41 21 2
SOLU 6DIM ENSE ET EULER 234.6 0.7 305.0 FRAC 1.00 0.49 -0.17 BFAC -0.14
Ensemble ET RMS variance(s): 0.96
 
 However, when i tried to refine, the Rfree is high as 0.51 at the first 
 round. Does this mean this is not the right solution or maybe some problems 
 with the space group?Any suggestions for next step? Thanks very much.
 
 

[ccp4bb] wrong space group or wrong refinement strategy

[ruisher hu]

Hi, Dear CCP4 group,

I recently collect one dataset and indexed as P4 space group. When I try  to do 
MR with a tetramer as input, I found the solution file suggested P41. 

SOLU SET RFZ=5.2 TFZ=10.3 PAK=0 LLG=239 LLG=366 TFZ==20.9
SOLU SPAC P 41
SOLU 6DIM ENSE ensemble1 EULER 50.265 0.217 219.800 FRAC 0.50029 0.49916 
-0.00408 BFAC -0.04000
SOLU ENSE ensemble1 VRMS 0.639
SOLU SET RFZ=5.2 TFZ=10.0 PAK=0 LLG=239 TFZ==11.2 LLG=365
SOLU SPAC P 41
SOLU 6DIM ENSE ensemble1 EULER 128.607 179.813 38.677 FRAC 0.49991 0.49905 
-0.00208 BFAC -0.06264
SOLU ENSE ensemble1 VRMS 0.642

However when I did refinement in phenix, I have some trouble getting the 
R/Rfree down. It complains about some twinning or maybe higher symmetry like 
P422. When I apply twin law, h,-k,-l, I'm able to refine to 0.34/0.37 but 
still, hard to continue the refinement. The strategy I used for refinement is 
xyz coordinates, real-space, individual B-factors, occupancies, with NCS 
restraints and twin law. 

So I tried to rescaled into P41212 space group, and run MR again, with two 
chains as an input and found one solution
   SOLU SET  RFZ=4.5 TFZ=9.5 PAK=0 LLG=115 TFZ==10.0 LLG=118 TFZ==10.4
   SOLU SPAC P 41 21 2
   SOLU 6DIM ENSE ET EULER 234.6 0.7 305.0 FRAC 1.00 0.49 -0.17 BFAC -0.14
   Ensemble ET RMS variance(s): 0.96

However, when i tried to refine, the Rfree is high as 0.51 at the first round. 
Does this mean this is not the right solution or maybe some problems with the 
space group?Any suggestions for next step? Thanks very much.

Re: [ccp4bb] wrong space group or wrong refinement strategy

[vellieux]

Hello,

What about the enantiomorphic space groups (the 4(3) screw axes instead 
of the 4(1) screw axes) ? These cannot be distinguised on the basis of 
structure factor amplitudes (unless you have an anomalous scatterer) nor 
on the basis of the specific extinctions (both screw axes extinguish the 
same reflections).


However molecular replacement distinguishes between the two. I did not 
see any mention of these enantiomorphic space groups in your post hence 
my asking... Phaser allows to test everything. The CCP4 program 
Pointless is also good at letting you know what is the most likely space 
group.


Hence you may have a combination of wrong space group and twinning. I 
can't really say with the information provided. I have had one case 
(also molecular replacement) where I had to test every single space 
group (a hexagonal lattice) in order to hit the correct one (that was 
before the days of Phaser).


Also, with molecular replacement the first thing I do is to compare the 
initial R-f / R-free to the R-factors that are expected for a random 
distribution of atoms in the asymmetric unit (from memory, ca. 0.6). 
Once you have refined, the numbers go down so you can't really say 
anything any more.


Furthermore, sometimes it is necessary to carry out the molecular 
replacement searches with a smaller set of atoms (for example when you 
are expecting to find a tetramer you carry out the searches with a 
dimer, or with a monomer - and sometimes you have the surprise to 
discover that the solvent content of your crystal is quite high and that 
the tetramer is formed by 2 dimers that are related by a 
crystallographic 2-fold axis - or the arrangement of molecules in your 
multimer is different from that in the search model, to sum it up: in 
crystallography, everything goes!).


HTH,

Fred.

On 01/12/12 01:59, ruisher hu wrote:

Hi, Dear CCP4 group,

I recently collect one dataset and indexed as P4 space group. When I 
try to do MR with a tetramer as input, I found the solution file 
suggested P41.


SOLU SET RFZ=5.2 TFZ=10.3 PAK=0 LLG=239 LLG=366 TFZ==20.9
SOLU SPAC P 41
SOLU 6DIM ENSE ensemble1 EULER 50.265 0.217 219.800 FRAC 0.50029 
0.49916 -0.00408 BFAC -0.04000

SOLU ENSE ensemble1 VRMS 0.639
SOLU SET RFZ=5.2 TFZ=10.0 PAK=0 LLG=239 TFZ==11.2 LLG=365
SOLU SPAC P 41
SOLU 6DIM ENSE ensemble1 EULER 128.607 179.813 38.677 FRAC 0.49991 
0.49905 -0.00208 BFAC -0.06264

SOLU ENSE ensemble1 VRMS 0.642

However when I did refinement in phenix, I have some trouble getting 
the R/Rfree down. It complains about some twinning or maybe higher 
symmetry like P422. When I apply twin law, h,-k,-l, I'm able to refine 
to 0.34/0.37 but still, hard to continue the refinement. The strategy 
I used for refinement is xyz coordinates, real-space, individual 
B-factors, occupancies, with NCS restraints and twin law.


So I tried to rescaled into P41212 space group, and run MR again, with 
two chains as an input and found one solution

   SOLU SET  RFZ=4.5 TFZ=9.5 PAK=0 LLG=115 TFZ==10.0 LLG=118 TFZ==10.4
   SOLU SPAC P 41 21 2
   SOLU 6DIM ENSE ET EULER 234.6 0.7 305.0 tel:234.6%200.7%20305.0 
FRAC 1.00 0.49 -0.17 BFAC -0.14

   Ensemble ET RMS variance(s): 0.96

However, when i tried to refine, the Rfree is high as 0.51 at the 
first round. Does this mean this is not the right solution or maybe 
some problems with the space group?Any suggestions for next step? 
Thanks very much.






--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] P321 space group reindex problem

[Laurent Maveyraud]

Hi,

it is therefore likely that your spacegroup is really P321... hopefully, 
your data set is not twinned, did you check that ?


You are left with 2 possible indexing schemes, as already mentionned. 
Chek scaling derivative / native scaling for each indexation of the 
derivative : the lowest Rfactor will likely indicate the right one.
It appears that you end up with Rfactor of about 29 %, which suggest 
that your derivatives are not isomorphous to your native dataset. How do 
cell parameters compare for each data set ?
Check also how the Rfactor varies with resolution, you might still have 
usefull phasing info at low resolution.


hope this helps

laurent



Le 30/05/2012 07:50, Qixu Cai a écrit :

At first, I processed the data at P3 space group. But after
phenix.xtriage analysis, the Xtriage told me the space group must be
P321, so I used P321 to process my data, and got an acceptable Rmerge.

Qixu Cai



2012/5/29 Phil Evans p...@mrc-lmb.cam.ac.uk mailto:p...@mrc-lmb.cam.ac.uk

How do you know the point group is 321? What does Pointless tell you
if you put in the unmerged data?

Despite some of the things said earlier (by me!), the possible
indexing schemes in 321 are h,k,l and -h,-k,l
If that doesn't work, it suggests that the point group is a lower
symmetry eg P3

Phil


On 29 May 2012, at 16:29, Qixu Cai wrote:

  Dear all,
 
  thank you for your help.
 
  I think I must describe my case in detail. I collected a native
dataset and two heavy atom derivant datasets （in fact, i don not
know whether these two kind of heavy atom have soked into the
crystal, i just collect the data to check it）.
 
  i processed all of three datasets with automar, and merged them
by CAD. I used scaleit to get the Rfactor between datasets and got a
strange result. the R factor between derivant1 and native is 26% and
the R factor between derivant2 and native is 59%!
 
  so I think it may be the problem of index （space group is
P321）.  so i exchange the h and k of derivant2 by the some awk
script and merged to native data by CAD. After scaleit analysis, I
got the R factor 29% between derivant2 and native.
 
  Here is my questions,
 
  1, at my case, is that right to invert the hand? is that the
special problem of the P3 or p321 space group?
 
  2, I have carryed out some suggestion of yours, such as use
pointless （use native data as reference for derivant2 reindex）, or
reindex the derivant2 dataset by （k, h, -l）, and I always got the
high R factor 59% between derivant2 and native.
 
  Any suggestion?
 
  thanks a lot!
 
  Qixu Cai
 
 
  在 2012-5-29，下午10:36，Laurent Maveyraud
laurent.maveyr...@ipbs.fr mailto:laurent.maveyr...@ipbs.fr 写道：
 
  Hi... and apologies !
 
  I was a little quick in my answer... in P321, h k l and -h -k l
are valid indexing schemes...
  It is in P3 that you can have  h k l and k h -l
  as Ian and Phil agreed on the BB !
 
  sorry,
  laurent
 
  Hi,
 
  you might have several possible spacegroups possible when
processing your data (at the indexation step). These will be based
on the metrics of your cell (vector length and angles). If you
happen to have something like a = b, and alpha=beta90° and
gamma=120°, then it is likely that your crystal is trigonal or
hexagonal.
 
  You will have to wait until the scaling step (or pointless after
integration) in order to decide which spacegroup is the right one,
based on the symmetry operations in your dataset and on systematic
absences. There you have to choose between P3, P31, P32, P312, P321
in trigonal.
 
  When comparing two datasets from trigonal crystals, even for
identical crystals and hence identical spacegroups, you have
different ways to index your dataset...
  In P321, one dataset might be indexed one way (eg. h k l), the
other might be index the other way (k h -l). When you compared this
two dataset, they will appear to be different, because both indexing
schemes, although valid, are not equivalent.
 
  Take one reflection; e.g. 3 2 1 from your crystal A. The very
same reflection will be indexed 2 3 -1 for your crystal B, and the
one indexed 3 2 1 for crytal B will not be equivalent to the 3 2 1
reflection from crystal A.
  If you try to merge your two datasets, you will have huge
Rmerge, because you are trying to average non equivalent reflections.
 
  You will have to ensure that the same indexing scheme is used
for both datasets, eg reindex B using the reindex k h -l command in
reindex, before being able to merge A and B.
 
  hope this helps... please feel free to as if I am not clear...
 
  best regards
 
  laurent
 
  Le 29/05/2012 16:03, Qixu Cai a écrit :
 

Re: [ccp4bb] P321 space group reindex problem

[Qixu Cai]

Why the 29% Rfactor indicate the derivatives are not isomorphous to native
dataset?

Native dataset cell constant: 181.39 181.39 110.217 90 90 120
derivative1 cell constant: 181.909 181.909 109.62 90 90
120Rfactor to native: 26%
derivative2 cell constant: 181.527 181.527 109.32 90 90
120Rfactor to native: 29%

The Rfactor at low resolution is larger than in high resolution.

Could you please to help me figure out where the heavy atoms had been
soaked into the crystal?

Thank you very much.

Best wishe,

Qixu Cai





2012/5/30 Laurent Maveyraud laurent.maveyr...@ipbs.fr

 Hi,

 it is therefore likely that your spacegroup is really P321... hopefully,
 your data set is not twinned, did you check that ?

 You are left with 2 possible indexing schemes, as already mentionned. Chek
 scaling derivative / native scaling for each indexation of the derivative :
 the lowest Rfactor will likely indicate the right one.
 It appears that you end up with Rfactor of about 29 %, which suggest that
 your derivatives are not isomorphous to your native dataset. How do cell
 parameters compare for each data set ?
 Check also how the Rfactor varies with resolution, you might still have
 usefull phasing info at low resolution.

 hope this helps

 laurent



 Le 30/05/2012 07:50, Qixu Cai a écrit :

 At first, I processed the data at P3 space group. But after
 phenix.xtriage analysis, the Xtriage told me the space group must be
 P321, so I used P321 to process my data, and got an acceptable Rmerge.

 Qixu Cai



 2012/5/29 Phil Evans p...@mrc-lmb.cam.ac.uk mailto:p...@mrc-lmb.cam.ac.uk
 **


How do you know the point group is 321? What does Pointless tell you
if you put in the unmerged data?

Despite some of the things said earlier (by me!), the possible
indexing schemes in 321 are h,k,l and -h,-k,l
If that doesn't work, it suggests that the point group is a lower
symmetry eg P3

Phil


On 29 May 2012, at 16:29, Qixu Cai wrote:

  Dear all,
 
  thank you for your help.
 
  I think I must describe my case in detail. I collected a native
dataset and two heavy atom derivant datasets （in fact, i don not
know whether these two kind of heavy atom have soked into the
crystal, i just collect the data to check it）.
 
  i processed all of three datasets with automar, and merged them
by CAD. I used scaleit to get the Rfactor between datasets and got a
strange result. the R factor between derivant1 and native is 26% and
the R factor between derivant2 and native is 59%!
 
  so I think it may be the problem of index （space group is
P321）.  so i exchange the h and k of derivant2 by the some awk
script and merged to native data by CAD. After scaleit analysis, I
got the R factor 29% between derivant2 and native.
 
  Here is my questions,
 
  1, at my case, is that right to invert the hand? is that the
special problem of the P3 or p321 space group?
 
  2, I have carryed out some suggestion of yours, such as use
pointless （use native data as reference for derivant2 reindex）, or
reindex the derivant2 dataset by （k, h, -l）, and I always got the
high R factor 59% between derivant2 and native.
 
  Any suggestion?
 
  thanks a lot!
 
  Qixu Cai
 
 
  在 2012-5-29，下午10:36，Laurent Maveyraud
laurent.maveyr...@ipbs.fr 
 mailto:laurent.maveyraud@**ipbs.frlaurent.maveyr...@ipbs.fr
 写道：

 
  Hi... and apologies !
 
  I was a little quick in my answer... in P321, h k l and -h -k l
are valid indexing schemes...
  It is in P3 that you can have  h k l and k h -l
  as Ian and Phil agreed on the BB !
 
  sorry,
  laurent
 
  Hi,
 
  you might have several possible spacegroups possible when
processing your data (at the indexation step). These will be based
on the metrics of your cell (vector length and angles). If you
happen to have something like a = b, and alpha=beta90° and
gamma=120°, then it is likely that your crystal is trigonal or
hexagonal.
 
  You will have to wait until the scaling step (or pointless after
integration) in order to decide which spacegroup is the right one,
based on the symmetry operations in your dataset and on systematic
absences. There you have to choose between P3, P31, P32, P312, P321
in trigonal.
 
  When comparing two datasets from trigonal crystals, even for
identical crystals and hence identical spacegroups, you have
different ways to index your dataset...
  In P321, one dataset might be indexed one way (eg. h k l), the
other might be index the other way (k h -l). When you compared this
two dataset, they will appear to be different, because both indexing
schemes, although valid, are not equivalent.
 
  Take one reflection; e.g. 3 2 1 from your crystal A. The very
same 

Re: [ccp4bb] P321 space group reindex problem

[Qixu Cai]

 Thank you for your remind of the twin problem.

I checked all of the datasets by Xtriage, and found that the native is not
twinned, but the derivant1 and derivant2 are both twinned.

So is the Rfactor between derivants and native useful for the judgement of
the success of the heavy atom soaking?

Thanks.

Best wishes,

Qixu Cai




2012/5/30 Laurent Maveyraud laurent.maveyr...@ipbs.fr

 Hi,

 it is therefore likely that your spacegroup is really P321... hopefully,
 your data set is not twinned, did you check that ?

 You are left with 2 possible indexing schemes, as already mentionned. Chek
 scaling derivative / native scaling for each indexation of the derivative :
 the lowest Rfactor will likely indicate the right one.
 It appears that you end up with Rfactor of about 29 %, which suggest that
 your derivatives are not isomorphous to your native dataset. How do cell
 parameters compare for each data set ?
 Check also how the Rfactor varies with resolution, you might still have
 usefull phasing info at low resolution.

 hope this helps

 laurent



 Le 30/05/2012 07:50, Qixu Cai a écrit :

 At first, I processed the data at P3 space group. But after
 phenix.xtriage analysis, the Xtriage told me the space group must be
 P321, so I used P321 to process my data, and got an acceptable Rmerge.

 Qixu Cai



 2012/5/29 Phil Evans p...@mrc-lmb.cam.ac.uk mailto:p...@mrc-lmb.cam.ac.uk
 **


How do you know the point group is 321? What does Pointless tell you
if you put in the unmerged data?

Despite some of the things said earlier (by me!), the possible
indexing schemes in 321 are h,k,l and -h,-k,l
If that doesn't work, it suggests that the point group is a lower
symmetry eg P3

Phil


On 29 May 2012, at 16:29, Qixu Cai wrote:

  Dear all,
 
  thank you for your help.
 
  I think I must describe my case in detail. I collected a native
dataset and two heavy atom derivant datasets （in fact, i don not
know whether these two kind of heavy atom have soked into the
crystal, i just collect the data to check it）.
 
  i processed all of three datasets with automar, and merged them
by CAD. I used scaleit to get the Rfactor between datasets and got a
strange result. the R factor between derivant1 and native is 26% and
the R factor between derivant2 and native is 59%!
 
  so I think it may be the problem of index （space group is
P321）.  so i exchange the h and k of derivant2 by the some awk
script and merged to native data by CAD. After scaleit analysis, I
got the R factor 29% between derivant2 and native.
 
  Here is my questions,
 
  1, at my case, is that right to invert the hand? is that the
special problem of the P3 or p321 space group?
 
  2, I have carryed out some suggestion of yours, such as use
pointless （use native data as reference for derivant2 reindex）, or
reindex the derivant2 dataset by （k, h, -l）, and I always got the
high R factor 59% between derivant2 and native.
 
  Any suggestion?
 
  thanks a lot!
 
  Qixu Cai
 
 
  在 2012-5-29，下午10:36，Laurent Maveyraud
laurent.maveyr...@ipbs.fr 
 mailto:laurent.maveyraud@**ipbs.frlaurent.maveyr...@ipbs.fr
 写道：

 
  Hi... and apologies !
 
  I was a little quick in my answer... in P321, h k l and -h -k l
are valid indexing schemes...
  It is in P3 that you can have  h k l and k h -l
  as Ian and Phil agreed on the BB !
 
  sorry,
  laurent
 
  Hi,
 
  you might have several possible spacegroups possible when
processing your data (at the indexation step). These will be based
on the metrics of your cell (vector length and angles). If you
happen to have something like a = b, and alpha=beta90° and
gamma=120°, then it is likely that your crystal is trigonal or
hexagonal.
 
  You will have to wait until the scaling step (or pointless after
integration) in order to decide which spacegroup is the right one,
based on the symmetry operations in your dataset and on systematic
absences. There you have to choose between P3, P31, P32, P312, P321
in trigonal.
 
  When comparing two datasets from trigonal crystals, even for
identical crystals and hence identical spacegroups, you have
different ways to index your dataset...
  In P321, one dataset might be indexed one way (eg. h k l), the
other might be index the other way (k h -l). When you compared this
two dataset, they will appear to be different, because both indexing
schemes, although valid, are not equivalent.
 
  Take one reflection; e.g. 3 2 1 from your crystal A. The very
same reflection will be indexed 2 3 -1 for your crystal B, and the
one indexed 3 2 1 for crytal B will not be equivalent to the 3 2 1
reflection from crystal A.
  If you try to merge your two datasets, you will have huge

Re: [ccp4bb] P321 space group reindex problem

[Laurent Maveyraud]

Hi,

Le 30/05/2012 08:29, Qixu Cai a écrit :

Thank you for your remind of the twin problem.

It is always a pleasure to be helpful ;-)
By the way, you stated the spacegoup is P321... did you check systematic 
absences  ? could it be P3121 / P3221 ?




I checked all of the datasets by Xtriage, and found that the native is
not twinned, but the derivant1 and derivant2 are both twinned.

So is the Rfactor between derivants and native useful for the judgement
of the success of the heavy atom soaking?


Well, the unhelpful answer will be : it depends
what is your twin fraction ? how does the scaling derivative/native 
perfom (in details... not only global Rfactors)


Did you try to calculate Patterson maps (isomorphous and anomalous) ?

I would try to find a good MIR tutorial (CCP4 website might be a good 
place to look at, but have a look at phenix website...), and try to 
adapt it to your specific case...


good luck !

laurent


Thanks.

Best wishes,

Qixu Cai




2012/5/30 Laurent Maveyraud laurent.maveyr...@ipbs.fr
mailto:laurent.maveyr...@ipbs.fr

Hi,

it is therefore likely that your spacegroup is really P321...
hopefully, your data set is not twinned, did you check that ?

You are left with 2 possible indexing schemes, as already
mentionned. Chek scaling derivative / native scaling for each
indexation of the derivative : the lowest Rfactor will likely
indicate the right one.
It appears that you end up with Rfactor of about 29 %, which suggest
that your derivatives are not isomorphous to your native dataset.
How do cell parameters compare for each data set ?
Check also how the Rfactor varies with resolution, you might still
have usefull phasing info at low resolution.

hope this helps

laurent



Le 30/05/2012 07:50, Qixu Cai a écrit :

At first, I processed the data at P3 space group. But after
phenix.xtriage analysis, the Xtriage told me the space group must be
P321, so I used P321 to process my data, and got an acceptable
Rmerge.

Qixu Cai



2012/5/29 Phil Evans p...@mrc-lmb.cam.ac.uk
mailto:p...@mrc-lmb.cam.ac.uk mailto:p...@mrc-lmb.cam.ac.uk
mailto:p...@mrc-lmb.cam.ac.uk__


How do you know the point group is 321? What does Pointless
tell you
if you put in the unmerged data?

Despite some of the things said earlier (by me!), the possible
indexing schemes in 321 are h,k,l and -h,-k,l
If that doesn't work, it suggests that the point group is a
lower
symmetry eg P3

Phil


On 29 May 2012, at 16:29, Qixu Cai wrote:

  Dear all,
 
  thank you for your help.
 
