Re: [ccp4bb] P21221 to P21212 conversion

[Shya Biswas]

Hi,
i just repeated the MR using the reindexed dataset (hkl to lhk) and it gave
me the right solution.
thanks,
Shya

On Mon, May 7, 2012 at 5:39 PM, Edward A. Berry  wrote:

> Now given that the MR soluiton was obtained in the (preparing to duck)
> "nonstandard" setting, what is the transform to apply to that solution
> in pdbset to get the solution in the "standard" setting? Or is it easier
> to just repeat the MR?
> eab
>
> Shya Biswas wrote:
>
>> Hi Matt,
>> It worked really well in HKL 2000 reindex option, sorry about the
>> confusion before, I wanted hkl to lhk. as you pointed out the second one
>> gave me what I wanted.
>> thanks,
>> Shya
>>
>> On Mon, May 7, 2012 at 4:47 PM, Matthew Franklin > > wrote:
>>
>>On 5/7/12 4:09 PM, Shya Biswas wrote:
>>
>>Hi all,
>>I was wondering if anyone knows how to convert the P21221 to
>>P21212 spacegroup in HKL2000. I scaled the data set in P21212 in
>>HKL 2000 but I got a correct MR solution in P21221 spacegroup. I
>>have a script file that runs with scalepack but was wondering if
>>there is an easier way to do it with HKL2000 gui mode.
>>thanks,
>>Shya
>>
>>Hi Shya -
>>
>>Under the Scale tab of HKL2000, you'll see a button near the bottom
>>labeled "Reindex".  Clicking this brings up a dialog box with the
>>reindexing conventions appropriate to your spacegroup.  For P
>>orthorhombic, there are only two choices: hkl -> klh, or hkl -> lhk.
>>  If you have P21221, and want to go to P21212, you want hkl ->lhk.
>>
>>HOWEVER, there seems to be a bug in this particular reindexing (or
>>maybe the options are written confusingly).  You want to choose the
>>"wrong" option (number 2 in the list presented), as the two options
>>seem to be reversed.  You'll know that you got it right by
>>inspection of the scaling log file - look at the systematic absence
>>table at the bottom.  Also check that the unit cell axes were
>>permuted in the correct way - you want your old b axis to be your
>>new c axis.
>>
>>Once you select the correct reindexing (make sure you apply it to
>>all datasets being scaled at the same time), you click "Reindex" in
>>the popup dialog, and this triggers another round of scaling with
>>the reindexing included.  This reindexing is "sticky" - you don't
>>need to select it again for subsequent rounds of scaling.
>>
>>Hope that helps - feel free to contact me if you want more explanation.
>>
>>- Matt
>>
>>
>>--
>>Matthew Franklin, Ph. D.
>>Senior Scientist
>>New York Structural Biology Center
>>89 Convent Avenue, New York, NY 10027
>>(212) 939-0660 ext. 9374 
>>
>>
>>
>>

Re: [ccp4bb] P21221 to P21212 conversion

[Edward A. Berry]

Now given that the MR soluiton was obtained in the (preparing to duck)
"nonstandard" setting, what is the transform to apply to that solution
in pdbset to get the solution in the "standard" setting? Or is it easier
to just repeat the MR?
eab

Shya Biswas wrote:

Hi Matt,
It worked really well in HKL 2000 reindex option, sorry about the
confusion before, I wanted hkl to lhk. as you pointed out the second one
gave me what I wanted.
thanks,
Shya

On Mon, May 7, 2012 at 4:47 PM, Matthew Franklin mailto:mfrank...@nysbc.org>> wrote:

On 5/7/12 4:09 PM, Shya Biswas wrote:

Hi all,
I was wondering if anyone knows how to convert the P21221 to
P21212 spacegroup in HKL2000. I scaled the data set in P21212 in
HKL 2000 but I got a correct MR solution in P21221 spacegroup. I
have a script file that runs with scalepack but was wondering if
there is an easier way to do it with HKL2000 gui mode.
thanks,
Shya

Hi Shya -

Under the Scale tab of HKL2000, you'll see a button near the bottom
labeled "Reindex".  Clicking this brings up a dialog box with the
reindexing conventions appropriate to your spacegroup.  For P
orthorhombic, there are only two choices: hkl -> klh, or hkl -> lhk.
  If you have P21221, and want to go to P21212, you want hkl ->lhk.

