[ccp4bb] AW: [ccp4bb] Hi

[Herman . Schreuder]

Hi Wei,
if you tried both P3 and P6 and all subgroups, the right space group should 
have been in there. By the way, the number of monomers in the a.u. will depend 
on the exact space group (e.g. 1 in P622, 2 in P6 or P321, 4 in P3). There 
might be a conformational change, which causes the MR programs to reject the 
solution because of clashes. In this case you should examine your structure 
e.g. in coot and look for loops or domains, which might be able to move and 
delete them. If you get an MR solution with the truncated search model, you can 
always do a second MR run with the deleted domain as a search model. Single 
loops you have to rebuild from scratch. Alternatively, you could also increase 
the number of allowed clashes, so the MR programs won't reject potential 
solutions.

Good luck!
Herman


Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Wei Shi
Gesendet: Montag, 10. Juni 2013 20:57
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Hi

Hi all,
I was trying to solve the structure of a protein in several different datasets 
using xds and phenix. I could solve the structure from one dataset in space 
group P4. For another dataset, I could solve the structure using the monomer of 
the structure I got from the first dataset as search model and solve the 
structure in space group mC. For the third dataset, in IDXREF.LP, the space 
group of the highest symmetry is hp: 101.2, 101.3, 58.8, 90, 90, 120. According 
to Mathiews coefficient, 1 monomer is expected in the asymmetric unit. But I 
couldn't get the molecular replacement solution using the same method as for 
the second dataset. I also tried several other search models (eg. deletion of 
the potential flexible region in the search model) and tried to find the 
solution in all possible pointgroup. I also tried to process the data in oC 
(C222), the space group of the second highest symmetry in IDXREF.LP, but, still 
I could not get right molecular replacement solution.  I don't whether this 
means that there is a big conformational change for the structure in the third 
dataset or the space group I use is not right. Let me know if any of you would 
have any comments or suggestions for me. Thank you so much!

Best,
Wei

Re: [ccp4bb] pdbset

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Swastik Phulera,

after the word 'output.pdb' you must first hit the Enter-key which
takes you into the program pdbset.
Then you type

B_reset Minimum 0
END

and the program runs.
If you wish to do it without interaction, e.g. in a script, you can
use the shell construct '<<':

pdbset XYZIN input.pdb XYZOUT output.pdb << eof
B_reset MINIMUM 0
eof

Best,
Tim

On 06/11/2013 08:15 AM, Swastik Phulera wrote:
> Dear All, I am trying to use pdbset from the terminal and am
> constantly getting an error:
> 
> [XYZ@NCCS3 110613]$ pdbset XYZIN input.pdb XYZOUT output.pdb
> B_reset MINIMUM 0
> 
>>> CCP4 library signal ccp4_general:Use: 
>>> 
> (Error) raised in ccp4fyp << pdbset:  Use:   name> pdbset:  Use:   Times: User:
> 0.0s System:0.0s Elapsed: 0:00
> 
> Does any one have any idea what's wrong here?
> 
> 
> Swastik Phulera

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

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFRtsaJUxlJ7aRr7hoRAiAsAKCuDDip6GFczecze/Y18+YaD4+SqACdGnSU
fG1/zzDml0ynkX8uOBN7S+o=
=2I5+
-END PGP SIGNATURE-

[ccp4bb] pdbset

[Swastik Phulera]

Dear All,
I am trying to use pdbset from the terminal and am constantly getting an
error:

[XYZ@NCCS3 110613]$ pdbset XYZIN input.pdb XYZOUT output.pdb B_reset
MINIMUM 0

>> CCP4 library signal ccp4_general:Use:  
(Error)
 raised in ccp4fyp <<
 pdbset:  Use:  
 pdbset:  Use:  
Times: User:   0.0s System:0.0s Elapsed: 0:00

Does any one have any idea what's wrong here?


Swastik Phulera
-- 
--
स्वस्तिक फुलेरा
वरिष्ठ अनुसंधान कर्ता
राष्ट्रीय कोशिका विज्ञान केंद्र
पुणे विश्वविद्यालय परिसर,
गणेशखिंड
पुना,  ४११,००७

Re: [ccp4bb] Protein concentration for crystallization

[Debasish Chattopadhyay]

Perhaps my question was not expressed well.  I wanted to know if proteins 
crystallize more frequently when the protein concentration is in the range 
5-30mg/ml.
The answer pointed out by my colleague Todd Green is on the page
http://www.douglas.co.uk/PDB_data.htm

Thanks for your inputs.