  I think I must describe my case in detail. I collected a native
dataset and two heavy atom derivant datasets （in fact, i
don not
know whether these two kind of heavy atom have soked into the
crystal, i just collect the data to check it）.
 
  i processed all of three datasets with automar, and merged them
by CAD. I used scaleit to get the Rfactor between datasets
and got a
strange result. the R factor between derivant1 and native is
26% and
the R factor between derivant2 and native is 59%!
 
  so I think it may be the problem of index （space group is
P321）.  so i exchange the h and k of derivant2 by the some awk
script and merged to native data by CAD. After scaleit
analysis, I
got the R factor 29% between derivant2 and native.
 
  Here is my questions,
 
  1, at my case, is that right to invert the hand? is that the
special problem of the P3 or p321 space group?
 
  2, I have carryed out some suggestion of yours, such as use
pointless （use native data as reference for derivant2
reindex）, or
reindex the derivant2 dataset by （k, h, -l）, and I always
got the
high R factor 59% between derivant2 and native.
 
  Any suggestion?
 
  thanks a lot!
 
  Qixu Cai
 
 
  在 2012-5-29，下午10:36，Laurent Maveyraud
laurent.maveyr...@ipbs.fr mailto:laurent.maveyr...@ipbs.fr
mailto:laurent.maveyraud@__ipbs.fr
mailto:laurent.maveyr...@ipbs.fr 写道：

 
  Hi... and apologies !
 
  I was a little quick in my answer... in P321, h k l and -h -k l
are valid indexing schemes...
  It is in P3 that you can have  h k l and k h -l
  as Ian and Phil agreed on the BB !
 
  sorry,
  laurent
 
  Hi,
 
  you might have several possible spacegroups possible when
processing your data (at the indexation step). 

Re: [ccp4bb] P321 space group reindex problem

[Vellieux Frederic]

Hi there,

I am not certain that the thread is P321 space group reindex problem 
any more.


But: trigonal (and hexagonal) space groups are (usually?) polar. The 
cell axis c  can go up or can go down, and in order to get a 
consistent indexing you need to check both indexing systems when you 
scale additional data to your native (the indexing chosen by your first 
crystals defines the standard indexing - I must say that I haven't 
checked in the drawings of the international tables if having c going up 
or going down leads to a difference in that particular space group, 
P321, I'd need to draw both possibilities and check but I'm sorry I do 
not have the time right now - in fact it's too bad that the 
International Tables do not indicate Polar or Non-polar).


For practical purposes, a derivative is considered non isomorphous 
when the differences in unit cell parameters exceed ca. 1% (this is 
because if you take 2 crystals from the same crystallisation drop and 
collect and process diffraction crystals from these 2 crystals, you will 
never get exactly the very same values for the unit cell parameters; 
non-isomorphism effects start at ca. 1% change and you'll never get 2 
perfectly isomorphous crystals - even if you collect diffraction data 
twice from the same crystals you will not get perfect isomorphism).


From the values mentioned, 1% of the cell parameters of the native for 
a and b is 1.81 Angstroem and for c 1.1 Angstroem (the angles do not 
matter for a trigonal space group).


Had you obtained a value for a, b larger than ca. 183 Angstroem, or 
below ca. 109.2 Angstroem (only in the direction indicated by the 
changes mentioned in your mail - I ignored changes in the opposite 
direction) then you would have been able to say that the crystals were 
non-isomorphous to each other. For me they are isomorphous to each other 
and I ignore these small differences in unit cell parameters.


The difference of 3% in Rfactor (I suppose this is |FP - FPH| / |FP|, no 
Sigma character on my keyboard to indicate the summations over h k l) 
is I think due to 2 different chemicals (heavy-atom compounds) in 
derivative 1 and derivative 2. Differences in R-factors at low 
resolutions are often associated with solvent effects, and I think you 
will have 2 different mother liquors and hence 2 different solvents in 
derivative 1 and in derivative 2. That is assuming that derivative 1 and 
derivative 2 were prepared using 2 different chemicals. And typically 
low-resolution data (below 15 Angstroem resolution or so) is kept out 
during phasing by the MIR method.


To locate the heavy atom constellations in the 2 derivatives, you could 
compute and interpret difference Patterson maps - including automated 
interpretation, vector search and the likes -, you could use direct 
methods (the heavy atom constellation is similar to a small molecule 
because there are far fewer atoms there than in the full macromolecule, 
and direct methods work extremely well for small molecules - you would 
need to use the isomorphous differences in order to use direct methods; 
no mention is made of any anomalous signal so I do not know if you could 
this as well).


HTH,

Fred.

Qixu Cai wrote:
Why the 29% Rfactor indicate the derivatives are not isomorphous to 
native dataset?


Native dataset cell constant: 181.39 181.39 110.217 90 90 120
derivative1 cell constant: 181.909 181.909 109.62 90 90 
120Rfactor to native: 26%
derivative2 cell constant: 181.527 181.527 109.32 90 90 
120Rfactor to native: 29%


The Rfactor at low resolution is larger than in high resolution.

Could you please to help me figure out where the heavy atoms had been 
soaked into the crystal?


Thank you very much.

Best wishe,

Qixu Cai





2012/5/30 Laurent Maveyraud laurent.maveyr...@ipbs.fr 
mailto:laurent.maveyr...@ipbs.fr


Hi,

it is therefore likely that your spacegroup is really P321...
hopefully, your data set is not twinned, did you check that ?

You are left with 2 possible indexing schemes, as already
mentionned. Chek scaling derivative / native scaling for each
indexation of the derivative : the lowest Rfactor will likely
indicate the right one.
It appears that you end up with Rfactor of about 29 %, which
suggest that your derivatives are not isomorphous to your native
dataset. How do cell parameters compare for each data set ?
Check also how the Rfactor varies with resolution, you might still
have usefull phasing info at low resolution.

hope this helps

laurent



Le 30/05/2012 07:50, Qixu Cai a écrit :

At first, I processed the data at P3 space group. But after
phenix.xtriage analysis, the Xtriage told me the space group
must be
P321, so I used P321 to process my data, and got an acceptable
Rmerge.

Qixu Cai



2012/5/29 Phil Evans p...@mrc-lmb.cam.ac.uk
mailto:p...@mrc-lmb.cam.ac.uk 

Re: [ccp4bb] P321 space group reindex problem

[Adrian Goldman]

If the data sets are twinned, large differences between derivatives are to be 
expected unless the twin fraction is very, very low (1-2%).  Given the above, 
I think nothing can be said until the data are all detwinned - and of course 
the correct axial interchange done.

Adrian


On 30 May 2012, at 09:55, Vellieux Frederic wrote:

 Hi there,
 
 I am not certain that the thread is P321 space group reindex problem any 
 more.
 
 But: trigonal (and hexagonal) space groups are (usually?) polar. The cell 
 axis c  can go up or can go down, and in order to get a consistent 
 indexing you need to check both indexing systems when you scale additional 
 data to your native (the indexing chosen by your first crystals defines the 
 standard indexing - I must say that I haven't checked in the drawings of 
 the international tables if having c going up or going down leads to a 
 difference in that particular space group, P321, I'd need to draw both 
 possibilities and check but I'm sorry I do not have the time right now - in 
 fact it's too bad that the International Tables do not indicate Polar or 
 Non-polar).
 
 For practical purposes, a derivative is considered non isomorphous when the 
 differences in unit cell parameters exceed ca. 1% (this is because if you 
 take 2 crystals from the same crystallisation drop and collect and process 
 diffraction crystals from these 2 crystals, you will never get exactly the 
 very same values for the unit cell parameters; non-isomorphism effects start 
 at ca. 1% change and you'll never get 2 perfectly isomorphous crystals - even 
 if you collect diffraction data twice from the same crystals you will not get 
 perfect isomorphism).
 
 From the values mentioned, 1% of the cell parameters of the native for a and 
 b is 1.81 Angstroem and for c 1.1 Angstroem (the angles do not matter for a 
 trigonal space group).
 
 Had you obtained a value for a, b larger than ca. 183 Angstroem, or below ca. 
 109.2 Angstroem (only in the direction indicated by the changes mentioned in 
 your mail - I ignored changes in the opposite direction) then you would have 
 been able to say that the crystals were non-isomorphous to each other. For me 
 they are isomorphous to each other and I ignore these small differences in 
 unit cell parameters.
 
 The difference of 3% in Rfactor (I suppose this is |FP - FPH| / |FP|, no 
 Sigma character on my keyboard to indicate the summations over h k l) is I 
 think due to 2 different chemicals (heavy-atom compounds) in derivative 1 and 
 derivative 2. Differences in R-factors at low resolutions are often 
 associated with solvent effects, and I think you will have 2 different 
 mother liquors and hence 2 different solvents in derivative 1 and in 
 derivative 2. That is assuming that derivative 1 and derivative 2 were 
 prepared using 2 different chemicals. And typically low-resolution data 
 (below 15 Angstroem resolution or so) is kept out during phasing by the MIR 
 method.
 
 To locate the heavy atom constellations in the 2 derivatives, you could 
 compute and interpret difference Patterson maps - including automated 
 interpretation, vector search and the likes -, you could use direct methods 
 (the heavy atom constellation is similar to a small molecule because there 
 are far fewer atoms there than in the full macromolecule, and direct methods 
 work extremely well for small molecules - you would need to use the 
 isomorphous differences in order to use direct methods; no mention is made of 
 any anomalous signal so I do not know if you could this as well).
 
 HTH,
 
 Fred.
 
 Qixu Cai wrote:
 Why the 29% Rfactor indicate the derivatives are not isomorphous to native 
 dataset?
 
 Native dataset cell constant: 181.39 181.39 110.217 90 90 120
 derivative1 cell constant: 181.909 181.909 109.62 90 90 120  
   Rfactor to native: 26%
 derivative2 cell constant: 181.527 181.527 109.32 90 90 120  
   Rfactor to native: 29%
 
 The Rfactor at low resolution is larger than in high resolution.
 
 Could you please to help me figure out where the heavy atoms had been soaked 
 into the crystal?
 
 Thank you very much.
 
 Best wishe,
 
 Qixu Cai
 
 
 
 
 
 2012/5/30 Laurent Maveyraud laurent.maveyr...@ipbs.fr 
 mailto:laurent.maveyr...@ipbs.fr
 
Hi,
 
it is therefore likely that your spacegroup is really P321...
hopefully, your data set is not twinned, did you check that ?
 
You are left with 2 possible indexing schemes, as already
mentionned. Chek scaling derivative / native scaling for each
indexation of the derivative : the lowest Rfactor will likely
indicate the right one.
It appears that you end up with Rfactor of about 29 %, which
suggest that your derivatives are not isomorphous to your native
dataset. How do cell parameters compare for each data set ?
Check also how the Rfactor varies with resolution, you might still
have usefull phasing info at low resolution.
 
hope this helps

Re: [ccp4bb] P321 space group reindex problem

[Clemens Vonrhein]

Hi Fred,

On Wed, May 30, 2012 at 08:55:35AM +0200, Vellieux Frederic wrote:
 For practical purposes, a derivative is considered non isomorphous
 when the differences in unit cell parameters exceed ca. 1% (this is
 because if you take 2 crystals from the same crystallisation drop
 and collect and process diffraction crystals from these 2 crystals,
 you will never get exactly the very same values for the unit cell
 parameters; non-isomorphism effects start at ca. 1% change and
 you'll never get 2 perfectly isomorphous crystals - even if you
 collect diffraction data twice from the same crystals you will not
 get perfect isomorphism).
 
 From the values mentioned, 1% of the cell parameters of the native
 for a and b is 1.81 Angstroem and for c 1.1 Angstroem (the angles do
 not matter for a trigonal space group).
 
 Had you obtained a value for a, b larger than ca. 183 Angstroem, or
 below ca. 109.2 Angstroem (only in the direction indicated by the
 changes mentioned in your mail - I ignored changes in the opposite
 direction) then you would have been able to say that the crystals
 were non-isomorphous to each other. For me they are isomorphous to
 each other and I ignore these small differences in unit cell
 parameters.

I would be careful with the (popular) percentage-rule here: the
absolute value of cell differences is much more important. At least if
we assume that the change in cell parameters roughly corresponds with
a shift in actual atoms.  If you have a 1000A cell then a 1%
difference could mean a shift of 10A ... clearly, a helix moved 10A
away results in something completely different. But with a cell of 20A
you could have a 0.2A shift, which you might hardly notice.

See eg. 5.2 in Garman  Murray (2003):

  http://journals.iucr.org/d/issues/2003/11/00/ba5042/index.html

which shows

  5.2. Non-isomorphism

One of the biggest problems of heavy-atom derivatization is that
incorporation of a heavy atom into the lattice often induces a
change in the unit cell away from the native crystal values,
i.e. the derivatized crystal is non-isomorphous to the native
crystals. The heavy atom may perturb the arrangement of protein
molecules in the crystal or distort the protein molecule, causing
a change in unit-cell lengths. Note, however, that it is also
possible for the protein to move within the original unit cell
(resulting in a different sampling of the molecular
transform). The same unit cell is thus a necessary but not
sufficient condition for isomorphism.

Crick  Magdoff (1956[Crick, F. H. C.  Magdoff,
B. S. (1956). Acta Cryst. 9, 901-908.]) calculated that a 0.5 Å
change in all three unit-cell edges of a 100 Å cubed unit cell
would change the diffraction intensities by an average of 15% in a
3 Å resolution sphere. The predicted intensity changes induced by
non-isomorphism increase at higher resolution. When faced with a
non-isomorphous derivative, it is the absolute change in the cell
which should be considered compared with the working resolution,
rather than the relative change, i.e. a change of 1.0% in a 100 Å
unit cell edge has a similar effect to that of a 0.5% change in a
200 Å unit cell edge, if compared at similar resolutions. As a
general rule of thumb, a change in cell dimensions of dmin/4 is
tolerable, where dmin is the resolution limit (Drenth,
1999[Drenth, J. (1999). Principles of Protein X-ray
Crystallography, 2nd ed. Berlin: Springer-Verlag.]). For instance,
for 2.5 Å data, a 0.6 Å change in the unit cell might be
acceptable, whereas at 3.5 Å this could rise to 0.8 Å.

Cheers

Clemens

-- 

***
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--
* BUSTER Development Group  (http://www.globalphasing.com)
***

Re: [ccp4bb] P321 space group reindex problem

[Ian Tickle]

Hello Fred

On 30 May 2012 07:55, Vellieux Frederic frederic.velli...@ibs.fr wrote:
 Hi there,

 But: trigonal (and hexagonal) space groups are (usually?) polar. The cell
 axis c  can go up or can go down, and in order to get a consistent
 indexing you need to check both indexing systems when you scale additional
 data to your native (the indexing chosen by your first crystals defines the
 standard indexing - I must say that I haven't checked in the drawings of
 the international tables if having c going up or going down leads to a
 difference in that particular space group, P321, I'd need to draw both
 possibilities and check but I'm sorry I do not have the time right now - in
 fact it's too bad that the International Tables do not indicate Polar or
 Non-polar).

It does, at least my edition (Vol. A: 5th ed., 2002, Table 10.2.1.2,
p.806) does - ITC has everything you need to know about space groups
(and a lot more besides)!

See also this table that I made where all polar  non-polar SGs are
listed individually:

http://www.ccp4.ac.uk/dist/html/alternate_origins.html

Counting only the non-enantiomorphic ones, PG3 (4 SGs) and PG6 (6 SGs)
are polar, whereas PG321 (3 SGs), PG312 (3 SGs), PG32 (1 SG) and PG622
(6 SGs) are non-polar.  So in all 10 are polar and 13 are non-polar.
A 2-fold axis perp to another axis always implies that there's no
preferred direction along the other axis, so it's non-polar.

Cheers

-- Ian

Re: [ccp4bb] P321 space group reindex problem

[Vellieux Frederic]

Hi Ian,

You're right the information is there... but not where I was expecting 
it (on the page corresponding to an individual space group). It had 
never occurred to me that it could be somewhere else.


So thanks, and regards to Jasmine.

Fred.

Ian Tickle wrote:

Hello Fred

On 30 May 2012 07:55, Vellieux Frederic frederic.velli...@ibs.fr wrote:
  

Hi there,



  

But: trigonal (and hexagonal) space groups are (usually?) polar. The cell
axis c  can go up or can go down, and in order to get a consistent
indexing you need to check both indexing systems when you scale additional
data to your native (the indexing chosen by your first crystals defines the
standard indexing - I must say that I haven't checked in the drawings of
the international tables if having c going up or going down leads to a
difference in that particular space group, P321, I'd need to draw both
possibilities and check but I'm sorry I do not have the time right now - in
fact it's too bad that the International Tables do not indicate Polar or
Non-polar).



It does, at least my edition (Vol. A: 5th ed., 2002, Table 10.2.1.2,
p.806) does - ITC has everything you need to know about space groups
(and a lot more besides)!

See also this table that I made where all polar  non-polar SGs are
listed individually:

http://www.ccp4.ac.uk/dist/html/alternate_origins.html

Counting only the non-enantiomorphic ones, PG3 (4 SGs) and PG6 (6 SGs)
are polar, whereas PG321 (3 SGs), PG312 (3 SGs), PG32 (1 SG) and PG622
(6 SGs) are non-polar.  So in all 10 are polar and 13 are non-polar.
A 2-fold axis perp to another axis always implies that there's no
preferred direction along the other axis, so it's non-polar.

Cheers

-- Ian


  

Re: [ccp4bb] P321 space group reindex problem

[Ian Tickle]

 It does, at least my edition (Vol. A: 5th ed., 2002, Table 10.2.1.2,
 p.806) does - ITC has everything you need to know about space groups
 (and a lot more besides)!

Actually, as the aforementioned table indicates, it's not correct to
talk about polar and non-polar space groups, but only about polar
and non-polar directions in space groups.  Many space-groups have
both polar and non-polar directions, which would seem to imply that
these space groups are both polar and non-polar at the same time!!!
For example, P3 has a polar direction parallel to the 3-fold and no
non-polar directions, whereas P321, even though it's classed as a
non-polar space group, nevertheless has 3 polar directions [100],
[010], [-1-10] parallel to the 3 2-folds in the xy plane, plus 4
non-polar directions (including the 3-fold).  Note that any direction
perpendicular to an even-fold rotation axis is always non-polar: these
'trivial' cases are not shown explicitly in the above table.

From the point of view of deciding which are the alternate settings I
don't think it's helpful to consider polar directions anyway.  What
matters is which symmetry axes of the lattice are not present in the
point group.  So in the case of P321 the hexagonal lattice has a
6-fold parallel to c which can be thought of as the product of a 3-
and a 2-fold both || c, and also 2-folds perp to the 6-fold.  The
3-fold and the perp 2-folds are all present in P321 but the 2-fold ||
c is not, so that is what gives rise to the 2 alternate settings
(h,k,l) and (-h,-k,l).  In P3 all 2-folds are missing so you get 4
alternate settings.  The same missing symmetry can also give rise to
merohedral twinning, so it's nice to kill 2 birds with 1 stone!

Cheers

-- Ian

Re: [ccp4bb] P321 space group reindex problem

[Thomas White]

On Wed, 30 May 2012 13:16:12 +0100
Ian Tickle ianj...@gmail.com wrote:

 From the point of view of deciding which are the alternate settings I
 don't think it's helpful to consider polar directions anyway.  What
 matters is which symmetry axes of the lattice are not present in the
 point group. 

Possibly relevant here is a set of tables I put together for our
free-electron laser experiments, where tens or even hundreds of
thousands of patterns have to be indexed independently:

https://www.desy.de/~twhite/crystfel/twin-calculator.pdf

Underlying these tables is the same underlying information as
everything else mentioned on this thread, but these ones tell you
what the apparent symmetry would be if the intensities were mixed up
according to all the available indexing ambiguities.  So far, no-one
has been able to reliably resolve these ambiguities in our case: the
intensities are just obscured by too much noise, partiality, a spiky
X-ray spectrum and so on.  That's why we have to have so many
patterns.  For the time being, we just merge according to the higher
symmetry, accept that the data may be (perfectly) twinned, and handle
it at the later stages.  Later on when we've hopefully solved this
problem, these tables will serve as a menu of options for doing the
whole thing backwards.

I agree that polarity isn't the right criterion.  Point group 2 is
polar but does not exhibit any indexing ambiguity.  Point group
4/m, which is most definitely not polar, does.  This paper, Le Page et
al., has some similar tables but lists the actual ambiguity operators:
http://scripts.iucr.org/cgi-bin/paper?S0108767384001392

Of course, all of this only covers merohedral ambiguities, not
pseudo-merohedral ones which might arise by accident in special
cases.

Comments on and corrections to the tables are welcome!

Tom

[ccp4bb] P321 space group reindex problem

[Qixu Cai]

Dear all,

I have a dataset at P321 space group. And I want to reindex from (h,k,l) 
to (k,h,l) or (h,k,-l), because I want to merge this dataset to the 
native dataset.
At first, I used the reindex program in CCP4i, and got an error:  
(either for (k,h,l) or (h,k,-l))



 Data line--- reindex HKL h, k, -l
 Data line--- end

 $TEXT:Warning: $$ comment $$
 WARNING:    Reindexing matrix INVERTS hand 
 $$
 REINDEX: You are NOT allowed to do this - Changing all signs 
in reindexing matrix

Times: User:   0.0s System:0.0s Elapsed: 0:00
=

Could you please tell me the reason?

At last, I converted the mtz file to CNS format, and write a script to 
exchange the h and k, and converted to mtz file.
When I tried to use cad to merge this dataset to the native dataset, 
if I chose Automatically check and enforce consistent indexing between 
different files,

the index would be changed back to the original index. Why?

Thank you very much for your attention.

Best wishes,

Qixu Cai

Re: [ccp4bb] P321 space group reindex problem

[Ian Tickle]

In principle there's no reason why you can't invert the hand of the
indices, as long as the program which does it also takes care to
convert any hand-dependent columns such as anomalous differences,
F+/F- etc in the appropriate manner at the same time.  The program
will also need to convert any phase or phase-coefficient columns, but
it will have to do this anyway, even if the hand is not inverted, in
those cases where the space group contains screw axes (since then you
will get phase shifts on reindexing for certain subsets of
reflections).