HOWEVER, there seems to be a bug in this particular reindexing (or
maybe the options are written confusingly).  You want to choose the
"wrong" option (number 2 in the list presented), as the two options
seem to be reversed.  You'll know that you got it right by
inspection of the scaling log file - look at the systematic absence
table at the bottom.  Also check that the unit cell axes were
permuted in the correct way - you want your old b axis to be your
new c axis.

Once you select the correct reindexing (make sure you apply it to
all datasets being scaled at the same time), you click "Reindex" in
the popup dialog, and this triggers another round of scaling with
the reindexing included.  This reindexing is "sticky" - you don't
need to select it again for subsequent rounds of scaling.

Hope that helps - feel free to contact me if you want more explanation.

- Matt


--
Matthew Franklin, Ph. D.
Senior Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(212) 939-0660 ext. 9374 

Re: [ccp4bb] P21221 to P21212 conversion

[Shya Biswas]

Hi Matt,
It worked really well in HKL 2000 reindex option, sorry about the confusion
before, I wanted hkl to lhk. as you pointed out the second one gave me what
I wanted.
thanks,
Shya

On Mon, May 7, 2012 at 4:47 PM, Matthew Franklin wrote:

> On 5/7/12 4:09 PM, Shya Biswas wrote:
>
>> Hi all,
>> I was wondering if anyone knows how to convert the P21221 to P21212
>> spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I
>> got a correct MR solution in P21221 spacegroup. I have a script file that
>> runs with scalepack but was wondering if there is an easier way to do it
>> with HKL2000 gui mode.
>> thanks,
>> Shya
>>
> Hi Shya -
>
> Under the Scale tab of HKL2000, you'll see a button near the bottom
> labeled "Reindex".  Clicking this brings up a dialog box with the
> reindexing conventions appropriate to your spacegroup.  For P orthorhombic,
> there are only two choices: hkl -> klh, or hkl -> lhk.  If you have P21221,
> and want to go to P21212, you want hkl ->lhk.
>
> HOWEVER, there seems to be a bug in this particular reindexing (or maybe
> the options are written confusingly).  You want to choose the "wrong"
> option (number 2 in the list presented), as the two options seem to be
> reversed.  You'll know that you got it right by inspection of the scaling
> log file - look at the systematic absence table at the bottom.  Also check
> that the unit cell axes were permuted in the correct way - you want your
> old b axis to be your new c axis.
>
> Once you select the correct reindexing (make sure you apply it to all
> datasets being scaled at the same time), you click "Reindex" in the popup
> dialog, and this triggers another round of scaling with the reindexing
> included.  This reindexing is "sticky" - you don't need to select it again
> for subsequent rounds of scaling.
>
> Hope that helps - feel free to contact me if you want more explanation.
>
> - Matt
>
>
> --
> Matthew Franklin, Ph. D.
> Senior Scientist
> New York Structural Biology Center
> 89 Convent Avenue, New York, NY 10027
> (212) 939-0660 ext. 9374
>
>
>

Re: [ccp4bb] P21221 to P21212 conversion

[Ethan Merritt]

On Monday, May 07, 2012 02:00:43 pm Phil Jeffrey wrote:
> On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt
>  > Scaling is done in a point group, not a space group.
> 
> My quibble with this statement is that the output reflection data from 
> Scalepack differs depending on what space group you tell it, since 
> systematic absences along h00, 0k0 and 00l in P2x2x2x are not written 
> out.  The number of reflections affected is quite small, of course.

The statement is correct, but the scalepack behavior is IMHO a bad thing.
Therefore I always tell it to scale in the pointgroup (P222 in this case)
and I correct the space group later.