Debasish

From: Orru, Roberto [mailto:roberto.o...@emory.edu]
Sent: Monday, June 10, 2013 5:04 PM
To: Debasish Chattopadhyay
Subject: RE: Protein concentration for crystallization

Dear Debasish,

On my memory there are 2 way (but I cannot say that are the only 2!)
First: if you have the structure and you know the water content, you can guess 
the amount of protein crystallized in your drop by calculating the volume of 
the crystals.
Second (if you can waste your drops): Fish all the crytsals in any drop for a 
given concentration, load a sds page w/ silver staining developing and compare 
it with a calibration curve done with your same protein in the same gel.

Best
R.

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Debasish 
Chattopadhyay [debas...@uab.edu]
Sent: Monday, June 10, 2013 10:49
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Protein concentration for crystallization
What would be a convenient way to estimate what percentages of proteins have 
been crystallized in a concentration range, for example 5-30 mg?

Debasish Chattopadhyay

University of Alabama at Birmingham
CBSE-250
1025 18th Street South, Birmingham, Al-35294
USA
Ph: (205)934-0124; Fax: (205)934-0480




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Re: [ccp4bb] Off-topic: NMR and crystallography

[Valerie Pye]

Hi Theresa,

I think you have to be very careful with NMR of homo-oligomers, even if
they’re small proteins: the NMR model/structure (backbone only) of a small
integral membrane kinase was a huge effort -
http://www.ncbi.nlm.nih.gov/pubmed/19556511

but is very different from the recently published crystal structure -
http://www.ncbi.nlm.nih.gov/pubmed/23676677

There’s some commentary here:
http://www.nature.com/nature/journal/v497/n7450/full/nature12245.html

I’m fairly biased but i don’t think that both states could exist – and
going from the NMR model to the crystal structure would require a huge
amount of energy – a morph between the two can be found here:
http://youtu.be/5vpEGSvVe04

Needless to say we couldn’t (try as we might!) get an MR solution using the
NMR model/structure

Best wishes, val


On 9 June 2013 16:36, Theresa Hsu  wrote:

> Dear all
>
> A question for the cross-trained members of this forum - for small sized
> proteins, is NMR better than crystallography in terms of data collection
> (having crystals in the first place) and data processing? How about
> membrane proteins?
>
> I would appreciate replies to the board, instead of off-board, to allow
> for a good discussion.
>
> Thank you.
>
> Theresa
>

Re: [ccp4bb] Hi

[Bernhard Rupp]

I guess Wei means just the lattice symbol, taken from the indexing program?
br

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Eleanor Dodson
Sent: Monday, June 10, 2013 10:52 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Hi

I don't really understand what your space group is? space group mC??? 
Eleanor
On 10 Jun 2013, at 19:57, Wei Shi wrote:

> Hi all,
> I was trying to solve the structure of a protein in several different
datasets using xds and phenix. I could solve the structure from one dataset
in space group P4. For another dataset, I could solve the structure using
the monomer of the structure I got from the first dataset as search model
and solve the structure in space group mC. For the third dataset, in
IDXREF.LP, the space group of the highest symmetry is hp: 101.2, 101.3,
58.8, 90, 90, 120. According to Mathiews coefficient, 1 monomer is expected
in the asymmetric unit. But I couldn't get the molecular replacement
solution using the same method as for the second dataset. I also tried
several other search models (eg. deletion of the potential flexible region
in the search model) and tried to find the solution in all possible
pointgroup. I also tried to process the data in oC (C222), the space group
of the second highest symmetry in IDXREF.LP, but, still I could not get
right molecular replacement solution.  I don't whether this means that there
is a big conformational change for the structure in the third dataset or the
space group I use is not right. Let me know if any of you would have any
comments or suggestions for me. Thank you so much!
> 
> Best,
> Wei 
> 
> 

Re: [ccp4bb] Hi

[Bosch, Juergen]

The other obvious conclusion would be that dataset #3 is a different protein 
perhaps ?
How about pointless for your third dataset ?
Jürgen

On Jun 10, 2013, at 2:57 PM, Wei Shi wrote:

Hi all,
I was trying to solve the structure of a protein in several different datasets 
using xds and phenix. I could solve the structure from one dataset in space 
group P4. For another dataset, I could solve the structure using the monomer of 
the structure I got from the first dataset as search model and solve the 
structure in space group mC. For the third dataset, in IDXREF.LP, the space 
group of the highest symmetry is hp: 101.2, 101.3, 58.8, 90, 90, 120. According 
to Mathiews coefficient, 1 monomer is expected in the asymmetric unit. But I 
couldn't get the molecular replacement solution using the same method as for 
the second dataset. I also tried several other search models (eg. deletion of 
the potential flexible region in the search model) and tried to find the 
solution in all possible pointgroup. I also tried to process the data in oC 
(C222), the space group of the second highest symmetry in IDXREF.LP, but, still 
I could not get right molecular replacement solution.  I don't whether this 
means that there is a big conformational change for the structure in the third 
dataset or the space group I use is not right. Let me know if any of you would 
have any comments or suggestions for me. Thank you so much!

Best,
Wei



..
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

Re: [ccp4bb] Hi

[Bosch, Juergen]

Hi Eleanor,

C2 - this was XDS lingo or Bravais talk :-)

Jürgen


** LATTICE SYMMETRY IMPLICATED BY SPACE GROUP SYMMETRY **

BRAVAIS-POSSIBLE SPACE-GROUPS FOR PROTEIN CRYSTALS
 TYPE [SPACE GROUP NUMBER,SYMBOL]
 aP  [1,P1]
 mP  [3,P2] [4,P2(1)]
mC,mI[5,C2]
 oP  [16,P222] [17,P222(1)] [18,P2(1)2(1)2] [19,P2(1)2(1)2(1)]
 oC  [21,C222] [20,C222(1)]
 oF  [22,F222]
 oI  [23,I222] [24,I2(1)2(1)2(1)]
 tP  [75,P4] [76,P4(1)] [77,P4(2)] [78,P4(3)] [89,P422] [90,P42(1)2]
 [91,P4(1)22] [92,P4(1)2(1)2] [93,P4(2)22] [94,P4(2)2(1)2]
 [95,P4(3)22] [96,P4(3)2(1)2]
 tI  [79,I4] [80,I4(1)] [97,I422] [98,I4(1)22]
 hP  [143,P3] [144,P3(1)] [145,P3(2)] [149,P312] [150,P321] [151,P3(1)12]
 [152,P3(1)21] [153,P3(2)12] [154,P3(2)21] [168,P6] [169,P6(1)]
 [170,P6(5)] [171,P6(2)] [172,P6(4)] [173,P6(3)] [177,P622]
 [178,P6(1)22] [179,P6(5)22] [180,P6(2)22] [181,P6(4)22] [182,P6(3)22]
 hR  [146,R3] [155,R32]
 cP  [195,P23] [198,P2(1)3] [207,P432] [208,P4(2)32] [212,P4(3)32]
 [213,P4(1)32]
 cF  [196,F23] [209,F432] [210,F4(1)32]
 cI  [197,I23] [199,I2(1)3] [211,I432] [214,I4(1)32]

On Jun 10, 2013, at 4:51 PM, Eleanor Dodson wrote:

I don't really understand what your space group is? space group mC???
Eleanor
On 10 Jun 2013, at 19:57, Wei Shi wrote:

Hi all,
I was trying to solve the structure of a protein in several different datasets 
using xds and phenix. I could solve the structure from one dataset in space 
group P4. For another dataset, I could solve the structure using the monomer of 
the structure I got from the first dataset as search model and solve the 
structure in space group mC. For the third dataset, in IDXREF.LP, the space 
group of the highest symmetry is hp: 101.2, 101.3, 58.8, 90, 90, 120. According 
to Mathiews coefficient, 1 monomer is expected in the asymmetric unit. But I 
couldn't get the molecular replacement solution using the same method as for 
the second dataset. I also tried several other search models (eg. deletion of 
the potential flexible region in the search model) and tried to find the 
solution in all possible pointgroup. I also tried to process the data in oC 
(C222), the space group of the second highest symmetry in IDXREF.LP, but, still 
I could not get right molecular replacement solution.  I don't whether this 
means that there is a big conformational change for the structure in the third 
dataset or the space group I use is not right. Let me know if any of you would 
have any comments or suggestions for me. Thank you so much!