So if the data consist only of I's or F's without anomalous data or
phases then inverting the hand will have absolutely no effect (it's
called Friedel's Law).

I note from the documentation that reindex will invert the hand if the
keyword 'LEFT' is supplied, though whether it then treats the
anomalous data and phases correctly is anyone's guess!

The question is really whether it's likely ever to be _necessary_ to
invert the hand; this will depend on the reciprocal space asymmetric
unit chosen by the processing program.  One could imagine a situation
where the a.u. chosen by one processing program was on a different
hand from the a.u. required by another.  In such a situation you would
have no choice but to invert the hand of the indices, though I suspect
you would be better off doing it with CAD which will do it reliably,
rather than reindex which may not (judging by the comments in the
reindex code!).  Whether such a situation ever occurs in practice, I
don't know, maybe not.

Cheers

-- Ian

On 29 May 2012 09:57, Graeme Winter graeme.win...@gmail.com wrote:
 Hello Qixu Cai,

 What you want is a reindexing operator which permutes the axes rather
 than one which changes the sign of an axis. The easiest way to do this
 is with pointless:

 pointless hklin input.mtz hklref reference.mtz hklout output.mtz

 and let pointless figure out the right operation to use. You may find
 the following helpful:

 http://www.ccp4.ac.uk/html/reindexing.html

 Best wishes,

 Graeme

 On 29 May 2012 09:48, Qixu Cai caiq...@gmail.com wrote:
 Dear all,

 I have a dataset at P321 space group. And I want to reindex from (h,k,l) to
 (k,h,l) or (h,k,-l), because I want to merge this dataset to the native
 dataset.
 At first, I used the reindex program in CCP4i, and got an error:  (either
 for (k,h,l) or (h,k,-l))

 
  Data line--- reindex HKL h, k, -l
  Data line--- end

  $TEXT:Warning: $$ comment $$
  WARNING:    Reindexing matrix INVERTS hand 
  $$
  REINDEX:     You are NOT allowed to do this - Changing all signs in
 reindexing matrix
 Times: User:   0.0s System:    0.0s Elapsed: 0:00
 =

 Could you please tell me the reason?

 At last, I converted the mtz file to CNS format, and write a script to
 exchange the h and k, and converted to mtz file.
 When I tried to use cad to merge this dataset to the native dataset, if I
 chose Automatically check and enforce consistent indexing between different
 files,
 the index would be changed back to the original index. Why?

 Thank you very much for your attention.

 Best wishes,

 Qixu Cai

Re: [ccp4bb] P321 space group reindex problem

[Mark J van Raaij]

In different datasets of P321 crystals, when you index them separately, the 
hand may be different and you may need to invert it for some. They 
prohibition in reindex is really a warning, and can be overridden.

Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij



On 29 May 2012, at 13:52, Ian Tickle wrote:

 In principle there's no reason why you can't invert the hand of the
 indices, as long as the program which does it also takes care to
 convert any hand-dependent columns such as anomalous differences,
 F+/F- etc in the appropriate manner at the same time.  The program
 will also need to convert any phase or phase-coefficient columns, but
 it will have to do this anyway, even if the hand is not inverted, in
 those cases where the space group contains screw axes (since then you
 will get phase shifts on reindexing for certain subsets of
 reflections).
 
 So if the data consist only of I's or F's without anomalous data or
 phases then inverting the hand will have absolutely no effect (it's
 called Friedel's Law).
 
 I note from the documentation that reindex will invert the hand if the
 keyword 'LEFT' is supplied, though whether it then treats the
 anomalous data and phases correctly is anyone's guess!
 
 The question is really whether it's likely ever to be _necessary_ to
 invert the hand; this will depend on the reciprocal space asymmetric
 unit chosen by the processing program.  One could imagine a situation
 where the a.u. chosen by one processing program was on a different
 hand from the a.u. required by another.  In such a situation you would
 have no choice but to invert the hand of the indices, though I suspect
 you would be better off doing it with CAD which will do it reliably,
 rather than reindex which may not (judging by the comments in the
 reindex code!).  Whether such a situation ever occurs in practice, I
 don't know, maybe not.
 
 Cheers
 
 -- Ian
 
 On 29 May 2012 09:57, Graeme Winter graeme.win...@gmail.com wrote:
 Hello Qixu Cai,
 
 What you want is a reindexing operator which permutes the axes rather
 than one which changes the sign of an axis. The easiest way to do this
 is with pointless:
 
 pointless hklin input.mtz hklref reference.mtz hklout output.mtz
 
 and let pointless figure out the right operation to use. You may find
 the following helpful:
 
 http://www.ccp4.ac.uk/html/reindexing.html
 
 Best wishes,
 
 Graeme
 
 On 29 May 2012 09:48, Qixu Cai caiq...@gmail.com wrote:
 Dear all,
 
 I have a dataset at P321 space group. And I want to reindex from (h,k,l) to
 (k,h,l) or (h,k,-l), because I want to merge this dataset to the native
 dataset.
 At first, I used the reindex program in CCP4i, and got an error:  (either
 for (k,h,l) or (h,k,-l))
 
 
  Data line--- reindex HKL h, k, -l
  Data line--- end
 
  $TEXT:Warning: $$ comment $$
  WARNING:    Reindexing matrix INVERTS hand 
  $$
  REINDEX: You are NOT allowed to do this - Changing all signs in
 reindexing matrix
 Times: User:   0.0s System:0.0s Elapsed: 0:00
 =
 
 Could you please tell me the reason?
 
 At last, I converted the mtz file to CNS format, and write a script to
 exchange the h and k, and converted to mtz file.
 When I tried to use cad to merge this dataset to the native dataset, if I
 chose Automatically check and enforce consistent indexing between different
 files,
 the index would be changed back to the original index. Why?
 
 Thank you very much for your attention.
 
 Best wishes,
 
 Qixu Cai

Re: [ccp4bb] P321 space group reindex problem

[Qixu Cai]

Thanks for your help.

How to use CAD to invert the hand?


2012/5/29 Ian Tickle ianj...@gmail.com

 In principle there's no reason why you can't invert the hand of the
 indices, as long as the program which does it also takes care to
 convert any hand-dependent columns such as anomalous differences,
 F+/F- etc in the appropriate manner at the same time.  The program
 will also need to convert any phase or phase-coefficient columns, but
 it will have to do this anyway, even if the hand is not inverted, in
 those cases where the space group contains screw axes (since then you
 will get phase shifts on reindexing for certain subsets of
 reflections).

 So if the data consist only of I's or F's without anomalous data or
 phases then inverting the hand will have absolutely no effect (it's
 called Friedel's Law).

 I note from the documentation that reindex will invert the hand if the
 keyword 'LEFT' is supplied, though whether it then treats the
 anomalous data and phases correctly is anyone's guess!

 The question is really whether it's likely ever to be _necessary_ to
 invert the hand; this will depend on the reciprocal space asymmetric
 unit chosen by the processing program.  One could imagine a situation
 where the a.u. chosen by one processing program was on a different
 hand from the a.u. required by another.  In such a situation you would
 have no choice but to invert the hand of the indices, though I suspect
 you would be better off doing it with CAD which will do it reliably,
 rather than reindex which may not (judging by the comments in the
 reindex code!).  Whether such a situation ever occurs in practice, I
 don't know, maybe not.

 Cheers

 -- Ian

 On 29 May 2012 09:57, Graeme Winter graeme.win...@gmail.com wrote:
  Hello Qixu Cai,
 
  What you want is a reindexing operator which permutes the axes rather
  than one which changes the sign of an axis. The easiest way to do this
  is with pointless:
 
  pointless hklin input.mtz hklref reference.mtz hklout output.mtz
 
  and let pointless figure out the right operation to use. You may find
  the following helpful:
 
  http://www.ccp4.ac.uk/html/reindexing.html
 
  Best wishes,
 
  Graeme
 
  On 29 May 2012 09:48, Qixu Cai caiq...@gmail.com wrote:
  Dear all,
 
  I have a dataset at P321 space group. And I want to reindex from
 (h,k,l) to
  (k,h,l) or (h,k,-l), because I want to merge this dataset to the native
  dataset.
  At first, I used the reindex program in CCP4i, and got an error:
 (either
  for (k,h,l) or (h,k,-l))
 
  
   Data line--- reindex HKL h, k, -l
   Data line--- end
 
   $TEXT:Warning: $$ comment $$
   WARNING:    Reindexing matrix INVERTS hand 
   $$
   REINDEX: You are NOT allowed to do this - Changing all signs in
  reindexing matrix
  Times: User:   0.0s System:0.0s Elapsed: 0:00
  =
 
  Could you please tell me the reason?
 
  At last, I converted the mtz file to CNS format, and write a script to
  exchange the h and k, and converted to mtz file.
  When I tried to use cad to merge this dataset to the native dataset,
 if I
  chose Automatically check and enforce consistent indexing between
 different
  files,
  the index would be changed back to the original index. Why?
 
  Thank you very much for your attention.
 
  Best wishes,
 
  Qixu Cai

Re: [ccp4bb] P321 space group reindex problem

[Qixu Cai]

Thanks for your help.

How to override the warning?


2012/5/29 Mark J van Raaij mjvanra...@cnb.csic.es

 In different datasets of P321 crystals, when you index them separately,
 the hand may be different and you may need to invert it for some. They
 prohibition in reindex is really a warning, and can be overridden.

 Mark J van Raaij
 Laboratorio M-4
 Dpto de Estructura de Macromoleculas
 Centro Nacional de Biotecnologia - CSIC
 c/Darwin 3
 E-28049 Madrid, Spain
 tel. (+34) 91 585 4616
 http://www.cnb.csic.es/~mjvanraaij



 On 29 May 2012, at 13:52, Ian Tickle wrote:

  In principle there's no reason why you can't invert the hand of the
  indices, as long as the program which does it also takes care to
  convert any hand-dependent columns such as anomalous differences,
  F+/F- etc in the appropriate manner at the same time.  The program
  will also need to convert any phase or phase-coefficient columns, but
  it will have to do this anyway, even if the hand is not inverted, in
  those cases where the space group contains screw axes (since then you
  will get phase shifts on reindexing for certain subsets of
  reflections).
 
  So if the data consist only of I's or F's without anomalous data or
  phases then inverting the hand will have absolutely no effect (it's
  called Friedel's Law).
 
  I note from the documentation that reindex will invert the hand if the
  keyword 'LEFT' is supplied, though whether it then treats the
  anomalous data and phases correctly is anyone's guess!
 
  The question is really whether it's likely ever to be _necessary_ to
  invert the hand; this will depend on the reciprocal space asymmetric
  unit chosen by the processing program.  One could imagine a situation
  where the a.u. chosen by one processing program was on a different
  hand from the a.u. required by another.  In such a situation you would
  have no choice but to invert the hand of the indices, though I suspect
  you would be better off doing it with CAD which will do it reliably,
  rather than reindex which may not (judging by the comments in the
  reindex code!).  Whether such a situation ever occurs in practice, I
  don't know, maybe not.
 
  Cheers
 
  -- Ian
 
  On 29 May 2012 09:57, Graeme Winter graeme.win...@gmail.com wrote:
  Hello Qixu Cai,
 
  What you want is a reindexing operator which permutes the axes rather
  than one which changes the sign of an axis. The easiest way to do this
  is with pointless:
 
  pointless hklin input.mtz hklref reference.mtz hklout output.mtz
 
  and let pointless figure out the right operation to use. You may find
  the following helpful:
 
  http://www.ccp4.ac.uk/html/reindexing.html
 
  Best wishes,
 
  Graeme
 
  On 29 May 2012 09:48, Qixu Cai caiq...@gmail.com wrote:
  Dear all,
 
  I have a dataset at P321 space group. And I want to reindex from
 (h,k,l) to
  (k,h,l) or (h,k,-l), because I want to merge this dataset to the native
  dataset.
  At first, I used the reindex program in CCP4i, and got an error:
  (either
  for (k,h,l) or (h,k,-l))
 
  
   Data line--- reindex HKL h, k, -l
   Data line--- end
 
   $TEXT:Warning: $$ comment $$
   WARNING:    Reindexing matrix INVERTS hand 
   $$
   REINDEX: You are NOT allowed to do this - Changing all signs
 in
  reindexing matrix
  Times: User:   0.0s System:0.0s Elapsed: 0:00
  =
 
  Could you please tell me the reason?
 
  At last, I converted the mtz file to CNS format, and write a script to
  exchange the h and k, and converted to mtz file.
  When I tried to use cad to merge this dataset to the native dataset,
 if I
  chose Automatically check and enforce consistent indexing between
 different
  files,
  the index would be changed back to the original index. Why?
 
  Thank you very much for your attention.
 
  Best wishes,
 
  Qixu Cai

Re: [ccp4bb] P321 space group reindex problem

[Phil Evans]

NO do NOT invert the hand. If you do you will end up with left-handed helices 
etc

The alternative indexing systems all need to preserve the right-handed axis 
system imposed by the data integration program (eg k,h,-l)

The ONLY time it is valid to invert the hand is if the indexing/integration 
program itself inverted the hand due to a bug (this has been know, but not for 
a long time)

Phil

On 29 May 2012, at 12:55, Mark J van Raaij wrote:

 In different datasets of P321 crystals, when you index them separately, the 
 hand may be different and you may need to invert it for some. They 
 prohibition in reindex is really a warning, and can be overridden.
 
 Mark J van Raaij
 Laboratorio M-4
 Dpto de Estructura de Macromoleculas
 Centro Nacional de Biotecnologia - CSIC
 c/Darwin 3
 E-28049 Madrid, Spain
 tel. (+34) 91 585 4616
 http://www.cnb.csic.es/~mjvanraaij
 
 
 
 On 29 May 2012, at 13:52, Ian Tickle wrote:
 
 In principle there's no reason why you can't invert the hand of the
 indices, as long as the program which does it also takes care to
 convert any hand-dependent columns such as anomalous differences,
 F+/F- etc in the appropriate manner at the same time.  The program
 will also need to convert any phase or phase-coefficient columns, but
 it will have to do this anyway, even if the hand is not inverted, in
 those cases where the space group contains screw axes (since then you
 will get phase shifts on reindexing for certain subsets of
 reflections).
 
 So if the data consist only of I's or F's without anomalous data or
 phases then inverting the hand will have absolutely no effect (it's
 called Friedel's Law).
 
 I note from the documentation that reindex will invert the hand if the
 keyword 'LEFT' is supplied, though whether it then treats the
 anomalous data and phases correctly is anyone's guess!
 
 The question is really whether it's likely ever to be _necessary_ to
 invert the hand; this will depend on the reciprocal space asymmetric
 unit chosen by the processing program.  One could imagine a situation
 where the a.u. chosen by one processing program was on a different
 hand from the a.u. required by another.  In such a situation you would
 have no choice but to invert the hand of the indices, though I suspect
 you would be better off doing it with CAD which will do it reliably,
 rather than reindex which may not (judging by the comments in the
 reindex code!).  Whether such a situation ever occurs in practice, I
 don't know, maybe not.
 
 Cheers
 
 -- Ian
 
 On 29 May 2012 09:57, Graeme Winter graeme.win...@gmail.com wrote:
 Hello Qixu Cai,
 
 What you want is a reindexing operator which permutes the axes rather
 than one which changes the sign of an axis. The easiest way to do this
 is with pointless:
 
 pointless hklin input.mtz hklref reference.mtz hklout output.mtz
 
 and let pointless figure out the right operation to use. You may find
 the following helpful:
 
 http://www.ccp4.ac.uk/html/reindexing.html
 
 Best wishes,
 
 Graeme
 
 On 29 May 2012 09:48, Qixu Cai caiq...@gmail.com wrote:
 Dear all,
 
 I have a dataset at P321 space group. And I want to reindex from (h,k,l) to
 (k,h,l) or (h,k,-l), because I want to merge this dataset to the native
 dataset.
 At first, I used the reindex program in CCP4i, and got an error:  (either
 for (k,h,l) or (h,k,-l))
 
 
 Data line--- reindex HKL h, k, -l
 Data line--- end
 
 $TEXT:Warning: $$ comment $$
 WARNING:    Reindexing matrix INVERTS hand 
 $$
 REINDEX: You are NOT allowed to do this - Changing all signs in
 reindexing matrix
 Times: User:   0.0s System:0.0s Elapsed: 0:00
 =
 
 Could you please tell me the reason?
 
 At last, I converted the mtz file to CNS format, and write a script to
 exchange the h and k, and converted to mtz file.
 When I tried to use cad to merge this dataset to the native dataset, if I
 chose Automatically check and enforce consistent indexing between 
 different
 files,
 the index would be changed back to the original index. Why?
 
 Thank you very much for your attention.
 
 Best wishes,
 
 Qixu Cai

Re: [ccp4bb] P321 space group reindex problem

[Ian Tickle]

Mark, thanks for pointing that out, I see it now:

In P321 the only possible alternate indexing is (-h, -k, l): this is a
2-fold || c which is an operator of the hexagonal lattice but is not
an equivalent reflection.

The standard CCP4 a.u. is h = k, l = 0 or h  k, k = 0, so for
example (3,2,1) would be in the standard a.u. (3  2 and 2 = 0).  In
the alternate indexing this would be (-3, -2, 1); however it's
impossible to transform this to the a.u. with any non-inverting
equivalent.  The only possibility is to invert the hand, i.e. to (3,
2, -1) which is again in the a.u..

So the required re-indexing operator to match (3, 2, -1) with (3, 2,
1) is (h, k, -l) which reindex won't allow without the LEFT keyword
(and you would be well-advised to avoid doing it with phase columns!).

Cheers

-- Ian

On 29 May 2012 12:55, Mark J van Raaij mjvanra...@cnb.csic.es wrote:
 In different datasets of P321 crystals, when you index them separately, the 
 hand may be different and you may need to invert it for some. They 
 prohibition in reindex is really a warning, and can be overridden.

 Mark J van Raaij
 Laboratorio M-4
 Dpto de Estructura de Macromoleculas
 Centro Nacional de Biotecnologia - CSIC
 c/Darwin 3
 E-28049 Madrid, Spain
 tel. (+34) 91 585 4616
 http://www.cnb.csic.es/~mjvanraaij



 On 29 May 2012, at 13:52, Ian Tickle wrote:

 In principle there's no reason why you can't invert the hand of the
 indices, as long as the program which does it also takes care to
 convert any hand-dependent columns such as anomalous differences,
 F+/F- etc in the appropriate manner at the same time.  The program
 will also need to convert any phase or phase-coefficient columns, but
 it will have to do this anyway, even if the hand is not inverted, in
 those cases where the space group contains screw axes (since then you
 will get phase shifts on reindexing for certain subsets of
 reflections).

 So if the data consist only of I's or F's without anomalous data or
 phases then inverting the hand will have absolutely no effect (it's
 called Friedel's Law).

 I note from the documentation that reindex will invert the hand if the
 keyword 'LEFT' is supplied, though whether it then treats the
 anomalous data and phases correctly is anyone's guess!

 The question is really whether it's likely ever to be _necessary_ to
 invert the hand; this will depend on the reciprocal space asymmetric
 unit chosen by the processing program.  One could imagine a situation
 where the a.u. chosen by one processing program was on a different
 hand from the a.u. required by another.  In such a situation you would
 have no choice but to invert the hand of the indices, though I suspect
 you would be better off doing it with CAD which will do it reliably,
 rather than reindex which may not (judging by the comments in the
 reindex code!).  Whether such a situation ever occurs in practice, I
 don't know, maybe not.

 Cheers

 -- Ian

 On 29 May 2012 09:57, Graeme Winter graeme.win...@gmail.com wrote:
 Hello Qixu Cai,

 What you want is a reindexing operator which permutes the axes rather
 than one which changes the sign of an axis. The easiest way to do this
 is with pointless:

 pointless hklin input.mtz hklref reference.mtz hklout output.mtz

 and let pointless figure out the right operation to use. You may find
 the following helpful:

 http://www.ccp4.ac.uk/html/reindexing.html

 Best wishes,

 Graeme

 On 29 May 2012 09:48, Qixu Cai caiq...@gmail.com wrote:
 Dear all,

 I have a dataset at P321 space group. And I want to reindex from (h,k,l) to
 (k,h,l) or (h,k,-l), because I want to merge this dataset to the native
 dataset.
 At first, I used the reindex program in CCP4i, and got an error:  (either
 for (k,h,l) or (h,k,-l))

 
  Data line--- reindex HKL h, k, -l
  Data line--- end

  $TEXT:Warning: $$ comment $$
  WARNING:    Reindexing matrix INVERTS hand 
  $$
  REINDEX:     You are NOT allowed to do this - Changing all signs in
 reindexing matrix
 Times: User:       0.0s System:    0.0s Elapsed:     0:00
 =

 Could you please tell me the reason?

 At last, I converted the mtz file to CNS format, and write a script to
 exchange the h and k, and converted to mtz file.
 When I tried to use cad to merge this dataset to the native dataset, if I
 chose Automatically check and enforce consistent indexing between 
 different
 files,
 the index would be changed back to the original index. Why?

 Thank you very much for your attention.

 Best wishes,

 Qixu Cai

Re: [ccp4bb] P321 space group reindex problem

[Ian Tickle]

Phil,

On 29 May 2012 14:08, Phil Evans p...@mrc-lmb.cam.ac.uk wrote:
 NO do NOT invert the hand. If you do you will end up with left-handed helices 
 etc

Surely not if you take care to also change the signs of the anomalous
differences?

 The alternative indexing systems all need to preserve the right-handed axis 
 system imposed by the data integration program (eg k,h,-l)

 The ONLY time it is valid to invert the hand is if the indexing/integration 
 program itself inverted the hand due to a bug (this has been know, but not 
 for a long time)

Assuming I've got the correct transformations and a.u. in P321 it's
only possible to re-index from the alternate setting if the hand is
inverted (and the anomalous data  any phase columns converted).