Ethan


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

Re: [ccp4bb] P21221 to P21212 conversion

[Jacob Keller]

Why do you like P21212 better than P22121?

JPK

On Mon, May 7, 2012 at 4:00 PM, Phil Jeffrey  wrote:

> The program that does the indexing in HKL is Denzo.  Denzo doesn't care
> about the space group.  It cares about the point group (cf. Ethan's point)
> and the cell dimensions, because it integrates the data without regard to
> the symmetry expressed in the intensities - however it does take notice of
> the restrictions placed on cell dimensions by point groups.  Denzo
> therefore picks primitive orthorhombic cells in a
> Scalepack scales the integrated data but does not reindex the data if you
> tell it the space group is P22121.  Therefore unit cell choice in HKL is by
> default driven by cell edge size.  Scalepack has the ability to reindex the
> data, for those of us that like to work in P21212 rather than P22121.
>
>
> On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt
> > Scaling is done in a point group, not a space group.
>
> My quibble with this statement is that the output reflection data from
> Scalepack differs depending on what space group you tell it, since
> systematic absences along h00, 0k0 and 00l in P2x2x2x are not written out.
>  The number of reflections affected is quite small, of course.
>
>
> Phil Jeffrey
> Princeton
>
>
>
>
>
> On 5/7/12 4:48 PM, Jacob Keller wrote:
>
>> Is it true that HKL adopts the naming convention of putting the screw
>> axes first and then naming a> the cell a> or would it automatically be p21212?
>>
>> JPK
>>
>> On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt > > wrote:
>>
>>On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote:
>> > Hi all,
>> > I was wondering if anyone knows how to convert the P21221 to P21212
>> > spacegroup in HKL2000. I scaled the data set in P21212 in HKL
>>2000 but I
>> > got a correct MR solution in P21221 spacegroup.
>>
>>Shya:
>>
>>Scaling is done in a point group, not a space group.
>>
>>The point group P222 contains both space groups P2(1)22(1) and
>>P2(1)2(1)2,
>>so your original scaling is correct in either case.
>>
>>It is not clear from your query which of two things happened:
>>
>>1) The MR solution kept the same a, b, and c axis assignments but made
>> a
>>different call on whether each axis did or did not correspond to a
>>2(1) screw.
>>In this case you don't need to do anything to your files. Just make
>> sure
>>that you keep the new space group as you go forward into refinement.
>>
>>2) The MR solution kept the orginal screw-axis identifications but
>>permuted the axes to the standard setting (non-screw axis is
>>labelled "c").
>>In this case you will need to construct a file containing the permuted
>>indices. For example, the reflection originally labeled (h=1 k=2
>>l=3) is now
>>(h=3 k=1 l=2). There are several programs that can help you do this,
>>including the HKL2000 GUI. But you do not need to go back into HKL
>>if you don't want to. You could, for example, use the ccp4i GUI to
>>select
>>-> Reflection Data Utilities
>>-> Reindex Reflections
>>Define Transformation Matrix by entering reflection transformation
>>h=l k=h l=k
>>
>>
>>Ethan
>>
>>
>> > I have a script file that
>> > runs with scalepack but was wondering if there is an easier way
>>to do it
>> > with HKL2000 gui mode.
>> > thanks,
>> > Shya
>> >
>>
>>--
>>Ethan A Merritt
>>Biomolecular Structure Center, K-428 Health Sciences Bldg
>>University of Washington, Seattle 98195-7742
>>
>>
>>
>>
>> --
>> *
>> Jacob Pearson Keller
>> Northwestern University
>> Medical Scientist Training Program
>> email: j-kell...@northwestern.edu 
>> > >
>> *
>>
>
>


-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] P21221 to P21212 conversion

[Felix Frolow]

If one make a proper transformation :-/ and supply a correct space group, 
absent reflections will be printed in the end of scale.log
Dr Felix Frolow   
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfro...@post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On May 8, 2012, at 24:00 , Phil Jeffrey wrote:

> The program that does the indexing in HKL is Denzo.  Denzo doesn't care about 
> the space group.  It cares about the point group (cf. Ethan's point) and the 
> cell dimensions, because it integrates the data without regard to the 
> symmetry expressed in the intensities - however it does take notice of the 
> restrictions placed on cell dimensions by point groups.  Denzo therefore 
> picks primitive orthorhombic cells in a 
> Scalepack scales the integrated data but does not reindex the data if you 
> tell it the space group is P22121.  Therefore unit cell choice in HKL is by 
> default driven by cell edge size.  Scalepack has the ability to reindex the 
> data, for those of us that like to work in P21212 rather than P22121.
> 
> On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt
> > Scaling is done in a point group, not a space group.
> 
> My quibble with this statement is that the output reflection data from 
> Scalepack differs depending on what space group you tell it, since systematic 
> absences along h00, 0k0 and 00l in P2x2x2x are not written out.  The number 
> of reflections affected is quite small, of course.
> 
> 
> Phil Jeffrey
> Princeton
> 
> 
> 
> 
> On 5/7/12 4:48 PM, Jacob Keller wrote:
>> Is it true that HKL adopts the naming convention of putting the screw
>> axes first and then naming a> the cell a> or would it automatically be p21212?
>> 
>> JPK
>> 
>> On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt > > wrote:
>> 
>>On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote:
>> > Hi all,
>> > I was wondering if anyone knows how to convert the P21221 to P21212
>> > spacegroup in HKL2000. I scaled the data set in P21212 in HKL
>>2000 but I
>> > got a correct MR solution in P21221 spacegroup.
>> 
>>Shya:
>> 
>>Scaling is done in a point group, not a space group.
>> 
>>The point group P222 contains both space groups P2(1)22(1) and
>>P2(1)2(1)2,
>>so your original scaling is correct in either case.
>> 
>>It is not clear from your query which of two things happened:
>> 
>>1) The MR solution kept the same a, b, and c axis assignments but made a
>>different call on whether each axis did or did not correspond to a
>>2(1) screw.
>>In this case you don't need to do anything to your files. Just make sure
>>that you keep the new space group as you go forward into refinement.
>> 
>>2) The MR solution kept the orginal screw-axis identifications but
>>permuted the axes to the standard setting (non-screw axis is
>>labelled "c").
>>In this case you will need to construct a file containing the permuted
>>indices. For example, the reflection originally labeled (h=1 k=2
>>l=3) is now
>>(h=3 k=1 l=2). There are several programs that can help you do this,
>>including the HKL2000 GUI. But you do not need to go back into HKL
>>if you don't want to. You could, for example, use the ccp4i GUI to
>>select
>>-> Reflection Data Utilities
>>-> Reindex Reflections
>>Define Transformation Matrix by entering reflection transformation
>>h=l k=h l=k
>> 
>> 
>>Ethan
>> 
>> 
>> > I have a script file that
>> > runs with scalepack but was wondering if there is an easier way
>>to do it
>> > with HKL2000 gui mode.
>> > thanks,
>> > Shya
>> >
>> 
>>--
>>Ethan A Merritt
>>Biomolecular Structure Center, K-428 Health Sciences Bldg
>>University of Washington, Seattle 98195-7742
>> 
>> 
>> 
>> 
>> --
>> ***
>> Jacob Pearson Keller
>> Northwestern University
>> Medical Scientist Training Program
>> email: j-kell...@northwestern.edu 
>> ***

Re: [ccp4bb] P21221 to P21212 conversion

[Phil Jeffrey]

The program that does the indexing in HKL is Denzo.  Denzo doesn't care 
about the space group.  It cares about the point group (cf. Ethan's 
point) and the cell dimensions, because it integrates the data without 
regard to the symmetry expressed in the intensities - however it does 
take notice of the restrictions placed on cell dimensions by point 
groups.  Denzo therefore picks primitive orthorhombic cells in a

Scalepack scales the integrated data but does not reindex the data if 
you tell it the space group is P22121.  Therefore unit cell choice in 
HKL is by default driven by cell edge size.  Scalepack has the ability 
to reindex the data, for those of us that like to work in P21212 rather 
than P22121.