Best,
Wei



..
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

Re: [ccp4bb] Hi

[Eleanor Dodson]

I don't really understand what your space group is? space group mC??? 
Eleanor
On 10 Jun 2013, at 19:57, Wei Shi wrote:

> Hi all,
> I was trying to solve the structure of a protein in several different 
> datasets using xds and phenix. I could solve the structure from one dataset 
> in space group P4. For another dataset, I could solve the structure using the 
> monomer of the structure I got from the first dataset as search model and 
> solve the structure in space group mC. For the third dataset, in IDXREF.LP, 
> the space group of the highest symmetry is hp: 101.2, 101.3, 58.8, 90, 90, 
> 120. According to Mathiews coefficient, 1 monomer is expected in the 
> asymmetric unit. But I couldn't get the molecular replacement solution using 
> the same method as for the second dataset. I also tried several other search 
> models (eg. deletion of the potential flexible region in the search model) 
> and tried to find the solution in all possible pointgroup. I also tried to 
> process the data in oC (C222), the space group of the second highest symmetry 
> in IDXREF.LP, but, still I could not get right molecular replacement 
> solution.  I don't whether this means that there is a big conformational 
> change for the structure in the third dataset or the space group I use is not 
> right. Let me know if any of you would have any comments or suggestions for 
> me. Thank you so much!
> 
> Best,
> Wei 
> 
> 

Re: [ccp4bb] Protein concentration for crystallization

[rana ibd]

Dear Debasish 
What do you mean by percentage? do you mean consentration? so if you mean cons. 
I think you should test you protein using a TCP kit to observe at what cons. 
would your protein  precipitate, this way you would verify the convinient cons. 
for your protein before crystallization
Best Regards
Rana

From: Debasish Chattopadhyay 
To: CCP4BB@JISCMAIL.AC.UK 
Sent: Monday, June 10, 2013 4:49 PM
Subject: [ccp4bb] Protein concentration for crystallization



What would be a convenient way to estimate what percentages of proteins have 
been crystallized in a concentration range, for example 5-30 mg?
 
Debasish Chattopadhyay
 
University of Alabama at Birmingham
CBSE-250
1025 18th Street South, Birmingham, Al-35294
USA
Ph: (205)934-0124; Fax: (205)934-0480

[ccp4bb] Hi

[Wei Shi]

 Hi all,
I was trying to solve the structure of a protein in several different
datasets using xds and phenix. I could solve the structure from one dataset
in space group P4. For another dataset, I could solve the structure using
the monomer of the structure I got from the first dataset as search model
and solve the structure in space group mC. For the third dataset, in
IDXREF.LP, the space group of the highest symmetry is hp: 101.2, 101.3,
58.8, 90, 90, 120. According to Mathiews coefficient, 1 monomer is expected
in the asymmetric unit. But I couldn't get the molecular replacement
solution using the same method as for the second dataset. I also tried
several other search models (eg. deletion of the potential flexible region
in the search model) and tried to find the solution in all possible
pointgroup. I also tried to process the data in oC (C222), the space group
of the second highest symmetry in IDXREF.LP, but, still I could not get
right molecular replacement solution.  I don't whether this means that
there is a big conformational change for the structure in the third dataset
or the space group I use is not right. Let me know if any of you would have
any comments or suggestions for me. Thank you so much!

Best,
Wei

Re: [ccp4bb] Protein concentration for crystallization

[Evgeny Osipov]

Dear Debasish,
you can use REMARK 200 field in pdb file. Sadly, this field is not 
mandatory so not everyone provide protein concentration info.


10.06.2013 18:49, Debasish Chattopadhyay ?:


What would be a convenient way to estimate what percentages of 
proteins have been crystallized in a concentration range, for example 
5-30 mg?


Debasish Chattopadhyay

University of Alabama at Birmingham

CBSE-250

1025 18th Street South, Birmingham, Al-35294

USA

Ph: (205)934-0124; Fax: (205)934-0480




--
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
A.N. Bach Institute of Biochemistry
Russian Academy of Sciences
Leninsky pr. 33, 119071 Moscow, Russia
e-mail: e.m.osi...@gmail.com

[ccp4bb] Protein concentration for crystallization

[Debasish Chattopadhyay]

What would be a convenient way to estimate what percentages of proteins have 
been crystallized in a concentration range, for example 5-30 mg?

Debasish Chattopadhyay

University of Alabama at Birmingham
CBSE-250
1025 18th Street South, Birmingham, Al-35294
USA
Ph: (205)934-0124; Fax: (205)934-0480