Cheers

-- Ian

Re: [ccp4bb] P321 space group reindex problem

[Qixu Cai]

P3 is another possible alternate indexing? is that correct?


2012/5/29 Ian Tickle ianj...@gmail.com

 Mark, thanks for pointing that out, I see it now:

 In P321 the only possible alternate indexing is (-h, -k, l): this is a
 2-fold || c which is an operator of the hexagonal lattice but is not
 an equivalent reflection.

 The standard CCP4 a.u. is h = k, l = 0 or h  k, k = 0, so for
 example (3,2,1) would be in the standard a.u. (3  2 and 2 = 0).  In
 the alternate indexing this would be (-3, -2, 1); however it's
 impossible to transform this to the a.u. with any non-inverting
 equivalent.  The only possibility is to invert the hand, i.e. to (3,
 2, -1) which is again in the a.u..

 So the required re-indexing operator to match (3, 2, -1) with (3, 2,
 1) is (h, k, -l) which reindex won't allow without the LEFT keyword
 (and you would be well-advised to avoid doing it with phase columns!).

 Cheers

 -- Ian

 On 29 May 2012 12:55, Mark J van Raaij mjvanra...@cnb.csic.es wrote:
  In different datasets of P321 crystals, when you index them separately,
 the hand may be different and you may need to invert it for some. They
 prohibition in reindex is really a warning, and can be overridden.
 
  Mark J van Raaij
  Laboratorio M-4
  Dpto de Estructura de Macromoleculas
  Centro Nacional de Biotecnologia - CSIC
  c/Darwin 3
  E-28049 Madrid, Spain
  tel. (+34) 91 585 4616
  http://www.cnb.csic.es/~mjvanraaij
 
 
 
  On 29 May 2012, at 13:52, Ian Tickle wrote:
 
  In principle there's no reason why you can't invert the hand of the
  indices, as long as the program which does it also takes care to
  convert any hand-dependent columns such as anomalous differences,
  F+/F- etc in the appropriate manner at the same time.  The program
  will also need to convert any phase or phase-coefficient columns, but
  it will have to do this anyway, even if the hand is not inverted, in
  those cases where the space group contains screw axes (since then you
  will get phase shifts on reindexing for certain subsets of
  reflections).
 
  So if the data consist only of I's or F's without anomalous data or
  phases then inverting the hand will have absolutely no effect (it's
  called Friedel's Law).
 
  I note from the documentation that reindex will invert the hand if the
  keyword 'LEFT' is supplied, though whether it then treats the
  anomalous data and phases correctly is anyone's guess!
 
  The question is really whether it's likely ever to be _necessary_ to
  invert the hand; this will depend on the reciprocal space asymmetric
  unit chosen by the processing program.  One could imagine a situation
  where the a.u. chosen by one processing program was on a different
  hand from the a.u. required by another.  In such a situation you would
  have no choice but to invert the hand of the indices, though I suspect
  you would be better off doing it with CAD which will do it reliably,
  rather than reindex which may not (judging by the comments in the
  reindex code!).  Whether such a situation ever occurs in practice, I
  don't know, maybe not.
 
  Cheers
 
  -- Ian
 
  On 29 May 2012 09:57, Graeme Winter graeme.win...@gmail.com wrote:
  Hello Qixu Cai,
 
  What you want is a reindexing operator which permutes the axes rather
  than one which changes the sign of an axis. The easiest way to do this
  is with pointless:
 
  pointless hklin input.mtz hklref reference.mtz hklout output.mtz
 
  and let pointless figure out the right operation to use. You may find
  the following helpful:
 
  http://www.ccp4.ac.uk/html/reindexing.html
 
  Best wishes,
 
  Graeme
 
  On 29 May 2012 09:48, Qixu Cai caiq...@gmail.com wrote:
  Dear all,
 
  I have a dataset at P321 space group. And I want to reindex from
 (h,k,l) to
  (k,h,l) or (h,k,-l), because I want to merge this dataset to the
 native
  dataset.
  At first, I used the reindex program in CCP4i, and got an error:
  (either
  for (k,h,l) or (h,k,-l))
 
  
   Data line--- reindex HKL h, k, -l
   Data line--- end
 
   $TEXT:Warning: $$ comment $$
   WARNING:    Reindexing matrix INVERTS hand 
   $$
   REINDEX: You are NOT allowed to do this - Changing all signs
 in
  reindexing matrix
  Times: User:   0.0s System:0.0s Elapsed: 0:00
  =
 
  Could you please tell me the reason?
 
  At last, I converted the mtz file to CNS format, and write a script to
  exchange the h and k, and converted to mtz file.
  When I tried to use cad to merge this dataset to the native
 dataset, if I
  chose Automatically check and enforce consistent indexing between
 different
  files,
  the index would be changed back to the original index. Why?
 
  Thank you very much for your attention.
 
  Best wishes,
 
  Qixu Cai

Re: [ccp4bb] P321 space group reindex problem

[Ian Tickle]

Qixu, yes obviously any sub-group is a possible indexing (all the way
down to P1 !).  You need to compare your Rpims etc.

Cheers

-- Ian

On 29 May 2012 15:03, Qixu Cai caiq...@gmail.com wrote:
 P3 is another possible alternate indexing? is that correct?



 2012/5/29 Ian Tickle ianj...@gmail.com

 Mark, thanks for pointing that out, I see it now:

 In P321 the only possible alternate indexing is (-h, -k, l): this is a
 2-fold || c which is an operator of the hexagonal lattice but is not
 an equivalent reflection.

 The standard CCP4 a.u. is h = k, l = 0 or h  k, k = 0, so for
 example (3,2,1) would be in the standard a.u. (3  2 and 2 = 0).  In
 the alternate indexing this would be (-3, -2, 1); however it's
 impossible to transform this to the a.u. with any non-inverting
 equivalent.  The only possibility is to invert the hand, i.e. to (3,
 2, -1) which is again in the a.u..

 So the required re-indexing operator to match (3, 2, -1) with (3, 2,
 1) is (h, k, -l) which reindex won't allow without the LEFT keyword
 (and you would be well-advised to avoid doing it with phase columns!).

 Cheers

 -- Ian

 On 29 May 2012 12:55, Mark J van Raaij mjvanra...@cnb.csic.es wrote:
  In different datasets of P321 crystals, when you index them separately,
  the hand may be different and you may need to invert it for some. They
  prohibition in reindex is really a warning, and can be overridden.
 
  Mark J van Raaij
  Laboratorio M-4
  Dpto de Estructura de Macromoleculas
  Centro Nacional de Biotecnologia - CSIC
  c/Darwin 3
  E-28049 Madrid, Spain
  tel. (+34) 91 585 4616
  http://www.cnb.csic.es/~mjvanraaij
 
 
 
  On 29 May 2012, at 13:52, Ian Tickle wrote:
 
  In principle there's no reason why you can't invert the hand of the
  indices, as long as the program which does it also takes care to
  convert any hand-dependent columns such as anomalous differences,
  F+/F- etc in the appropriate manner at the same time.  The program
  will also need to convert any phase or phase-coefficient columns, but
  it will have to do this anyway, even if the hand is not inverted, in
  those cases where the space group contains screw axes (since then you
  will get phase shifts on reindexing for certain subsets of
  reflections).
 
  So if the data consist only of I's or F's without anomalous data or
  phases then inverting the hand will have absolutely no effect (it's
  called Friedel's Law).
 
  I note from the documentation that reindex will invert the hand if the
  keyword 'LEFT' is supplied, though whether it then treats the
  anomalous data and phases correctly is anyone's guess!
 
  The question is really whether it's likely ever to be _necessary_ to
  invert the hand; this will depend on the reciprocal space asymmetric
  unit chosen by the processing program.  One could imagine a situation
  where the a.u. chosen by one processing program was on a different
  hand from the a.u. required by another.  In such a situation you would
  have no choice but to invert the hand of the indices, though I suspect
  you would be better off doing it with CAD which will do it reliably,
  rather than reindex which may not (judging by the comments in the
  reindex code!).  Whether such a situation ever occurs in practice, I
  don't know, maybe not.
 
  Cheers
 
  -- Ian
 
  On 29 May 2012 09:57, Graeme Winter graeme.win...@gmail.com wrote:
  Hello Qixu Cai,
 
  What you want is a reindexing operator which permutes the axes rather
  than one which changes the sign of an axis. The easiest way to do this
  is with pointless:
 
  pointless hklin input.mtz hklref reference.mtz hklout output.mtz
 
  and let pointless figure out the right operation to use. You may find
  the following helpful:
 
  http://www.ccp4.ac.uk/html/reindexing.html
 
  Best wishes,
 
  Graeme
 
  On 29 May 2012 09:48, Qixu Cai caiq...@gmail.com wrote:
  Dear all,
 
  I have a dataset at P321 space group. And I want to reindex from
  (h,k,l) to
  (k,h,l) or (h,k,-l), because I want to merge this dataset to the
  native
  dataset.
  At first, I used the reindex program in CCP4i, and got an error:
   (either
  for (k,h,l) or (h,k,-l))
 
  
   Data line--- reindex HKL h, k, -l
   Data line--- end
 
   $TEXT:Warning: $$ comment $$
   WARNING:    Reindexing matrix INVERTS hand 
   $$
   REINDEX:     You are NOT allowed to do this - Changing all signs
  in
  reindexing matrix
  Times: User:       0.0s System:    0.0s Elapsed:     0:00
  =
 
  Could you please tell me the reason?
 
  At last, I converted the mtz file to CNS format, and write a script
  to
  exchange the h and k, and converted to mtz file.
  When I tried to use cad to merge this dataset to the native
  dataset, if I
  chose Automatically check and enforce consistent indexing between
  different
  files,
  the index would be changed back to the original index. Why?
 
  Thank you very much for your attention.
 

Re: [ccp4bb] P321 space group reindex problem

[Phil Evans]

On 29 May 2012, at 15:02, Ian Tickle wrote:

 Phil,
 
 On 29 May 2012 14:08, Phil Evans p...@mrc-lmb.cam.ac.uk wrote:
 NO do NOT invert the hand. If you do you will end up with left-handed 
 helices etc
 
 Surely not if you take care to also change the signs of the anomalous
 differences?

I suppose that's true (I think) but it's no harder to do it properly (ie 
preserving the hand


 
 The alternative indexing systems all need to preserve the right-handed axis 
 system imposed by the data integration program (eg k,h,-l)
 
 The ONLY time it is valid to invert the hand is if the indexing/integration 
 program itself inverted the hand due to a bug (this has been know, but not 
 for a long time)
 
 Assuming I've got the correct transformations and a.u. in P321 it's
 only possible to re-index from the alternate setting if the hand is
 inverted (and the anomalous data  any phase columns converted).
 


No the hand-preserving transformation in 321 is (k,h,-l)

Phil



 Cheers
 
 -- Ian

Re: [ccp4bb] P321 space group reindex problem

[George Sheldrick]

Which programs require that the data be the 'standard' a.u.? None of 
mine require this.


George

On 05/29/2012 03:44 PM, Ian Tickle wrote:

Mark, thanks for pointing that out, I see it now:

In P321 the only possible alternate indexing is (-h, -k, l): this is a
2-fold || c which is an operator of the hexagonal lattice but is not
an equivalent reflection.

The standard CCP4 a.u. is h = k, l= 0 or h  k, k= 0, so for
example (3,2,1) would be in the standard a.u. (3  2 and 2= 0).  In
the alternate indexing this would be (-3, -2, 1); however it's
impossible to transform this to the a.u. with any non-inverting
equivalent.  The only possibility is to invert the hand, i.e. to (3,
2, -1) which is again in the a.u..

So the required re-indexing operator to match (3, 2, -1) with (3, 2,
1) is (h, k, -l) which reindex won't allow without the LEFT keyword
(and you would be well-advised to avoid doing it with phase columns!).

Cheers

-- Ian


--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] P321 space group reindex problem

[Ian Tickle]

Phil,

On 29 May 2012 15:09, Phil Evans p...@mrc-lmb.cam.ac.uk wrote:

 No the hand-preserving transformation in 321 is (k,h,-l)

But that's an equivalent of the space group so it won't transform from
the alternate setting (-h, -k, l). It will just give you a _different_
a.u. of the _same_ setting.  We need the _same_ a.u. of the
_different_ setting!

Cheers

-- Ian

Re: [ccp4bb] P321 space group reindex problem

[Phil Evans]

Although there is no need for a standard reciprocal asu, it is convenient to 
have all your datasets in the same convention when it comes to comparing and 
combining different isomorphous datasets (ie to do it once rather than every 
time you compare them). It doesn't matter what the standard is as long as it 
is consistent

Reading Ian's Email more carefully, it is true that eg in 321 the reindexing 
k,h,-l may take it out of the standard asu, and need an inversion operator to 
put it back. In that case, Pointless (and Reindex) do reduce the hkl to the asu 
and swap anomalous columns, and pointless will also invert phase columns etc

 No the hand-preserving transformation in 321 is (k,h,-l)
 
 But that's an equivalent of the space group so it won't transform from
 the alternate setting (-h, -k, l). It will just give you a _different_
 a.u. of the _same_ setting.  We need the _same_ a.u. of the
 _different_ setting!


Apologies, you are right, for 321 the reindexing operator is (-h,-k,l). But 
Pointless will do it correctly (I believe!)

Phil


On 29 May 2012, at 14:29, George Sheldrick wrote:

 Which programs require that the data be the 'standard' a.u.? None of mine 
 require this.
 
 George
 
 On 05/29/2012 03:44 PM, Ian Tickle wrote:
 Mark, thanks for pointing that out, I see it now:
 
 In P321 the only possible alternate indexing is (-h, -k, l): this is a
 2-fold || c which is an operator of the hexagonal lattice but is not
 an equivalent reflection.
 
 The standard CCP4 a.u. is h = k, l= 0 or h  k, k= 0, so for
 example (3,2,1) would be in the standard a.u. (3  2 and 2= 0).  In
 the alternate indexing this would be (-3, -2, 1); however it's
 impossible to transform this to the a.u. with any non-inverting
 equivalent.  The only possibility is to invert the hand, i.e. to (3,
 2, -1) which is again in the a.u..
 
 So the required re-indexing operator to match (3, 2, -1) with (3, 2,
 1) is (h, k, -l) which reindex won't allow without the LEFT keyword
 (and you would be well-advised to avoid doing it with phase columns!).
 
 Cheers
 
 -- Ian
 
 -- 
 Prof. George M. Sheldrick FRS
 Dept. Structural Chemistry,
 University of Goettingen,
 Tammannstr. 4,
 D37077 Goettingen, Germany
 Tel. +49-551-39-3021 or -3068
 Fax. +49-551-39-22582

Re: [ccp4bb] P321 space group reindex problem

[Ian Tickle]

George

The CCP4 programs (I can't speak for others) involved with isomorphous
replacement, i.e. scaling, FFT for difference Pattersons  Fouriers,
and heavy-atom refinement (e.g. MLPHARE), mostly require that the
native data and that of all the derivatives be not only in the same
a.u. but sorted identically, so the preceding programs such as CAD go
to a lot of trouble to ensure this.

Cheers

-- Ian

On 29 May 2012 14:29, George Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote:
 Which programs require that the data be the 'standard' a.u.? None of mine
 require this.

 George


 On 05/29/2012 03:44 PM, Ian Tickle wrote:

 Mark, thanks for pointing that out, I see it now:

 In P321 the only possible alternate indexing is (-h, -k, l): this is a
 2-fold || c which is an operator of the hexagonal lattice but is not
 an equivalent reflection.

 The standard CCP4 a.u. is h = k, l= 0 or h  k, k= 0, so for
 example (3,2,1) would be in the standard a.u. (3  2 and 2= 0).  In
 the alternate indexing this would be (-3, -2, 1); however it's
 impossible to transform this to the a.u. with any non-inverting
 equivalent.  The only possibility is to invert the hand, i.e. to (3,
 2, -1) which is again in the a.u..

 So the required re-indexing operator to match (3, 2, -1) with (3, 2,
 1) is (h, k, -l) which reindex won't allow without the LEFT keyword
 (and you would be well-advised to avoid doing it with phase columns!).

 Cheers

 -- Ian


 --
 Prof. George M. Sheldrick FRS
 Dept. Structural Chemistry,
 University of Goettingen,
 Tammannstr. 4,
 D37077 Goettingen, Germany
 Tel. +49-551-39-3021 or -3068
 Fax. +49-551-39-22582

Re: [ccp4bb] P321 space group reindex problem

[Qixu Cai]

Dear all,

thank you for your help.

I think I must describe my case in detail. I collected a native dataset and two 
heavy atom derivant datasets （in fact, i don not know whether these two kind of 
heavy atom have soked into the crystal, i just collect the data to check it）.

i processed all of three datasets with automar, and merged them by CAD. I used 
scaleit to get the Rfactor between datasets and got a strange result. the R 
factor between derivant1 and native is 26% and the R factor between derivant2 
and native is 59%!

so I think it may be the problem of index （space group is P321）.  so i exchange 
the h and k of derivant2 by the some awk script and merged to native data by 
CAD. After scaleit analysis, I got the R factor 29% between derivant2 and 
native.

Here is my questions,

1, at my case, is that right to invert the hand? is that the special problem of 
the P3 or p321 space group?

2, I have carryed out some suggestion of yours, such as use pointless （use 
native data as reference for derivant2 reindex）, or reindex the derivant2 
dataset by （k, h, -l）, and I always got the high R factor 59% between derivant2 
and native.

Any suggestion?

thanks a lot!

Qixu Cai


在 2012-5-29，下午10:36，Laurent Maveyraud laurent.maveyr...@ipbs.fr 写道：

 Hi... and apologies !
 
 I was a little quick in my answer... in P321, h k l and -h -k l are valid 
 indexing schemes...
 It is in P3 that you can have  h k l and k h -l
 as Ian and Phil agreed on the BB !
 
 sorry,
 laurent
 
 Hi,
 
 you might have several possible spacegroups possible when processing your 
 data (at the indexation step). These will be based on the metrics of your 
 cell (vector length and angles). If you happen to have something like a = b, 
 and alpha=beta90° and gamma=120°, then it is likely that your crystal is 
 trigonal or hexagonal.
 
 You will have to wait until the scaling step (or pointless after integration) 
 in order to decide which spacegroup is the right one, based on the symmetry 
 operations in your dataset and on systematic absences. There you have to 
 choose between P3, P31, P32, P312, P321 in trigonal.
 
 When comparing two datasets from trigonal crystals, even for identical 
 crystals and hence identical spacegroups, you have different ways to index 
 your dataset...
 In P321, one dataset might be indexed one way (eg. h k l), the other might be 
 index the other way (k h -l). When you compared this two dataset, they will 
 appear to be different, because both indexing schemes, although valid, are 
 not equivalent.
 
 Take one reflection; e.g. 3 2 1 from your crystal A. The very same reflection 
 will be indexed 2 3 -1 for your crystal B, and the one indexed 3 2 1 for 
 crytal B will not be equivalent to the 3 2 1 reflection from crystal A.
 If you try to merge your two datasets, you will have huge Rmerge, because you 
 are trying to average non equivalent reflections.
 
 You will have to ensure that the same indexing scheme is used for both 
 datasets, eg reindex B using the reindex k h -l command in reindex, before 
 being able to merge A and B.
 
 hope this helps... please feel free to as if I am not clear...
 
 best regards
 
 laurent
 
 Le 29/05/2012 16:03, Qixu Cai a écrit :
 P3 is another possible alternate indexing? is that correct?
 
 
 2012/5/29 Ian Tickle ianj...@gmail.com mailto:ianj...@gmail.com
 
Mark, thanks for pointing that out, I see it now:
 
In P321 the only possible alternate indexing is (-h, -k, l): this is a
2-fold || c which is an operator of the hexagonal lattice but is not
an equivalent reflection.
 
The standard CCP4 a.u. is h = k, l = 0 or h  k, k = 0, so for
example (3,2,1) would be in the standard a.u. (3  2 and 2 = 0).  In
the alternate indexing this would be (-3, -2, 1); however it's
impossible to transform this to the a.u. with any non-inverting
equivalent.  The only possibility is to invert the hand, i.e. to (3,
2, -1) which is again in the a.u..
 
So the required re-indexing operator to match (3, 2, -1) with (3, 2,
1) is (h, k, -l) which reindex won't allow without the LEFT keyword
(and you would be well-advised to avoid doing it with phase columns!).
 
Cheers
 
-- Ian
 
On 29 May 2012 12:55, Mark J van Raaij mjvanra...@cnb.csic.es
mailto:mjvanra...@cnb.csic.es wrote:
  In different datasets of P321 crystals, when you index them
separately, the hand may be different and you may need to invert it
for some. They prohibition in reindex is really a warning, and can
be overridden.
 
  Mark J van Raaij
  Laboratorio M-4
  Dpto de Estructura de Macromoleculas
  Centro Nacional de Biotecnologia - CSIC
  c/Darwin 3
  E-28049 Madrid, Spain
  tel. (+34) 91 585 4616
  http://www.cnb.csic.es/~mjvanraaij
http://www.cnb.csic.es/%7Emjvanraaij
 
 
 
  On 29 May 2012, at 13:52, Ian Tickle wrote:
 
  In principle there's no reason why you can't invert the hand of 

Re: [ccp4bb] P321 space group reindex problem

[Phil Evans]

How do you know the point group is 321? What does Pointless tell you if you put 
in the unmerged data?

Despite some of the things said earlier (by me!), the possible indexing schemes 
in 321 are h,k,l and -h,-k,l
If that doesn't work, it suggests that the point group is a lower symmetry eg P3

Phil


On 29 May 2012, at 16:29, Qixu Cai wrote:

 Dear all,
 
 thank you for your help.
 
 I think I must describe my case in detail. I collected a native dataset and 
 two heavy atom derivant datasets （in fact, i don not know whether these two 
 kind of heavy atom have soked into the crystal, i just collect the data to 
 check it）.
 
 i processed all of three datasets with automar, and merged them by CAD. I 
 used scaleit to get the Rfactor between datasets and got a strange result. 
 the R factor between derivant1 and native is 26% and the R factor between 
 derivant2 and native is 59%!
 
 so I think it may be the problem of index （space group is P321）.  so i 
 exchange the h and k of derivant2 by the some awk script and merged to native 
 data by CAD. After scaleit analysis, I got the R factor 29% between derivant2 
 and native.
 
 Here is my questions,
 
 1, at my case, is that right to invert the hand? is that the special problem 
 of the P3 or p321 space group?
 
 2, I have carryed out some suggestion of yours, such as use pointless （use 
 native data as reference for derivant2 reindex）, or reindex the derivant2 
 dataset by （k, h, -l）, and I always got the high R factor 59% between 
 derivant2 and native.
 
 Any suggestion?
 
 thanks a lot!
 
 Qixu Cai
 
 
 在 2012-5-29，下午10:36，Laurent Maveyraud laurent.maveyr...@ipbs.fr 写道：
 
 Hi... and apologies !
 
 I was a little quick in my answer... in P321, h k l and -h -k l are valid 
 indexing schemes...
 It is in P3 that you can have  h k l and k h -l
 as Ian and Phil agreed on the BB !
 
 sorry,
 laurent
 
 Hi,
 
 you might have several possible spacegroups possible when processing your 
 data (at the indexation step). These will be based on the metrics of your 
 cell (vector length and angles). If you happen to have something like a = b, 
 and alpha=beta90° and gamma=120°, then it is likely that your crystal is 
 trigonal or hexagonal.
 
 You will have to wait until the scaling step (or pointless after 
 integration) in order to decide which spacegroup is the right one, based on 
 the symmetry operations in your dataset and on systematic absences. There 
 you have to choose between P3, P31, P32, P312, P321 in trigonal.
 
 When comparing two datasets from trigonal crystals, even for identical 
 crystals and hence identical spacegroups, you have different ways to index 
 your dataset...
 In P321, one dataset might be indexed one way (eg. h k l), the other might 
 be index the other way (k h -l). When you compared this two dataset, they 
 will appear to be different, because both indexing schemes, although valid, 
 are not equivalent.
 
 Take one reflection; e.g. 3 2 1 from your crystal A. The very same 
 reflection will be indexed 2 3 -1 for your crystal B, and the one indexed 3 
 2 1 for crytal B will not be equivalent to the 3 2 1 reflection from crystal 
 A.
 If you try to merge your two datasets, you will have huge Rmerge, because 
 you are trying to average non equivalent reflections.
 
 You will have to ensure that the same indexing scheme is used for both 
 datasets, eg reindex B using the reindex k h -l command in reindex, before 
 being able to merge A and B.
 
 hope this helps... please feel free to as if I am not clear...
 
 best regards
 
 laurent
 
 Le 29/05/2012 16:03, Qixu Cai a écrit :
 P3 is another possible alternate indexing? is that correct?
 
 
 2012/5/29 Ian Tickle ianj...@gmail.com mailto:ianj...@gmail.com
 
   Mark, thanks for pointing that out, I see it now:
 
   In P321 the only possible alternate indexing is (-h, -k, l): this is a
   2-fold || c which is an operator of the hexagonal lattice but is not
   an equivalent reflection.
 
   The standard CCP4 a.u. is h = k, l = 0 or h  k, k = 0, so for
   example (3,2,1) would be in the standard a.u. (3  2 and 2 = 0).  In
   the alternate indexing this would be (-3, -2, 1); however it's
   impossible to transform this to the a.u. with any non-inverting
   equivalent.  The only possibility is to invert the hand, i.e. to (3,
   2, -1) which is again in the a.u..
 
   So the required re-indexing operator to match (3, 2, -1) with (3, 2,
   1) is (h, k, -l) which reindex won't allow without the LEFT keyword
   (and you would be well-advised to avoid doing it with phase columns!).
 
   Cheers
 
   -- Ian
 
   On 29 May 2012 12:55, Mark J van Raaij mjvanra...@cnb.csic.es
   mailto:mjvanra...@cnb.csic.es wrote:
 In different datasets of P321 crystals, when you index them
   separately, the hand may be different and you may need to invert it
   for some. They prohibition in reindex is really a warning, and can
   be overridden.
 
 Mark J van Raaij
 Laboratorio M-4
 Dpto de Estructura de Macromoleculas
 

Re: [ccp4bb] P321 space group reindex problem

[Ian Tickle]

Hi Qixu

Whether it's valid to simply swap h and k depends on whether you have
anomalous data (I assume you don't have any phases at this stage).  If
not there's no issue with inverting the hand, but if you do then you
must either remove the anomalous data to avoid confusing yourself and
others later on, or change the sign of the anomalous differences (or
swap F-/F+ and/or I-/I+ as appropriate).

You swapped h and k i.e. (h, k, l) to (k, h, l): taken with the
equivalent reflection (k, h, -l) this gives (h, k, -l) which is
exactly the index transformation that I derived (see my previous
email).  You could have done the same thing with reindex using h,k,-l
and the LEFT keyword (in fact I would stick to well-tried programs!).
So with my proviso about anomalous data above, what you have done is
completely correct and the R factor of 29% that you got for derivative
2 (assuming I've understood you correctly) supports this.

I can't explain why pointless appears not to have worked, Phil is the
person to ask about that.

Cheers

-- Ian

On 29 May 2012 16:29, Qixu Cai caiq...@gmail.com wrote:
 Dear all,

 thank you for your help.

 I think I must describe my case in detail. I collected a native dataset and 
 two heavy atom derivant datasets （in fact, i don not know whether these two 
 kind of heavy atom have soked into the crystal, i just collect the data to 
 check it）.

 i processed all of three datasets with automar, and merged them by CAD. I 
 used scaleit to get the Rfactor between datasets and got a strange result. 
 the R factor between derivant1 and native is 26% and the R factor between 
 derivant2 and native is 59%!

 so I think it may be the problem of index （space group is P321）.  so i 
 exchange the h and k of derivant2 by the some awk script and merged to native 
 data by CAD. After scaleit analysis, I got the R factor 29% between derivant2 
 and native.

 Here is my questions,

 1, at my case, is that right to invert the hand? is that the special problem 
 of the P3 or p321 space group?

 2, I have carryed out some suggestion of yours, such as use pointless （use 
 native data as reference for derivant2 reindex）, or reindex the derivant2 
 dataset by （k, h, -l）, and I always got the high R factor 59% between 
 derivant2 and native.

 Any suggestion?

 thanks a lot!

 Qixu Cai


 在 2012-5-29，下午10:36，Laurent Maveyraud laurent.maveyr...@ipbs.fr 写道：

 Hi... and apologies !

 I was a little quick in my answer... in P321, h k l and -h -k l are valid 
 indexing schemes...
 It is in P3 that you can have  h k l and k h -l
 as Ian and Phil agreed on the BB !

 sorry,
 laurent

 Hi,

 you might have several possible spacegroups possible when processing your 
 data (at the indexation step). These will be based on the metrics of your 
 cell (vector length and angles). If you happen to have something like a = b, 
 and alpha=beta90° and gamma=120°, then it is likely that your crystal is 
 trigonal or hexagonal.

 You will have to wait until the scaling step (or pointless after 
 integration) in order to decide which spacegroup is the right one, based on 
 the symmetry operations in your dataset and on systematic absences. There 
 you have to choose between P3, P31, P32, P312, P321 in trigonal.

 When comparing two datasets from trigonal crystals, even for identical 
 crystals and hence identical spacegroups, you have different ways to index 
 your dataset...
 In P321, one dataset might be indexed one way (eg. h k l), the other might 
 be index the other way (k h -l). When you compared this two dataset, they 
 will appear to be different, because both indexing schemes, although valid, 
 are not equivalent.

 Take one reflection; e.g. 3 2 1 from your crystal A. The very same 
 reflection will be indexed 2 3 -1 for your crystal B, and the one indexed 3 
 2 1 for crytal B will not be equivalent to the 3 2 1 reflection from crystal 
 A.
 If you try to merge your two datasets, you will have huge Rmerge, because 
 you are trying to average non equivalent reflections.

 You will have to ensure that the same indexing scheme is used for both 
 datasets, eg reindex B using the reindex k h -l command in reindex, before 
 being able to merge A and B.

 hope this helps... please feel free to as if I am not clear...

 best regards

 laurent

 Le 29/05/2012 16:03, Qixu Cai a écrit :
 P3 is another possible alternate indexing? is that correct?


 2012/5/29 Ian Tickle ianj...@gmail.com mailto:ianj...@gmail.com

    Mark, thanks for pointing that out, I see it now:

    In P321 the only possible alternate indexing is (-h, -k, l): this is a
    2-fold || c which is an operator of the hexagonal lattice but is not
    an equivalent reflection.

    The standard CCP4 a.u. is h = k, l = 0 or h  k, k = 0, so for
    example (3,2,1) would be in the standard a.u. (3  2 and 2 = 0).  In
    the alternate indexing this would be (-3, -2, 1); however it's
    impossible to transform this to the a.u. with any non-inverting
    equivalent.  The 

Re: [ccp4bb] P321 space group reindex problem

[Qixu Cai]

At first, I processed the data at P3 space group. But after phenix.xtriage
analysis, the Xtriage told me the space group must be P321, so I used P321
to process my data, and got an acceptable Rmerge.

Qixu Cai



2012/5/29 Phil Evans p...@mrc-lmb.cam.ac.uk

 How do you know the point group is 321? What does Pointless tell you if
 you put in the unmerged data?

 Despite some of the things said earlier (by me!), the possible indexing
 schemes in 321 are h,k,l and -h,-k,l
 If that doesn't work, it suggests that the point group is a lower symmetry
 eg P3

 Phil


 On 29 May 2012, at 16:29, Qixu Cai wrote:

  Dear all,
 
  thank you for your help.
 
  I think I must describe my case in detail. I collected a native dataset
 and two heavy atom derivant datasets （in fact, i don not know whether these
 two kind of heavy atom have soked into the crystal, i just collect the data
 to check it）.
 
  i processed all of three datasets with automar, and merged them by CAD.
 I used scaleit to get the Rfactor between datasets and got a strange
 result. the R factor between derivant1 and native is 26% and the R factor
 between derivant2 and native is 59%!
 
  so I think it may be the problem of index （space group is P321）.  so i
 exchange the h and k of derivant2 by the some awk script and merged to
 native data by CAD. After scaleit analysis, I got the R factor 29% between
 derivant2 and native.
 
  Here is my questions,
 
  1, at my case, is that right to invert the hand? is that the special
 problem of the P3 or p321 space group?
 
  2, I have carryed out some suggestion of yours, such as use pointless
 （use native data as reference for derivant2 reindex）, or reindex the
 derivant2 dataset by （k, h, -l）, and I always got the high R factor 59%
 between derivant2 and native.
 
  Any suggestion?
 
  thanks a lot!
 
  Qixu Cai
 
 
  在 2012-5-29，下午10:36，Laurent Maveyraud laurent.maveyr...@ipbs.fr 写道：
 
  Hi... and apologies !
 
  I was a little quick in my answer... in P321, h k l and -h -k l are
 valid indexing schemes...
  It is in P3 that you can have  h k l and k h -l
  as Ian and Phil agreed on the BB !
 
  sorry,
  laurent
 
  Hi,
 
  you might have several possible spacegroups possible when processing
 your data (at the indexation step). These will be based on the metrics of
 your cell (vector length and angles). If you happen to have something like
 a = b, and alpha=beta90° and gamma=120°, then it is likely that your
 crystal is trigonal or hexagonal.
 
  You will have to wait until the scaling step (or pointless after
 integration) in order to decide which spacegroup is the right one, based on
 the symmetry operations in your dataset and on systematic absences. There
 you have to choose between P3, P31, P32, P312, P321 in trigonal.
 
  When comparing two datasets from trigonal crystals, even for identical
 crystals and hence identical spacegroups, you have different ways to index
 your dataset...
  In P321, one dataset might be indexed one way (eg. h k l), the other
 might be index the other way (k h -l). When you compared this two dataset,
 they will appear to be different, because both indexing schemes, although
 valid, are not equivalent.
 
  Take one reflection; e.g. 3 2 1 from your crystal A. The very same
 reflection will be indexed 2 3 -1 for your crystal B, and the one indexed 3
 2 1 for crytal B will not be equivalent to the 3 2 1 reflection from
 crystal A.
  If you try to merge your two datasets, you will have huge Rmerge,
 because you are trying to average non equivalent reflections.
 
  You will have to ensure that the same indexing scheme is used for both
 datasets, eg reindex B using the reindex k h -l command in reindex, before
 being able to merge A and B.
 
  hope this helps... please feel free to as if I am not clear...
 
  best regards
 
  laurent
 
  Le 29/05/2012 16:03, Qixu Cai a écrit :
  P3 is another possible alternate indexing? is that correct?
 
 
  2012/5/29 Ian Tickle ianj...@gmail.com mailto:ianj...@gmail.com
 
Mark, thanks for pointing that out, I see it now:
 
In P321 the only possible alternate indexing is (-h, -k, l): this is
 a
2-fold || c which is an operator of the hexagonal lattice but is not
an equivalent reflection.
 
The standard CCP4 a.u. is h = k, l = 0 or h  k, k = 0, so for
example (3,2,1) would be in the standard a.u. (3  2 and 2 = 0).  In
the alternate indexing this would be (-3, -2, 1); however it's
impossible to transform this to the a.u. with any non-inverting
equivalent.  The only possibility is to invert the hand, i.e. to (3,
2, -1) which is again in the a.u..
 
So the required re-indexing operator to match (3, 2, -1) with (3, 2,
1) is (h, k, -l) which reindex won't allow without the LEFT keyword
(and you would be well-advised to avoid doing it with phase
 columns!).
 
Cheers
 
-- Ian
 
On 29 May 2012 12:55, Mark J van Raaij mjvanra...@cnb.csic.es
mailto:mjvanra...@cnb.csic.es wrote:
  In different 

Re: [ccp4bb] Potential Space Group Issuetely..

[Eleanor Dodson]

If there is no indication of twinning and your Rmerge is sensible then 
it is probably point group P222


Run pointless - that gives you the quality of each of the 2 folds sepera 
tely..


Deciding on the spacegroup is a bit trickier.

That depends on absences along h00 0k0  and 00l, and if there is a 
non-crystallographic-translation with a 1/2 translation along a b or c 
then they can mislead you.


Eg if the pseudo-translation was (0.5,0.3,0.1) then the h00 would  have 
all h=odd weak and the spacegroup could be P212121 or P 2 21 21


truncate tells you whether there is non-crystallographic translation.

On 07/08/2011 04:30 AM, Raji Edayathumangalam wrote:

Hello Everyone,

I have a 3.1 Ang dataset for which I'd like to get to the bottom of what the
correct space group is.

The current unit cell in p212121 is 98.123   101.095   211.20190.000
90.00090.000
I fed the reflection data into Xtriage to look for twinning and
pseudotranslational NCS and there is no indication for either issue in the
Xtriage output. Also, all odd 00h, 00k, 00l reflections are systematically
absent as they should be for p212121.

However, my colleague who is also working on the same dataset recently
reprocessed the data in P21. Here's the cell in p21:
98.010  100.940  210.470  90.00  90.04  90.00 p21

I am not sure if BETA=90.04 is significant enough to treat as p21 (0.04%
deviation of beta angle from ideal lattice for p212121). I don't think so
but I could be wrong. Could someone please clarify?

Also, what kind of twinning and twinning operators can relate a p212121 cell
to a p21 cell with almost identical unit cell parameters as that of the
p212121 cell and leave all systematic absences intact?

Thanks much.
Raji


---
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University

Re: [ccp4bb] Potential Space Group Issue

[harry powell]

Hi

I'd run the reflection file through pointless rather than rely on  
cell dimensions and/or systematic absences. This is a quick and easy  
test to do and more reliable. As Bert suggests, the only real way to  
know the symmetry is after successful structure solution and  
refinement (but even then you can be fooled...).


On 8 Jul 2011, at 21:07, Van Den Berg, Bert wrote:

I'd say its very likely to be orthorhombic. Refinement should tell  
you.its the best way to determine the space group anyway. Why  
do you doubt its orthorhombic? Is Vm reasonable?
It could be monoclinic and merohedrally winned with the beta angle  
very close to 90 degrees, but my money is on orthorhombic. if  
refinement fails I would try monoclinic plus/minus twinning. As for  
the operators, xx.triage will tell you and xx.refine will  
apply them for you during refinement;-)


Bert

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Raji  
Edayathumangalam [r...@brandeis.edu]

Sent: Friday, July 08, 2011 3:24 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Potential Space Group Issue

Oops sorry for the slippery fingers. I meant h00, 0k0 and 00l in my  
original email and NOT 00h, 00k, 00l. Note the correction  
especially if you are a first-year graduate student trying to learn  
stuff from these emails :)


Raji



On Thu, Jul 7, 2011 at 11:30 PM, Raji Edayathumangalam  
r...@brandeis.edumailto:r...@brandeis.edu wrote:

Hello Everyone,

I have a 3.1 Ang dataset for which I'd like to get to the bottom of  
what the correct space group is.


The current unit cell in p212121 is 98.123   101.095   211.201 
90.00090.00090.000
I fed the reflection data into Xtriage to look for twinning and  
pseudotranslational NCS and there is no indication for either issue  
in the Xtriage output. Also, all odd 00h, 00k, 00l reflections are  
systematically absent as they should be for p212121.


However, my colleague who is also working on the same dataset  
recently reprocessed the data in P21. Here's the cell in p21:

98.010  100.940  210.470  90.00  90.04  90.00 p21

I am not sure if BETA=90.04 is significant enough to treat as p21  
(0.04% deviation of beta angle from ideal lattice for p212121). I  
don't think so but I could be wrong. Could someone please clarify?


Also, what kind of twinning and twinning operators can relate a  
p212121 cell to a p21 cell with almost identical unit cell  
parameters as that of the p212121 cell and leave all systematic  
absences intact?


Thanks much.
Raji


---
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University




--

--
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University


Harry
--
Dr Harry Powell,
MRC Laboratory of Molecular Biology,
Hills Road,
Cambridge,
CB2 0QH

Re: [ccp4bb] Potential Space Group Issue

[Frederic VELLIEUX]

Well you could have a monoclinic space group with beta = 90....0001, which 
for everyone would mean 90.0 degrees. You could also have beta = exactly 90 by 
pure chance. Normally the R-sym values should tell you which of the two 
possibilities is the correct one.

If you obtain (an example) R-sym = 0.045 for P2(1) and R-sym = 0.052 for 
P2(1)2(1)2(1), then the orthorhombic space group is most likely the correct one.

And a definitive proof is solving the structure in P2(1)2(1)2(1).

Fred.

 Message du 08/07/11 05:31
 De : Raji Edayathumangalam 
 A : CCP4BB@JISCMAIL.AC.UK
 Copie à : 
 Objet : [ccp4bb] Potential Space Group Issue
 
 Hello Everyone,
 
 I have a 3.1 Ang dataset for which I'd like to get to the bottom of what the
 correct space group is.
 
 The current unit cell in p212121 is 98.123 101.095 211.201 90.000
 90.000 90.000
 I fed the reflection data into Xtriage to look for twinning and
 pseudotranslational NCS and there is no indication for either issue in the
 Xtriage output. Also, all odd 00h, 00k, 00l reflections are systematically
 absent as they should be for p212121.
 
 However, my colleague who is also working on the same dataset recently
 reprocessed the data in P21. Here's the cell in p21:
 98.010 100.940 210.470 90.00 90.04 90.00 p21
 
 I am not sure if BETA=90.04 is significant enough to treat as p21 (0.04%
 deviation of beta angle from ideal lattice for p212121). I don't think so
 but I could be wrong. Could someone please clarify?
 
 Also, what kind of twinning and twinning operators can relate a p212121 cell
 to a p21 cell with almost identical unit cell parameters as that of the
 p212121 cell and leave all systematic absences intact?
 
 Thanks much.
 Raji
 
 
 ---
 Raji Edayathumangalam
 Instructor in Neurology, Harvard Medical School
 Research Associate, Brigham and Women's Hospital
 Visiting Research Scholar, Brandeis University
 

Re: [ccp4bb] Potential Space Group Issue

[Ed Pozharski]

Raji,

Assuming that the real space group is P212121, in P21 you will still get
a solution except for the extra NCS which will closely resemble the
extra 2-fold screw.  Then you can probably tell if there are any
significant differences between NCS-related copies that justify lower
symmetry space group.  It's not impossible, as Fred points out, that P21
is the true space group, but I think most people here would agree it may
be less likely.  Did your colleague actually try going orthorhombic?

One possibility is that symmetry breakdown results from lattice
distortion upon cryocooling.  I would expect that shifts/rotations are
small and naturally the effect on the refinement is
resolution-dependent.  I am sure there are more examples in the
literature, but this one should hit close to the hills of Waltham:

http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0040099

which is PDB ID 2PZV - check out that P1 with beta=89.98.  Colonel Pybus
could tell you more (if the brass lets him, of course :), but what I
recall is that most of the time and at lower resolution KSI can be
processed in C2221 without problems.  With that particular dataset (and
the goal was to get as high resolution as possible to discern minute
changes in hydrogen bonds) it processed fine too, except that R-values
stayed a little too high (lower 20s?) for authors comfort.  But they do
go down significantly in P1.

However, you are at much lower resolution.  My own unpublished example
was at 2.4A, processed fine in C2221, gave a clear MR solution, but then
stayed in R~40% zone and had every loop missing in electron density.
Turned out to be P21 with NCS resembling higher symmetry just enough to
confuse denzo (and me).

I guess the message is that everything is P1 and higher symmetry is just
a dream within a dream so you can experience a drop at any time :)

Cheers,

Ed.

On Thu, 2011-07-07 at 23:30 -0400, Raji Edayathumangalam wrote:
 Hello Everyone,
 
 I have a 3.1 Ang dataset for which I'd like to get to the bottom of
 what the correct space group is.
 
 The current unit cell in p212121 is 98.123   101.095   211.201
 90.00090.00090.000
 I fed the reflection data into Xtriage to look for twinning and
 pseudotranslational NCS and there is no indication for either issue in
 the Xtriage output. Also, all odd 00h, 00k, 00l reflections are
 systematically absent as they should be for p212121.
 
 However, my colleague who is also working on the same dataset recently
 reprocessed the data in P21. Here's the cell in p21:
 98.010  100.940  210.470  90.00  90.04  90.00 p21
 
 I am not sure if BETA=90.04 is significant enough to treat as p21
 (0.04% deviation of beta angle from ideal lattice for p212121). I
 don't think so but I could be wrong. Could someone please clarify? 
 
 Also, what kind of twinning and twinning operators can relate a
 p212121 cell to a p21 cell with almost identical unit cell parameters
 as that of the p212121 cell and leave all systematic absences intact?
 
 Thanks much.
 Raji
 
 
 ---
 Raji Edayathumangalam
 Instructor in Neurology, Harvard Medical School
 Research Associate, Brigham and Women's Hospital
 Visiting Research Scholar, Brandeis University
 

-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
--   / Lao Tse /

Re: [ccp4bb] Potential Space Group Issue

[Raji Edayathumangalam]

Oops sorry for the slippery fingers. I meant h00, 0k0 and 00l in my original
email and NOT 00h, 00k, 00l. Note the correction especially if you are a
first-year graduate student trying to learn stuff from these emails :)

Raji



On Thu, Jul 7, 2011 at 11:30 PM, Raji Edayathumangalam r...@brandeis.eduwrote:

 Hello Everyone,

 I have a 3.1 Ang dataset for which I'd like to get to the bottom of what
 the correct space group is.

 The current unit cell in p212121 is 98.123   101.095   211.20190.000
 90.00090.000
 I fed the reflection data into Xtriage to look for twinning and
 pseudotranslational NCS and there is no indication for either issue in the
 Xtriage output. Also, all odd 00h, 00k, 00l reflections are systematically
 absent as they should be for p212121.

 However, my colleague who is also working on the same dataset recently
 reprocessed the data in P21. Here's the cell in p21:
 98.010  100.940  210.470  90.00  90.04  90.00 p21

 I am not sure if BETA=90.04 is significant enough to treat as p21 (0.04%
 deviation of beta angle from ideal lattice for p212121). I don't think so
 but I could be wrong. Could someone please clarify?

 Also, what kind of twinning and twinning operators can relate a p212121
 cell to a p21 cell with almost identical unit cell parameters as that of the
 p212121 cell and leave all systematic absences intact?

 Thanks much.
 Raji


 ---
 Raji Edayathumangalam
 Instructor in Neurology, Harvard Medical School
 Research Associate, Brigham and Women's Hospital
 Visiting Research Scholar, Brandeis University




-- 

--
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University

Re: [ccp4bb] Potential Space Group Issue

[Van Den Berg, Bert]

I'd say its very likely to be orthorhombic. Refinement should tell you.its 
the best way to determine the space group anyway. Why do you doubt its 
orthorhombic? Is Vm reasonable?
It could be monoclinic and merohedrally winned with the beta angle very close 
to 90 degrees, but my money is on orthorhombic. if refinement fails I would try 
monoclinic plus/minus twinning. As for the operators, xx.triage will tell 
you and xx.refine will apply them for you during refinement;-)

Bert

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Raji 
Edayathumangalam [r...@brandeis.edu]
Sent: Friday, July 08, 2011 3:24 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Potential Space Group Issue

Oops sorry for the slippery fingers. I meant h00, 0k0 and 00l in my original 
email and NOT 00h, 00k, 00l. Note the correction especially if you are a 
first-year graduate student trying to learn stuff from these emails :)

Raji



On Thu, Jul 7, 2011 at 11:30 PM, Raji Edayathumangalam 
r...@brandeis.edumailto:r...@brandeis.edu wrote:
Hello Everyone,

I have a 3.1 Ang dataset for which I'd like to get to the bottom of what the 
correct space group is.

The current unit cell in p212121 is 98.123   101.095   211.20190.000
90.00090.000
I fed the reflection data into Xtriage to look for twinning and 
pseudotranslational NCS and there is no indication for either issue in the 
Xtriage output. Also, all odd 00h, 00k, 00l reflections are systematically 
absent as they should be for p212121.

However, my colleague who is also working on the same dataset recently 
reprocessed the data in P21. Here's the cell in p21:
98.010  100.940  210.470  90.00  90.04  90.00 p21

I am not sure if BETA=90.04 is significant enough to treat as p21 (0.04% 
deviation of beta angle from ideal lattice for p212121). I don't think so but I 
could be wrong. Could someone please clarify?

Also, what kind of twinning and twinning operators can relate a p212121 cell to 
a p21 cell with almost identical unit cell parameters as that of the p212121 
cell and leave all systematic absences intact?

Thanks much.
Raji


---
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University




--

--
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University

Re: [ccp4bb] Potential Space Group Issue

[Pavel Afonine]

Hi,

yes, that would be my preferred strategy: often (but not always), sampling
space by trying plausible options saves you more time than thinking hard
first... and then still ending up trying -:)

All the best,
Pavel.


On Fri, Jul 8, 2011 at 1:07 PM, Van Den Berg, Bert 
lambertus.vandenb...@umassmed.edu wrote:

 I'd say its very likely to be orthorhombic. Refinement should tell
 you.its the best way to determine the space group anyway. Why do you
 doubt its orthorhombic? Is Vm reasonable?
 It could be monoclinic and merohedrally winned with the beta angle very
 close to 90 degrees, but my money is on orthorhombic. if refinement fails I
 would try monoclinic plus/minus twinning. As for the operators,
 xx.triage will tell you and xx.refine will apply them for you during
 refinement;-)

 Bert
 
 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Raji
 Edayathumangalam [r...@brandeis.edu]
 Sent: Friday, July 08, 2011 3:24 PM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] Potential Space Group Issue

 Oops sorry for the slippery fingers. I meant h00, 0k0 and 00l in my
 original email and NOT 00h, 00k, 00l. Note the correction especially if
 you are a first-year graduate student trying to learn stuff from these
 emails :)

 Raji



 On Thu, Jul 7, 2011 at 11:30 PM, Raji Edayathumangalam r...@brandeis.edu
 mailto:r...@brandeis.edu wrote:
 Hello Everyone,

 I have a 3.1 Ang dataset for which I'd like to get to the bottom of what
 the correct space group is.

 The current unit cell in p212121 is 98.123   101.095   211.20190.000
  90.00090.000
 I fed the reflection data into Xtriage to look for twinning and
 pseudotranslational NCS and there is no indication for either issue in the
 Xtriage output. Also, all odd 00h, 00k, 00l reflections are systematically
 absent as they should be for p212121.

 However, my colleague who is also working on the same dataset recently
 reprocessed the data in P21. Here's the cell in p21:
 98.010  100.940  210.470  90.00  90.04  90.00 p21

 I am not sure if BETA=90.04 is significant enough to treat as p21 (0.04%
 deviation of beta angle from ideal lattice for p212121). I don't think so
 but I could be wrong. Could someone please clarify?

 Also, what kind of twinning and twinning operators can relate a p212121
 cell to a p21 cell with almost identical unit cell parameters as that of the
 p212121 cell and leave all systematic absences intact?

 Thanks much.
 Raji


 ---
 Raji Edayathumangalam
 Instructor in Neurology, Harvard Medical School
 Research Associate, Brigham and Women's Hospital
 Visiting Research Scholar, Brandeis University




 --

 --
 Raji Edayathumangalam
 Instructor in Neurology, Harvard Medical School
 Research Associate, Brigham and Women's Hospital
 Visiting Research Scholar, Brandeis University

[ccp4bb] Potential Space Group Issue

[Raji Edayathumangalam]

Hello Everyone,

I have a 3.1 Ang dataset for which I'd like to get to the bottom of what the
correct space group is.

The current unit cell in p212121 is 98.123   101.095   211.20190.000
90.00090.000
I fed the reflection data into Xtriage to look for twinning and
pseudotranslational NCS and there is no indication for either issue in the
Xtriage output. Also, all odd 00h, 00k, 00l reflections are systematically
absent as they should be for p212121.

However, my colleague who is also working on the same dataset recently
reprocessed the data in P21. Here's the cell in p21:
98.010  100.940  210.470  90.00  90.04  90.00 p21

I am not sure if BETA=90.04 is significant enough to treat as p21 (0.04%
deviation of beta angle from ideal lattice for p212121). I don't think so
but I could be wrong. Could someone please clarify?

Also, what kind of twinning and twinning operators can relate a p212121 cell
to a p21 cell with almost identical unit cell parameters as that of the
p212121 cell and leave all systematic absences intact?

Thanks much.
Raji


---
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University

Re: [ccp4bb] Regarding space group P1, P21

[Eleanor Dodson]

as others have said, there are many cases where the actual symmetry is 
lower than the apparent, because a small part of thesructure does not 
obey the higher symmetry. This seems to have happened to you - an 
inhibitor which has P21 symmetry in a structure with near P212121 symmetry..
In similar cases I found the pointless analysis very helpful. It gives 
you the CC for each symmetry operator seperately. If the P121 ones are 
marginally higher than the P2 1 1 then that isextra proof.
You need to integrate that data in P21 - the beta angle may not be 
exactly 90.


Eleanor


On 10/21/2010 04:31 PM, herman.schreu...@sanofi-aventis.com wrote:

Dear Mohinder and Ed,

If you process your data in a lower symmetry space group, you will have
more unique reflections, since reflections which are related by the
higher symmetry will be avaraged during scaling in a higher symmetry
space group (i.e. a 2fold or 3fold axis), while in lower symmetry space
groups they will not. So the observation to parameter ratio stays the
same and is only depending on resolution and solvent content.

The question one has to ask of course is: are these reflections really
different, or are they the same only not averaged? In the latter case,
you have more reflections, but not more information. As Ed mentions,
using tight NCS restraints would in this case mimick the
crystallographic symmetry.

I would calculate maps while leaving out the inhibitor (omit maps) and
check that the inhibitor indeed has a unique conformation in the lower
symmetry space group. In that case the symmetry of the inhibitor, and
therefore of your crystal, is the lower symmetry. If the inhibitor has a
twofold disorder in the lower symmetry space group, you really have a
higher symmetry space group and should work with this space group. In
that case you can fit a molecule on the twofold axis with an occupancy
of 0.5 and Refmac will automatically recognize the special position.

Best regards,
Herman

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ed
Pozharski
Sent: Thursday, October 21, 2010 5:05 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Regarding space group P1, P21

There is nothing fundamentally wrong with refining in P1 even if the
P21212 symmetry is present.  An effective way to reduce the number of
parameters wold be to introduce tight restraints.  If you decide to
lower the symmetry, go with P21 as it still keeps your ligand off
symmetry axes.  You can then add tight ncs restraints for the protein
part.

Alternatively, you can finish up the refinement in P21212 but get the
maps for your publication drawn in P21 (with appropriate explanation).
The reason to use the highest symmetry possible is because it presumably
gives you a more precise structure since data quality may be better in
P21212.

I am not quite sure what you mean by putting restraints on protein -
NCS?  If so, tight restraints should approximately reduce the number of
effective parameters by the number of copies.  It appears (perhaps
someone will correct me) that *constraints* are only available in CNS,
but tight restraints supposedly approach that limit.

Ed.

On Thu, 2010-10-21 at 13:05 +0100, Mohinder Pal wrote:

Dear CCP4BB members,

I have solved a protein-drug complex structure in P21212 space group.

In this structure, the drug molecule is  falling on the two-fold
symmetry axis having averaged electron density  with 0.5 occupancy. We
tried a lot to crystallize this protein-drug complex in different space
group but no success so far.  I have tried to solve the same data  in
space group P1 (statistics are fine as I have collected data for 360
degree). The map looks even better with one conformation for a drug.
Interestingly, then I reprocessed the same data using imosflm in P21
space group which have penalty 1 compared to 4 for P21212.  The
structure in P21 is  also refining well (with one conformation of the
drug compound without symmetry axis at the ligand position). The
question is , is it a good practice to solve this structure in P1 and
P21 even if the data has higher symmetry?


Secondly, I have been advised that I have to be careful to refine

structure in P1 as there will be problem regarding observation/parameter
ratio if I add too many water molecules. What will be the case if the
electron density present  for water molecules?


  I can put restrains to protein structure  but  I am just curious to

know one restrain equals how many observations.


I look forward to hear your suggestions.

Kind regards,

Mohinder Pal


--
I'd jump in myself, if I weren't so good at whistling.
Julian, King of Lemurs

Re: [ccp4bb] Regarding space group P1, P21

[Pal M.]

Dear CCP4BB members,

Thank you very much for your overwhelming  help and discussion about data 
analysis.

Kind regards,

Mohinder
--
Mohinder Pal
Ph.D Student
Protein Crystallography Group
School of Biological Sciences
University of Southampton
Bassett Crescent East
Southampton
SO16 7PX UK
m...@soton.ac.uk
Fax: +44 (0)23 8059 4459

From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Phil Evans 
[...@mrc-lmb.cam.ac.uk]
Sent: Thursday, October 21, 2010 9:45 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Regarding space group P1, P21

It's more complicated than that, since the tricky thing is to distinguish 
between reflections related eg by a putative crystallographic two-fold and by a 
parallel non-crystallographic two-fold, which would give very similar intensity 
relationships. Pointless does try to score these alternative models, but it is 
not fool-proof.

In the end, the best test is probably comparing refinements in different space 
groups (as is done by the Andrey Lebedev's Zanuda program, on the York 
University server), though it seems to me that in the limit you can't tell: how 
close does a non-crystallographic axis have to be to a crystal direction to be 
crystallographic, 1degree, 0.1 degrees, 0.01degrees?

Phil Evans

(incidentally, the algorithms used in Pointless are described in a paper due to 
appear in the Acta Cryst. D volume from the 2010 CCP4 Study Weekend, probably 
early next year. But I don't really know how best to calculate the 
probabilities)


On 21 Oct 2010, at 21:03, Ethan Merritt wrote:

 On Thursday, October 21, 2010 11:38:55 am Jacob Keller wrote:


 if the data really looks like P21-- what are the criteria for that?

 This is a straightforward statistical question.
 In testing for a possible 2-fold, you want to know:

 Do two random reflections related by the putative 2-fold agree with
 each other better than two random reflections not related by the
 putative 2-fold?

 To make this test less sensitive to scaling, one can formulate it
 as a correlation coefficient.  Have a look at the paper describing
 `pointless`.

  P Evans (2006), Acta Cryst. D62: 72-82

 Testing the for systematic absences indicating a screw axis can also
 be phrased as a statistical test, although generally there are a relatively
 small number of putative absences to inspect so the test is not all that
 strong.

   Ethan





 I believe p1 can have good-as-perfect 90deg angles, no?

 Correct. The cell angles don't really enter into it.



 And also
 equal cell dimensions? So I don't think you will be able to tell from the
 positions of the spots on the detector, necessarily. Also, would it not be
 more rigorous to say I can gain a lot by assuming these molecules are in
 p21? Look, nobody thinks that every molecule in the crystal is identical,
 so that is truly a convenient assumption. The symmetry, I think, is a
 similar assumption at a different level.

 By the way, I have always wondered whether anybody has looked into the
 degree of intermolecular differences possible given all of the parameters in
 our crystallographic models. In other words, would a microscopic observer
 look at the molecules in the crystal and see what looks like a crowd from a
 NYC street, or something more like an army formation? How much variety is
 there at the molecular lever, I wonder?

 True: but how do you judge that those differences are within or
 outside of experimental noise?

 Agreed!

 What if by refining in P1 the parametrisation makes those side-chains
 different in the first place? A poorly defined Lys side-chain suddenly
 becomes two significantly different poorly defined side-chain?

 I don't know--depends on last question I think.

 Jacob

 ***
 Jacob Pearson Keller
 Northwestern University
 Medical Scientist Training Program
 Dallos Laboratory
 F. Searle 1-240
 2240 Campus Drive
 Evanston IL 60208
 lab: 847.491.2438
 cel: 773.608.9185
 email: j-kell...@northwestern.edu
 ***


 --
 Ethan A Merritt
 Biomolecular Structure Center,  K-428 Health Sciences Bldg
 University of Washington, Seattle 98195-7742

[ccp4bb] Regarding space group P1, P21

[Mohinder Pal]

Dear CCP4BB members,

I have solved a protein-drug complex structure in P21212 space group.  In this 
structure, the drug molecule is  falling on the two-fold symmetry axis having 
averaged electron density  with 0.5 occupancy. We tried a lot to crystallize 
this protein-drug complex in different space group but no success so far.  I 
have tried to solve the same data  in space group P1 (statistics are fine as I 
have collected data for 360 degree). The map looks even better with one 
conformation for a drug. Interestingly, then I reprocessed the same data using 
imosflm in P21 space group which have penalty 1 compared to 4 for P21212.  The 
structure in P21 is  also refining well (with one conformation of the drug 
compound without symmetry axis at the ligand position). The question is , is it 
a good practice to solve this structure in P1 and P21 even if the data has 
higher symmetry?

Secondly, I have been advised that I have to be careful to refine structure in 
P1 as there will be problem regarding observation/parameter ratio if I add too 
many water molecules. What will be the case if the electron density present  
for water molecules?  

 I can put restrains to protein structure  but  I am just curious to know one 
restrain equals how many observations.

I look forward to hear your suggestions.

Kind regards,

Mohinder Pal

Re: [ccp4bb] Regarding space group P1, P21

[Harry Powell]

Hi

Since you're using iMosflm to process the data, it is well worthwhile running 
the Quickscale task following integration (I would actually run it after 
integrating ~5 - 10 degrees of data) to see if the true crystal symmetry 
determined by analysing agreement of the intensities of symmetry related 
reflections is actually the same as that indicated by the penalties from 
indexing.

Remember that the relationship between the unit cell dimensions is a 
consequence of the true symmetry, not vice versa - most crystallographers who 
have been in the game more than a few years have examples of lower symmetry 
crystals with apparently higher symmetry cell dimensions - a relatively common 
occurrence to have cell dimensions that look right for tetragonal when the 
true symmetry is orthorhombic.

Of course, following integration  scaling etc you would probably want to check 
for things like twinning etc...

In general, I think you should probably solve and refine in the highest 
symmetry space group that is most consistent with your data. If the experiment 
gives you just as good results in the higher symmetry space group as the lower, 
I would go for the higher symmetry. In your case, if P21 solution/refinement is 
as good as P1, but both are better than P21212, I would tend towards using the 
P21 solution.


On 21 Oct 2010, at 12:05, Mohinder Pal wrote:

 Dear CCP4BB members,
 
 I have solved a protein-drug complex structure in P21212 space group.  In 
 this structure, the drug molecule is  falling on the two-fold symmetry axis 
 having averaged electron density  with 0.5 occupancy. We tried a lot to 
 crystallize this protein-drug complex in different space group but no success 
 so far.  I have tried to solve the same data  in space group P1 (statistics 
 are fine as I have collected data for 360 degree). The map looks even better 
 with one conformation for a drug. Interestingly, then I reprocessed the same 
 data using imosflm in P21 space group which have penalty 1 compared to 4 for 
 P21212.  The structure in P21 is  also refining well (with one conformation 
 of the drug compound without symmetry axis at the ligand position). The 
 question is , is it a good practice to solve this structure in P1 and P21 
 even if the data has higher symmetry?
 
 Secondly, I have been advised that I have to be careful to refine structure 
 in P1 as there will be problem regarding observation/parameter ratio if I add 
 too many water molecules. What will be the case if the electron density 
 present  for water molecules?  
 
 I can put restrains to protein structure  but  I am just curious to know one 
 restrain equals how many observations.
 
 I look forward to hear your suggestions.
 
 Kind regards,
 
 Mohinder Pal

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
Cambridge, CB2 0QH

Re: [ccp4bb] Regarding space group P1, P21

[Ed Pozharski]

There is nothing fundamentally wrong with refining in P1 even if the
P21212 symmetry is present.  An effective way to reduce the number of
parameters wold be to introduce tight restraints.  If you decide to
lower the symmetry, go with P21 as it still keeps your ligand off
symmetry axes.  You can then add tight ncs restraints for the protein
part.

Alternatively, you can finish up the refinement in P21212 but get the
maps for your publication drawn in P21 (with appropriate explanation).
The reason to use the highest symmetry possible is because it presumably
gives you a more precise structure since data quality may be better in
P21212.

I am not quite sure what you mean by putting restraints on protein -
NCS?  If so, tight restraints should approximately reduce the number of
effective parameters by the number of copies.  It appears (perhaps
someone will correct me) that *constraints* are only available in CNS,
but tight restraints supposedly approach that limit.

Ed.

On Thu, 2010-10-21 at 13:05 +0100, Mohinder Pal wrote:
 Dear CCP4BB members,
 
 I have solved a protein-drug complex structure in P21212 space group.  In 
 this structure, the drug molecule is  falling on the two-fold symmetry axis 
 having averaged electron density  with 0.5 occupancy. We tried a lot to 
 crystallize this protein-drug complex in different space group but no success 
 so far.  I have tried to solve the same data  in space group P1 (statistics 
 are fine as I have collected data for 360 degree). The map looks even better 
 with one conformation for a drug. Interestingly, then I reprocessed the same 
 data using imosflm in P21 space group which have penalty 1 compared to 4 for 
 P21212.  The structure in P21 is  also refining well (with one conformation 
 of the drug compound without symmetry axis at the ligand position). The 
 question is , is it a good practice to solve this structure in P1 and P21 
 even if the data has higher symmetry?
 
 Secondly, I have been advised that I have to be careful to refine structure 
 in P1 as there will be problem regarding observation/parameter ratio if I add 
 too many water molecules. What will be the case if the electron density 
 present  for water molecules?  
 
  I can put restrains to protein structure  but  I am just curious to know one 
 restrain equals how many observations.
 
 I look forward to hear your suggestions.
 
 Kind regards,
 
 Mohinder Pal

-- 
I'd jump in myself, if I weren't so good at whistling.
   Julian, King of Lemurs

Re: [ccp4bb] Regarding space group P1, P21

[Herman . Schreuder]

Dear Mohinder and Ed,

If you process your data in a lower symmetry space group, you will have
more unique reflections, since reflections which are related by the
higher symmetry will be avaraged during scaling in a higher symmetry
space group (i.e. a 2fold or 3fold axis), while in lower symmetry space
groups they will not. So the observation to parameter ratio stays the
same and is only depending on resolution and solvent content. 

The question one has to ask of course is: are these reflections really
different, or are they the same only not averaged? In the latter case,
you have more reflections, but not more information. As Ed mentions,
using tight NCS restraints would in this case mimick the
crystallographic symmetry. 

I would calculate maps while leaving out the inhibitor (omit maps) and
check that the inhibitor indeed has a unique conformation in the lower
symmetry space group. In that case the symmetry of the inhibitor, and
therefore of your crystal, is the lower symmetry. If the inhibitor has a
twofold disorder in the lower symmetry space group, you really have a
higher symmetry space group and should work with this space group. In
that case you can fit a molecule on the twofold axis with an occupancy
of 0.5 and Refmac will automatically recognize the special position.

Best regards,
Herman

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ed
Pozharski
Sent: Thursday, October 21, 2010 5:05 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Regarding space group P1, P21

There is nothing fundamentally wrong with refining in P1 even if the
P21212 symmetry is present.  An effective way to reduce the number of
parameters wold be to introduce tight restraints.  If you decide to
lower the symmetry, go with P21 as it still keeps your ligand off
symmetry axes.  You can then add tight ncs restraints for the protein
part.

Alternatively, you can finish up the refinement in P21212 but get the
maps for your publication drawn in P21 (with appropriate explanation).
The reason to use the highest symmetry possible is because it presumably
gives you a more precise structure since data quality may be better in
P21212.

I am not quite sure what you mean by putting restraints on protein -
NCS?  If so, tight restraints should approximately reduce the number of
effective parameters by the number of copies.  It appears (perhaps
someone will correct me) that *constraints* are only available in CNS,
but tight restraints supposedly approach that limit.

Ed.

On Thu, 2010-10-21 at 13:05 +0100, Mohinder Pal wrote:
 Dear CCP4BB members,
 
 I have solved a protein-drug complex structure in P21212 space group.
In this structure, the drug molecule is  falling on the two-fold
symmetry axis having averaged electron density  with 0.5 occupancy. We
tried a lot to crystallize this protein-drug complex in different space
group but no success so far.  I have tried to solve the same data  in
space group P1 (statistics are fine as I have collected data for 360
degree). The map looks even better with one conformation for a drug.
Interestingly, then I reprocessed the same data using imosflm in P21
space group which have penalty 1 compared to 4 for P21212.  The
structure in P21 is  also refining well (with one conformation of the
drug compound without symmetry axis at the ligand position). The
question is , is it a good practice to solve this structure in P1 and
P21 even if the data has higher symmetry?
 
 Secondly, I have been advised that I have to be careful to refine
structure in P1 as there will be problem regarding observation/parameter
ratio if I add too many water molecules. What will be the case if the
electron density present  for water molecules?  
 
  I can put restrains to protein structure  but  I am just curious to
know one restrain equals how many observations.
 
 I look forward to hear your suggestions.
 
 Kind regards,
 
 Mohinder Pal

--
I'd jump in myself, if I weren't so good at whistling.
   Julian, King of Lemurs

Re: [ccp4bb] Regarding space group P1, P21

[Clemens Vonrhein]

Dear Mohinder,

On Thu, Oct 21, 2010 at 01:05:42PM +0100, Mohinder Pal wrote:
 The question is , is it a good practice to solve this structure in
 P1 and P21 even if the data has higher symmetry?

On a slightly philosophical note regarding the final model (and not
necessarily the 'good practice' leading to it): shouldn't our model
describe the experiment (intensities from a crystal of given symmetry)
and not the other way round (changing the experimental data to make
modeling easier)?

Or maybe I'm too strict here ...

If your crystal has P21212 then I would model it this way: having a
compound on a 2-fold with half occupancy isn't really a problem
nowadays with modern refinement programs.

And yes: it might confuse molecular biologists downloading the PDB
file. And since their needs often dictate how we are supposed to
produce models for our experiments, the time might come where all
structures being refined in P1 with only the A chain deposited ;-)

Cheers

Clemens

-- 

***
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--
* BUSTER Development Group  (http://www.globalphasing.com)
***

Re: [ccp4bb] Regarding space group P1, P21

[Clemens Vonrhein]

Hi Herman,

On Thu, Oct 21, 2010 at 05:31:51PM +0200, herman.schreu...@sanofi-aventis.com 
wrote:
 If you process your data in a lower symmetry space group, you will have
 more unique reflections, since reflections which are related by the
 higher symmetry will be avaraged during scaling in a higher symmetry
 space group (i.e. a 2fold or 3fold axis), while in lower symmetry space
 groups they will not. So the observation to parameter ratio stays the
 same and is only depending on resolution and solvent content. 

True - if you count Miller indices as observations. But if you think
about information content than probably not (as you discuss below).

 The question one has to ask of course is: are these reflections really
 different, or are they the same only not averaged?

Yes - by merging we're getting better data (better error estimate on
the intensity due to higher multiplicity). So there isn't really
independent information in 50% of the reflections if e.g. going from
P21 to P1 - we've only increased the noise because the multiplicity of
each reflection has been reduced.

 In the latter case, you have more reflections, but not more
 information. As Ed mentions, using tight NCS restraints would in
 this case mimick the crystallographic symmetry.

Apart from the (good) NCS argument, one could go even further:

We could also just collect 36000 degree of data on a 7A Lysozyme
crystal and refine against completely unmerged data. After all, why
should we stop at removing only the some symmetry operators from our
data merging ... lets get rid of all of them including th x,y,z
operator and use unmerged data. Then we could refine Lysozyme with
anisotropic hydrogens and no restraints against 7A data since we have
a huge number of 'observations' ... right?

But seriously: there is a difference in having reflections (H, K, L)
and independent data (I, SIGI). Maybe we should talk more about
(independent observations)/parameters ratio in the same way we
look at depdencies of parameters (e.g. restraints on Bfactors etc).

Cheers

Clemens

-- 

***
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--
* BUSTER Development Group  (http://www.globalphasing.com)
***

Re: [ccp4bb] Regarding space group P1, P21

[James Holton]

You pick the Rfree flags in the high-symmetry space group, and then use 
CAD with OUTLIM SPACE P1 to symmetry-expand them to P1 (or whatever 
you like).


Things get trickier, however, when your NCS is close to, (bot not 
exactly) crystallographic (NECS?).  Or if you are simply not sure.  The 
best way I can think of to deal with this situation is to road test 
your Rfree:
1) do something that you know is wrong, like delete a helix, or put 
some side chains in the wrong place

2) refine with NCS turned on
3) check that Rfree actually goes up
4) un-do the wrong things
5) refine again
6) check that Rfree actually goes down
7) try again with NCS turned off

Remembering these timeless words of wisdom: Control, Control, you must 
learn CONTROL! -Yoda (Jedi Master)


-James Holton
MAD Scientist

On 10/21/2010 8:46 AM, Christina Bourne wrote:

Dear all,
How would one properly select reflections for R-free in these 
situations?  Presumably if the selection is done in P1 then it mimics 
twinning or high NCS, such that reflections in both the work and free 
set will be (potentially?) related by symmetry.

-Christina


*From:* Mohinder Pal m...@soton.ac.uk
*To:* CCP4BB@JISCMAIL.AC.UK
*Sent:* Thu, October 21, 2010 7:05:42 AM
*Subject:* [ccp4bb] Regarding space group P1, P21

Dear CCP4BB members,

I have solved a protein-drug complex structure in P21212 space group.  
In this structure, the drug molecule is  falling on the two-fold 
symmetry axis having averaged electron density  with 0.5 occupancy. We 
tried a lot to crystallize this protein-drug complex in different 
space group but no success so far.  I have tried to solve the same 
data  in space group P1 (statistics are fine as I have collected data 
for 360 degree). The map looks even better with one conformation for a 
drug. Interestingly, then I reprocessed the same data using imosflm in 
P21 space group which have penalty 1 compared to 4 for P21212.  The 
structure in P21 is  also refining well (with one conformation of the 
drug compound without symmetry axis at the ligand position). The 
question is , is it a good practice to solve this structure in P1 and 
P21 even if the data has higher symmetry?


Secondly, I have been advised that I have to be careful to refine 
structure in P1 as there will be problem regarding 
observation/parameter ratio if I add too many water molecules. What 
will be the case if the electron density present  for water molecules?


I can put restrains to protein structure  but  I am just curious to 
know one restrain equals how many observations.


I look forward to hear your suggestions.

Kind regards,

Mohinder Pal

Re: [ccp4bb] Regarding space group P1, P21

[Jacob Keller]

I have heard many times that it is a black eye to refine in a lower-symmetry 
spacegroup, but I could never really understand why. The higher symmetry could 
be considered merely a helpful theoretical lens to improve signal-to-noise, and 
therefore imposing higher symmetry on the data could be seen as a sort of 
*leniency* of scientific (or at least empiric) rigor. I think similarly about 
using discrete spot intensities rather than the whole image--we assume Bragg 
conditions and neglect certain things about the image between the spots, which 
is usually valid, but not always. I wonder why it is considered maladroit to 
refine in a lower spacegroup, then--don't higher spacegroup impose more 
assumptions than p1?

Jacob Keller

  - Original Message - 
  From: James Holton 
  To: CCP4BB@JISCMAIL.AC.UK 
  Sent: Thursday, October 21, 2010 10:55 AM
  Subject: Re: [ccp4bb] Regarding space group P1, P21



  You pick the Rfree flags in the high-symmetry space group, and then use CAD 
with OUTLIM SPACE P1 to symmetry-expand them to P1 (or whatever you like).

  Things get trickier, however, when your NCS is close to, (bot not exactly) 
crystallographic (NECS?).  Or if you are simply not sure.  The best way I can 
think of to deal with this situation is to road test your Rfree:
  1) do something that you know is wrong, like delete a helix, or put some 
side chains in the wrong place
  2) refine with NCS turned on
  3) check that Rfree actually goes up
  4) un-do the wrong things
  5) refine again
  6) check that Rfree actually goes down
  7) try again with NCS turned off

  Remembering these timeless words of wisdom: Control, Control, you must learn 
CONTROL! -Yoda (Jedi Master)

  -James Holton
  MAD Scientist

  On 10/21/2010 8:46 AM, Christina Bourne wrote: 
Dear all,
How would one properly select reflections for R-free in these situations?  
Presumably if the selection is done in P1 then it mimics twinning or high NCS, 
such that reflections in both the work and free set will be (potentially?) 
related by symmetry.
-Christina





From: Mohinder Pal m...@soton.ac.uk
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thu, October 21, 2010 7:05:42 AM
Subject: [ccp4bb] Regarding space group P1, P21

Dear CCP4BB members,

I have solved a protein-drug complex structure in P21212 space group.  In 
this structure, the drug molecule is  falling on the two-fold symmetry axis 
having averaged electron density  with 0.5 occupancy. We tried a lot to 
crystallize this protein-drug complex in different space group but no success 
so far.  I have tried to solve the same data  in space group P1 (statistics are 
fine as I have collected data for 360 degree). The map looks even better with 
one conformation for a drug. Interestingly, then I reprocessed the same data 
using imosflm in P21 space group which have penalty 1 compared to 4 for P21212. 
 The structure in P21 is  also refining well (with one conformation of the drug 
compound without symmetry axis at the ligand position). The question is , is it 
a good practice to solve this structure in P1 and P21 even if the data has 
higher symmetry?

Secondly, I have been advised that I have to be careful to refine structure 
in P1 as there will be problem regarding observation/parameter ratio if I add 
too many water molecules. What will be the case if the electron density present 
 for water molecules?  

I can put restrains to protein structure  but  I am just curious to know 
one restrain equals how many observations.

I look forward to hear your suggestions.

Kind regards,

Mohinder Pal








***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] Regarding space group P1, P21

[Ronald E Stenkamp]

How you choose to make use of (or ignore) crystallographic symmetry comes down to your 
view of what constitutes the best model for the sample you're studying.  How 
similar do you believe the molecules are in your crystal?  If you describe the model in a 
higher symmetry space group, you believe that given the information content of the 
diffraction pattern, the molecules are identical.  If you describe it using fewer 
symmetry operations, you believe the molecules differ in some way.  So, how you describe 
the symmetry of your crystal comes down to determining the simplest model consistent with 
your experimental observations.  Ron

On Thu, 21 Oct 2010, Jacob Keller wrote:


 
I have heard many times that it is a black eye to refine in a lower-symmetry 
spacegroup, but I could never really
understand why. The higher symmetry could be considered merely a helpful 
theoretical lens to improve signal-to-noise,
and therefore imposing higher symmetry on the data could be seen as a sort of 
*leniency* of scientific (or at least
empiric) rigor. I think similarly about using discrete spot intensities rather 
than the whole image--we assume Bragg
conditions and neglect certain things about the image between the spots, which 
is usually valid, but not always. I
wonder why it is considered maladroit to refine in a lower spacegroup, 
then--don't higher spacegroup impose more
assumptions than p1?
 
Jacob Keller
 
  - Original Message -
From: James Holton
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thursday, October 21, 2010 10:55 AM
Subject: Re: [ccp4bb] Regarding space group P1, P21


You pick the Rfree flags in the high-symmetry space group, and then use CAD with 
OUTLIM SPACE P1 to
symmetry-expand them to P1 (or whatever you like).

Things get trickier, however, when your NCS is close to, (bot not exactly) 
crystallographic (NECS?).  Or if you
are simply not sure.  The best way I can think of to deal with this situation is to 
road test your Rfree:
1) do something that you know is wrong, like delete a helix, or put some side 
chains in the wrong place
2) refine with NCS turned on
3) check that Rfree actually goes up
4) un-do the wrong things
5) refine again
6) check that Rfree actually goes down
7) try again with NCS turned off

Remembering these timeless words of wisdom: Control, Control, you must learn 
CONTROL! -Yoda (Jedi Master)

-James Holton
MAD Scientist

On 10/21/2010 8:46 AM, Christina Bourne wrote:
  Dear all,
  How would one properly select reflections for R-free in these 
situations?  Presumably if the
  selection is done in P1 then it mimics twinning or high NCS, such that 
reflections in both the work
  and free set will be (potentially?) related by symmetry.
  -Christina

__
From: Mohinder Pal m...@soton.ac.uk
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thu, October 21, 2010 7:05:42 AM
Subject: [ccp4bb] Regarding space group P1, P21

Dear CCP4BB members,

I have solved a protein-drug complex structure in P21212 space group.  In this 
structure, the drug
molecule is  falling on the two-fold symmetry axis having averaged electron 
density  with 0.5 occupancy.
We tried a lot to crystallize this protein-drug complex in different space 
group but no success so far.  I
have tried to solve the same data  in space group P1 (statistics are fine as I 
have collected data for 360
degree). The map looks even better with one conformation for a drug. 
Interestingly, then I reprocessed the
same data using imosflm in P21 space group which have penalty 1 compared to 4 
for P21212.  The structure
in P21 is  also refining well (with one conformation of the drug compound 
without symmetry axis at the
ligand position). The question is , is it a good practice to solve this 
structure in P1 and P21 even if
the data has higher symmetry?

Secondly, I have been advised that I have to be careful to refine structure in 
P1 as there will be problem
regarding observation/parameter ratio if I add too many water molecules. What 
will be the case if the
electron density present  for water molecules? 

I can put restrains to protein structure  but  I am just curious to know one 
restrain equals how many
observations.

I look forward to hear your suggestions.

Kind regards,

Mohinder Pal



 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] Regarding space group P1, P21

[Ed Pozharski]

Because refining in the (right) higher symmetry space group leads to a
better model.

On Thu, 2010-10-21 at 11:34 -0500, Jacob Keller wrote:
  
 I have heard many times that it is a black eye to refine in a
 lower-symmetry spacegroup, but I could never really understand why.
 The higher symmetry could be considered merely a helpful theoretical
 lens to improve signal-to-noise, and therefore imposing higher
 symmetry on the data could be seen as a sort of *leniency* of
 scientific (or at least empiric) rigor. I think similarly about using
 discrete spot intensities rather than the whole image--we assume Bragg
 conditions and neglect certain things about the image between the
 spots, which is usually valid, but not always. I wonder why it is
 considered maladroit to refine in a lower spacegroup, then--don't
 higher spacegroup impose more assumptions than p1?
  
 Jacob Keller
  
 - Original Message - 
 From: James Holton 
 To: CCP4BB@JISCMAIL.AC.UK 
 Sent: Thursday, October 21, 2010 10:55 AM
 Subject: Re: [ccp4bb] Regarding space group P1, P21
 
 
 
 You pick the Rfree flags in the high-symmetry space group, and
 then use CAD with OUTLIM SPACE P1 to symmetry-expand them
 to P1 (or whatever you like).
 
 Things get trickier, however, when your NCS is close to, (bot
 not exactly) crystallographic (NECS?).  Or if you are simply
 not sure.  The best way I can think of to deal with this
 situation is to road test your Rfree:
 1) do something that you know is wrong, like delete a helix,
 or put some side chains in the wrong place
 2) refine with NCS turned on
 3) check that Rfree actually goes up
 4) un-do the wrong things
 5) refine again
 6) check that Rfree actually goes down
 7) try again with NCS turned off
 
 Remembering these timeless words of wisdom: Control, Control,
 you must learn CONTROL! -Yoda (Jedi Master)
 
 -James Holton
 MAD Scientist
 
 On 10/21/2010 8:46 AM, Christina Bourne wrote: 
  Dear all,
  How would one properly select reflections for R-free in
  these situations?  Presumably if the selection is done in P1
  then it mimics twinning or high NCS, such that reflections
  in both the work and free set will be (potentially?) related
  by symmetry.
  -Christina
  
  
  
  
  From: Mohinder Pal m...@soton.ac.uk
  To: CCP4BB@JISCMAIL.AC.UK
  Sent: Thu, October 21, 2010 7:05:42 AM
  Subject: [ccp4bb] Regarding space group P1, P21
  
  Dear CCP4BB members,
  
  I have solved a protein-drug complex structure in P21212
  space group.  In this structure, the drug molecule is
  falling on the two-fold symmetry axis having averaged
  electron density  with 0.5 occupancy. We tried a lot to
  crystallize this protein-drug complex in different space
  group but no success so far.  I have tried to solve the same
  data  in space group P1 (statistics are fine as I have
  collected data for 360 degree). The map looks even better
  with one conformation for a drug. Interestingly, then I
  reprocessed the same data using imosflm in P21 space group
  which have penalty 1 compared to 4 for P21212.  The
  structure in P21 is  also refining well (with one
  conformation of the drug compound without symmetry axis at
  the ligand position). The question is , is it a good
  practice to solve this structure in P1 and P21 even if the
  data has higher symmetry?
  
  Secondly, I have been advised that I have to be careful to
  refine structure in P1 as there will be problem regarding
  observation/parameter ratio if I add too many water
  molecules. What will be the case if the electron density
  present  for water molecules?  
  
  I can put restrains to protein structure  but  I am just
  curious to know one restrain equals how many observations.
  
  I look forward to hear your suggestions.
  
  Kind regards,
  
  Mohinder Pal
  
  
 
 
  
 ***
 Jacob Pearson Keller
 Northwestern University
 Medical Scientist Training Program
 Dallos Laboratory
 F. Searle 1-240
 2240 Campus Drive
 Evanston IL 60208
 lab: 847.491.2438
 cel: 773.608.9185
 email: j-kell...@northwestern.edu
 ***
 

-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When

Re: [ccp4bb] Regarding space group P1, P21

[Jacob Keller]

The black eye comes not from the treatment of the observations, but from 
the
treatment of the model.  If you want to refine the same model against 
lower
symmetry and/or unmerged data - go right ahead.  I think the result will 
not
usually be an improvement, but in some cases this may work around 
systematic

artefacts in the data.  What you should _not_ do is replicate the model to
produce multiple copies which are then refined as if they were 
independent.

That amounts to doubling/tripling/whatever the number of model parameters.

Ethan



I think that when you say as if they were independent, you are begging the 
question. You could say that refining in higher symmetry treats the 
molecules as if they were the same. Further, it really assumes more to 
posit that they are the same. Really the crux I think is weighing what 
benefits one gets from treating the data in different ways. If one can know 
somehow that the molecules when treated as p1 differ from each other only as 
a function of experimental noise, there would be no reason to treat them as 
p1. On the other hand, if somehow a few sidechains became systematically 
different between molecules in the p1 cell, it *would* make sense to refine 
in p1, no? (One could imagine an electric field around the crystal upon 
freezing or whatever.)


Jacob Keller 

Re: [ccp4bb] Regarding space group P1, P21

[Clemens Vonrhein]

Hi Ed,

On Thu, Oct 21, 2010 at 12:18:31PM -0400, Ed Pozharski wrote:
 Let's say I have a ligand on symmetry axes and so it appears in two
 conformations.  If I reduce symmetry, there are two possible scenarios.
 
 a. In lower symmetry, ligand still appears in two conformations.  Shall
 use higher symmetry.
 b. In lower symmetry, ligand appears to be in single conformation (this
 is what Mohinder says, if I am not mistaken).  In this case, the true
 symmetry is lower, and it is simply overwhelmed by the fact that most of
 the structure (but not all) obeys higher symmetry.

I think I understand what you're getting at: you have a lower symmetry
with a NCS axis that is basically perfectly aligned with the
corresponding crystallographic axis in the higher symmetry
spacegroup. And the only part of the model not obeying this NCS is the
ligand.

But then what about a water on a special position (2-fold with
occ=0.5)? If I remove that 2-fold from my spacegroup symmetry and
refine I get ... a single water with occupancy 1.0 ... or 2 waters
with occupancy 0.5? Hmmm, diffcult to decide on the true spacegroup
here ;-)

So it all depends

 * how clear the difference between high-symmetry/double conformation
   and low-symmetry/single-conformation is

 * how symmetrical the ligand is

 * how the refinement in the lower-symmetry spacegroup is done - since
   there is a real danger (in case it is the high-symmetry spacegroup
   after all) that because of model bias and poorer (independent
   observations)/parameter ratio what seems like a clear single
   conformation is difficult to confirm.

 I recall Bruce Foxman describing a b) case (I am sure there is more than
 one example) for a small molecule crystal, where a single heavy atom had
 higher symmetry than the rest of the molecule.

There is a recent nice example of a very interesting symmetry/disorder
siuation by Yves Muller: 2xgc. It took some time for me to get my head
around what it is in the PDB file and what it means ... but it's very
neat!

Cheers

Clemens

-- 

***
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--
* BUSTER Development Group  (http://www.globalphasing.com)
***

Re: [ccp4bb] Regarding space group P1, P21

[Ed Pozharski]

On Thu, 2010-10-21 at 12:58 -0500, Jacob Keller wrote:
 On the other hand, if somehow a few sidechains became systematically 
 different between molecules in the p1 cell, it *would* make sense to
 refine 
 in p1

And sometimes (but rarely) such differences become detectable at high
resolution (e.g. Kraut et al., PLOS Biology, 4:501).
 
-- 
I'd jump in myself, if I weren't so good at whistling.
   Julian, King of Lemurs

Re: [ccp4bb] Regarding space group P1, P21

[Clemens Vonrhein]

Hi,

 I think that when you say as if they were independent, you are begging 
 the question. You could say that refining in higher symmetry treats the  
 molecules as if they were the same. Further, it really assumes more to  
 posit that they are the same.

But we're still talking about crystals, right? The whole reason for
trying to crystallise our proteins/DNA/RNA is because we ideally want
a perfect arrangement of molecules. So taking as a starting hypotheses
the conservative approach that if the data really looks like P21 it
probably is P21 seems a good idea to me.

To me it is more a case of 

  refining in lower symmetry treats the molecules as if they were
  different

when initially we don't have an indication for it (from data
processing). Unless we take the fact that P1 will always give us lower
merging R-factors and better indexing scores as indication that
actually all our crystals are always P1 ... which they well might be,
but probably not within our experimental error.

 Really the crux I think is weighing what benefits one gets from
 treating the data in different ways. If one can know somehow that
 the molecules when treated as p1 differ from each other only as a
 function of experimental noise, there would be no reason to treat
 them as p1.

True: but how do you judge that those differences are within or
outside of experimental noise?

 On the other hand, if somehow a few sidechains became systematically
 different between molecules in the p1 cell, it *would* make sense to
 refine in p1, no?

What if by refining in P1 the parametrisation makes those side-chains
different in the first place? A poorly defined Lys side-chain suddenly
becomes two significantly different poorly defined side-chain?

Cheers

Clemens


-- 

***
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--
* BUSTER Development Group  (http://www.globalphasing.com)
***

Re: [ccp4bb] Regarding space group P1, P21

[Ed Pozharski]

On Thu, 2010-10-21 at 18:59 +0100, Clemens Vonrhein wrote:
 I think I understand what you're getting at: you have a lower symmetry
 with a NCS axis that is basically perfectly aligned with the
 corresponding crystallographic axis in the higher symmetry
 spacegroup. And the only part of the model not obeying this NCS is the
 ligand.
 

precisely

 But then what about a water on a special position (2-fold with
 occ=0.5)? If I remove that 2-fold from my spacegroup symmetry and
 refine I get ... a single water with occupancy 1.0 ... or 2 waters
 with occupancy 0.5? Hmmm, diffcult to decide on the true spacegroup
 here ;-)
 

water is symmetrical (no hydrogens, please), shall use the higher
symmetry

 So it all depends
 
  * how clear the difference between high-symmetry/double conformation
and low-symmetry/single-conformation is
 

Hard to put a specific number on it.  I'd inspect the density and play
Potter Stewart.

  * how symmetrical the ligand is
 

same deal as with water

  * how the refinement in the lower-symmetry spacegroup is done - since
there is a real danger (in case it is the high-symmetry spacegroup
after all) that because of model bias and poorer (independent
observations)/parameter ratio what seems like a clear single
conformation is difficult to confirm.

Absolutely true.  As we discussed before, restraining protein copies is
a must as well as maybe some bias removal.

Cheers,

Ed.

-- 
I'd jump in myself, if I weren't so good at whistling.
   Julian, King of Lemurs

Re: [ccp4bb] Regarding space group P1, P21

[Jacob Keller]

But we're still talking about crystals, right? The whole reason for
trying to crystallise our proteins/DNA/RNA is because we ideally want
a perfect arrangement of molecules. So taking as a starting hypotheses
the conservative approach that if the data really looks like P21 it
probably is P21 seems a good idea to me.


if the data really looks like P21-- what are the criteria for that? For 
example, I believe p1 can have good-as-perfect 90deg angles, no? And also 
equal cell dimensions? So I don't think you will be able to tell from the 
positions of the spots on the detector, necessarily. Also, would it not be 
more rigorous to say I can gain a lot by assuming these molecules are in 
p21? Look, nobody thinks that every molecule in the crystal is identical, 
so that is truly a convenient assumption. The symmetry, I think, is a 
similar assumption at a different level.


By the way, I have always wondered whether anybody has looked into the 
degree of intermolecular differences possible given all of the parameters in 
our crystallographic models. In other words, would a microscopic observer 
look at the molecules in the crystal and see what looks like a crowd from a 
NYC street, or something more like an army formation? How much variety is 
there at the molecular lever, I wonder?



True: but how do you judge that those differences are within or
outside of experimental noise?


Agreed!


What if by refining in P1 the parametrisation makes those side-chains
different in the first place? A poorly defined Lys side-chain suddenly
becomes two significantly different poorly defined side-chain?


I don't know--depends on last question I think.

Jacob

***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] Regarding space group P1, P21

[Ian Tickle]

Hi Clemens,

Sorry to be picky and start the 'definition game' over again, but
'Miller indices' are strictly not the numbers that index X-ray
reflections that everyone is familiar with (whether observed or not!).
 Miller indices were introduced in 1839 by the British mineralogist
William Hallowes Miller (it says in WIkipedia) as a way of describing
the direction of the perpendicular to the plane faces that he observed
on mineral crystals.  A condition is that no common denominator is
possible, since it defines only the direction of a vector; its
magnitude has no relevance in this context.  So you can have Miller
indices (1,0,0), (1,2,0), (1,2,3) etc but you can't have (2,0,0),
(3,0,0), {2,4,0), (3,6,9) etc., or at least (1,0,0) means exactly the
same thing as (2,0,0) etc.  You can multiply the MiIler index vector
by -1: this indicates the opposite face of the crystal.  Imagine what
an electron density map would look like if you only collected
intensities at the Miller indices!

Miller's observation of the plane faces of mineral crystals occurred
73 years before the discovery in 1912 of X-ray diffraction by Max Laue
in Munich (he became Max von Laue in 1913 when his father was raised
to the nobility), for which Laue received the Nobel Prize in Physics
in 1914.  Laue explained diffraction by means of the 'Laue equations'
which contain 3 integers corresponding exactly to the indices we are
all familiar with.  I prefer to call them 'reflection indices', though
strictly I suppose we should be calling them 'Laue indices'.  Almost
immediately after Laue's discovery, William Lawrence Bragg in
Cambridge devised what we now know as Bragg's Law, wherein the
factor 'n' relates the Miller indices to the Laue indices; thus the
reflection with indices (nh,nk,nl) is the n'th order of diffraction
from the set of crystal planes with Miller indices (h,k,l).  Bragg
also received the physics Nobel prize jointly with his father William
Henry Bragg in the following year, 1915, for their determination of
the crystal structures of NaCl, ZnS and diamond.

Cheers

-- Ian

On Thu, Oct 21, 2010 at 4:57 PM, Clemens Vonrhein
vonrh...@globalphasing.com wrote:
 Hi Herman,

 On Thu, Oct 21, 2010 at 05:31:51PM +0200, herman.schreu...@sanofi-aventis.com 
 wrote:
 If you process your data in a lower symmetry space group, you will have
 more unique reflections, since reflections which are related by the
 higher symmetry will be avaraged during scaling in a higher symmetry
 space group (i.e. a 2fold or 3fold axis), while in lower symmetry space
 groups they will not. So the observation to parameter ratio stays the
 same and is only depending on resolution and solvent content.

 True - if you count Miller indices as observations. But if you think
 about information content than probably not (as you discuss below).

 The question one has to ask of course is: are these reflections really
 different, or are they the same only not averaged?

 Yes - by merging we're getting better data (better error estimate on
 the intensity due to higher multiplicity). So there isn't really
 independent information in 50% of the reflections if e.g. going from
 P21 to P1 - we've only increased the noise because the multiplicity of
 each reflection has been reduced.

 In the latter case, you have more reflections, but not more
 information. As Ed mentions, using tight NCS restraints would in
 this case mimick the crystallographic symmetry.

 Apart from the (good) NCS argument, one could go even further:

 We could also just collect 36000 degree of data on a 7A Lysozyme
 crystal and refine against completely unmerged data. After all, why
 should we stop at removing only the some symmetry operators from our
 data merging ... lets get rid of all of them including th x,y,z
 operator and use unmerged data. Then we could refine Lysozyme with
 anisotropic hydrogens and no restraints against 7A data since we have
 a huge number of 'observations' ... right?

 But seriously: there is a difference in having reflections (H, K, L)
 and independent data (I, SIGI). Maybe we should talk more about
 (independent observations)/parameters ratio in the same way we
 look at depdencies of parameters (e.g. restraints on Bfactors etc).

 Cheers

 Clemens

 --

 ***
 * Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
 *
 *  Global Phasing Ltd.
 *  Sheraton House, Castle Park
 *  Cambridge CB3 0AX, UK
 *--
 * BUSTER Development Group      (http://www.globalphasing.com)
 ***

Re: [ccp4bb] Regarding space group P1, P21

[Ian Tickle]

Well no, I never did during my crystallography training: it seems to
be a change of definition that's occurred fairly recently, without
recognition of the fact that the original definition is still in use,
particularly in mineralogy of course, where, unlike often is the case
with protein crystals, you can usually see the crystal faces with the
naked eye!  I'm thinking particularly of this site that Bernhard
recently pointed out:

http://news.nationalgeographic.com/news/bigphotos/82948445.html

I remember the time when we did actually measure the faces of a
crystal (small molecule, not protein) and determine their Miller
indices, in order to calculate the absorption correction (no doubt
Shel-X still allows you to do it that way!).  So it would have been a
little confusing to call Miller indices and reflection/Laue indices by
the same name!

Cheers

-- Ian

On Thu, Oct 21, 2010 at 8:28 PM, Jacob Keller
j-kell...@fsm.northwestern.edu wrote:
 I like your more-accurate definition, but practically speaking, doesn't
 everyone call hkl Miller indices?

 Jacob

 - Original Message - From: Ian Tickle ianj...@gmail.com
 To: CCP4BB@JISCMAIL.AC.UK
 Sent: Thursday, October 21, 2010 2:00 PM
 Subject: Re: [ccp4bb] Regarding space group P1, P21


 Hi Clemens,

 Sorry to be picky and start the 'definition game' over again, but
 'Miller indices' are strictly not the numbers that index X-ray
 reflections that everyone is familiar with (whether observed or not!).
 Miller indices were introduced in 1839 by the British mineralogist
 William Hallowes Miller (it says in WIkipedia) as a way of describing
 the direction of the perpendicular to the plane faces that he observed
 on mineral crystals.  A condition is that no common denominator is
 possible, since it defines only the direction of a vector; its
 magnitude has no relevance in this context.  So you can have Miller
 indices (1,0,0), (1,2,0), (1,2,3) etc but you can't have (2,0,0),
 (3,0,0), {2,4,0), (3,6,9) etc., or at least (1,0,0) means exactly the
 same thing as (2,0,0) etc.  You can multiply the MiIler index vector
 by -1: this indicates the opposite face of the crystal.  Imagine what
 an electron density map would look like if you only collected
 intensities at the Miller indices!

 Miller's observation of the plane faces of mineral crystals occurred
 73 years before the discovery in 1912 of X-ray diffraction by Max Laue
 in Munich (he became Max von Laue in 1913 when his father was raised
 to the nobility), for which Laue received the Nobel Prize in Physics
 in 1914.  Laue explained diffraction by means of the 'Laue equations'
 which contain 3 integers corresponding exactly to the indices we are
 all familiar with.  I prefer to call them 'reflection indices', though
 strictly I suppose we should be calling them 'Laue indices'.  Almost
 immediately after Laue's discovery, William Lawrence Bragg in
 Cambridge devised what we now know as Bragg's Law, wherein the
 factor 'n' relates the Miller indices to the Laue indices; thus the
 reflection with indices (nh,nk,nl) is the n'th order of diffraction
 from the set of crystal planes with Miller indices (h,k,l).  Bragg
 also received the physics Nobel prize jointly with his father William
 Henry Bragg in the following year, 1915, for their determination of
 the crystal structures of NaCl, ZnS and diamond.

 Cheers

 -- Ian

 On Thu, Oct 21, 2010 at 4:57 PM, Clemens Vonrhein
 vonrh...@globalphasing.com wrote:

 Hi Herman,

 On Thu, Oct 21, 2010 at 05:31:51PM +0200,
 herman.schreu...@sanofi-aventis.com wrote:

 If you process your data in a lower symmetry space group, you will have
 more unique reflections, since reflections which are related by the
 higher symmetry will be avaraged during scaling in a higher symmetry
 space group (i.e. a 2fold or 3fold axis), while in lower symmetry space
 groups they will not. So the observation to parameter ratio stays the
 same and is only depending on resolution and solvent content.

 True - if you count Miller indices as observations. But if you think
 about information content than probably not (as you discuss below).

 The question one has to ask of course is: are these reflections really
 different, or are they the same only not averaged?

 Yes - by merging we're getting better data (better error estimate on
 the intensity due to higher multiplicity). So there isn't really
 independent information in 50% of the reflections if e.g. going from
 P21 to P1 - we've only increased the noise because the multiplicity of
 each reflection has been reduced.

 In the latter case, you have more reflections, but not more
 information. As Ed mentions, using tight NCS restraints would in
 this case mimick the crystallographic symmetry.

 Apart from the (good) NCS argument, one could go even further:

 We could also just collect 36000 degree of data on a 7A Lysozyme
 crystal and refine against completely unmerged data. After all, why
 should we stop at removing only the some symmetry operators

Re: [ccp4bb] Regarding space group P1, P21

[Ethan Merritt]

On Thursday, October 21, 2010 11:38:55 am Jacob Keller wrote:

 
 if the data really looks like P21-- what are the criteria for that?

This is a straightforward statistical question.
In testing for a possible 2-fold, you want to know:

 Do two random reflections related by the putative 2-fold agree with
 each other better than two random reflections not related by the
 putative 2-fold?

To make this test less sensitive to scaling, one can formulate it
as a correlation coefficient.  Have a look at the paper describing
`pointless`.

  P Evans (2006), Acta Cryst. D62: 72-82

Testing the for systematic absences indicating a screw axis can also
be phrased as a statistical test, although generally there are a relatively
small number of putative absences to inspect so the test is not all that
strong.

Ethan





 I believe p1 can have good-as-perfect 90deg angles, no? 

Correct. The cell angles don't really enter into it.



 And also 
 equal cell dimensions? So I don't think you will be able to tell from the 
 positions of the spots on the detector, necessarily. Also, would it not be 
 more rigorous to say I can gain a lot by assuming these molecules are in 
 p21? Look, nobody thinks that every molecule in the crystal is identical, 
 so that is truly a convenient assumption. The symmetry, I think, is a 
 similar assumption at a different level.
 
 By the way, I have always wondered whether anybody has looked into the 
 degree of intermolecular differences possible given all of the parameters in 
 our crystallographic models. In other words, would a microscopic observer 
 look at the molecules in the crystal and see what looks like a crowd from a 
 NYC street, or something more like an army formation? How much variety is 
 there at the molecular lever, I wonder?
 
  True: but how do you judge that those differences are within or
  outside of experimental noise?
 
 Agreed!
 
  What if by refining in P1 the parametrisation makes those side-chains
  different in the first place? A poorly defined Lys side-chain suddenly
  becomes two significantly different poorly defined side-chain?
 
 I don't know--depends on last question I think.
 
 Jacob
 
 ***
 Jacob Pearson Keller
 Northwestern University
 Medical Scientist Training Program
 Dallos Laboratory
 F. Searle 1-240
 2240 Campus Drive
 Evanston IL 60208
 lab: 847.491.2438
 cel: 773.608.9185
 email: j-kell...@northwestern.edu
 ***
 

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742

Re: [ccp4bb] Regarding space group P1, P21

[Phil Evans]

It's more complicated than that, since the tricky thing is to distinguish 
between reflections related eg by a putative crystallographic two-fold and by a 
parallel non-crystallographic two-fold, which would give very similar intensity 
relationships. Pointless does try to score these alternative models, but it is 
not fool-proof. 

In the end, the best test is probably comparing refinements in different space 
groups (as is done by the Andrey Lebedev's Zanuda program, on the York 
University server), though it seems to me that in the limit you can't tell: how 
close does a non-crystallographic axis have to be to a crystal direction to be 
crystallographic, 1degree, 0.1 degrees, 0.01degrees?

Phil Evans

(incidentally, the algorithms used in Pointless are described in a paper due to 
appear in the Acta Cryst. D volume from the 2010 CCP4 Study Weekend, probably 
early next year. But I don't really know how best to calculate the 
probabilities)   


On 21 Oct 2010, at 21:03, Ethan Merritt wrote:

 On Thursday, October 21, 2010 11:38:55 am Jacob Keller wrote:
 
 
 if the data really looks like P21-- what are the criteria for that?
 
 This is a straightforward statistical question.
 In testing for a possible 2-fold, you want to know:
 
 Do two random reflections related by the putative 2-fold agree with
 each other better than two random reflections not related by the
 putative 2-fold?
 
 To make this test less sensitive to scaling, one can formulate it
 as a correlation coefficient.  Have a look at the paper describing
 `pointless`.
 
  P Evans (2006), Acta Cryst. D62: 72-82
 
 Testing the for systematic absences indicating a screw axis can also
 be phrased as a statistical test, although generally there are a relatively
 small number of putative absences to inspect so the test is not all that
 strong.
 
   Ethan
 
 
 
 
 
 I believe p1 can have good-as-perfect 90deg angles, no? 
 
 Correct. The cell angles don't really enter into it.
 
 
 
 And also 
 equal cell dimensions? So I don't think you will be able to tell from the 
 positions of the spots on the detector, necessarily. Also, would it not be 
 more rigorous to say I can gain a lot by assuming these molecules are in 
 p21? Look, nobody thinks that every molecule in the crystal is identical, 
 so that is truly a convenient assumption. The symmetry, I think, is a 
 similar assumption at a different level.
 
 By the way, I have always wondered whether anybody has looked into the 
 degree of intermolecular differences possible given all of the parameters in 
 our crystallographic models. In other words, would a microscopic observer 
 look at the molecules in the crystal and see what looks like a crowd from a 
 NYC street, or something more like an army formation? How much variety is 
 there at the molecular lever, I wonder?
 
 True: but how do you judge that those differences are within or
 outside of experimental noise?
 
 Agreed!
 
 What if by refining in P1 the parametrisation makes those side-chains
 different in the first place? A poorly defined Lys side-chain suddenly
 becomes two significantly different poorly defined side-chain?
 
 I don't know--depends on last question I think.
 
 Jacob
 
 ***
 Jacob Pearson Keller
 Northwestern University
 Medical Scientist Training Program
 Dallos Laboratory
 F. Searle 1-240
 2240 Campus Drive
 Evanston IL 60208
 lab: 847.491.2438
 cel: 773.608.9185
 email: j-kell...@northwestern.edu
 ***
 
 
 -- 
 Ethan A Merritt
 Biomolecular Structure Center,  K-428 Health Sciences Bldg
 University of Washington, Seattle 98195-7742

[ccp4bb] Missing space group in ?.mtz file

[Petr Kolenko]

Dear colleagues,
I have a ?.mtz file from integration with missing info about the space 
group in the SYMINFO. I tried to modify the file with combat and 
mtzutils, but it always ends up in reading the original file with this 
message:


Failed to find spacegroup in SYMINFO!
MTZUTILS:  Fatal error in ccp4spg_register_by_symops
MTZUTILS:  Fatal error in ccp4spg_register_by_symops

Here is report from mtzdump:
Failed to find spacegroup in SYMINFO!
MTZDUMP:  Fatal error in ccp4spg_register_by_symops

I know the correct space group, but I do not know how to supply the .mtz 
file. Any suggestion, please? Thanks for all of them.


Best Regards,
Petr

Petr Kolenko
[EMAIL PROTECTED]

Re: [ccp4bb] Missing space group in ?.mtz file

[Eleanor Dodson]

When all else fails you can dump the file as an ASCII format using 
mtztona4, edit that file to correct the spacegroup and reconvert it to 
mtz using na4tomtz.

Eleanor

Petr Kolenko wrote:

Dear colleagues,
I have a ?.mtz file from integration with missing info about the space 
group in the SYMINFO. I tried to modify the file with combat and 
mtzutils, but it always ends up in reading the original file with this 
message:


Failed to find spacegroup in SYMINFO!
MTZUTILS:  Fatal error in ccp4spg_register_by_symops
MTZUTILS:  Fatal error in ccp4spg_register_by_symops

Here is report from mtzdump:
Failed to find spacegroup in SYMINFO!
MTZDUMP:  Fatal error in ccp4spg_register_by_symops

I know the correct space group, but I do not know how to supply the 
.mtz file. Any suggestion, please? Thanks for all of them.


Best Regards,
Petr

Petr Kolenko
[EMAIL PROTECTED]