On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt
> Scaling is done in a point group, not a space group.

My quibble with this statement is that the output reflection data from 
Scalepack differs depending on what space group you tell it, since 
systematic absences along h00, 0k0 and 00l in P2x2x2x are not written 
out.  The number of reflections affected is quite small, of course.



Phil Jeffrey
Princeton




On 5/7/12 4:48 PM, Jacob Keller wrote:

Is it true that HKL adopts the naming convention of putting the screw
axes first and then naming amailto:merr...@u.washington.edu>> wrote:

On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote:
 > Hi all,
 > I was wondering if anyone knows how to convert the P21221 to P21212
 > spacegroup in HKL2000. I scaled the data set in P21212 in HKL
2000 but I
 > got a correct MR solution in P21221 spacegroup.

Shya:

Scaling is done in a point group, not a space group.

The point group P222 contains both space groups P2(1)22(1) and
P2(1)2(1)2,
so your original scaling is correct in either case.

It is not clear from your query which of two things happened:

1) The MR solution kept the same a, b, and c axis assignments but made a
different call on whether each axis did or did not correspond to a
2(1) screw.
In this case you don't need to do anything to your files. Just make sure
that you keep the new space group as you go forward into refinement.

2) The MR solution kept the orginal screw-axis identifications but
permuted the axes to the standard setting (non-screw axis is
labelled "c").
In this case you will need to construct a file containing the permuted
indices. For example, the reflection originally labeled (h=1 k=2
l=3) is now
(h=3 k=1 l=2). There are several programs that can help you do this,
including the HKL2000 GUI. But you do not need to go back into HKL
if you don't want to. You could, for example, use the ccp4i GUI to
select
-> Reflection Data Utilities
-> Reindex Reflections
Define Transformation Matrix by entering reflection transformation
h=l k=h l=k


Ethan


 > I have a script file that
 > runs with scalepack but was wondering if there is an easier way
to do it
 > with HKL2000 gui mode.
 > thanks,
 > Shya
 >

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




--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu 
***

Re: [ccp4bb] P21221 to P21212 conversion

[Felix Frolow]

Forget to tell that all is done in the menu Macros : - (
FF
Dr Felix Frolow   
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfro...@post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On May 7, 2012, at 23:48 , Jacob Keller wrote:

> Is it true that HKL adopts the naming convention of putting the screw axes 
> first and then naming a a automatically be p21212?
> 
> JPK
> 
> On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt  
> wrote:
> On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote:
> > Hi all,
> > I was wondering if anyone knows how to convert the P21221 to P21212
> > spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I
> > got a correct MR solution in P21221 spacegroup.
> 
> Shya:
> 
> Scaling is done in a point group, not a space group.
> 
> The point group P222 contains both space groups P2(1)22(1) and P2(1)2(1)2,
> so your original scaling is correct in either case.
> 
> It is not clear from your query which of two things happened:
> 
> 1) The MR solution kept the same a, b, and c axis assignments but made a
> different call on whether each axis did or did not correspond to a 2(1) screw.
> In this case you don't need to do anything to your files.  Just make sure
> that you keep the new space group as you go forward into refinement.
> 
> 2) The MR solution kept the orginal screw-axis identifications but
> permuted the axes to the standard setting (non-screw axis is labelled "c").
> In this case you will need to construct a file containing the permuted
> indices.  For example, the reflection originally labeled  (h=1 k=2 l=3) is now
> (h=3 k=1 l=2).  There are several programs that can help you do this,
> including the HKL2000 GUI.   But you do not need to go back into HKL
> if you don't want to.  You could, for example, use the ccp4i GUI to
> select
> -> Reflection Data Utilities
>   -> Reindex Reflections
>  Define Transformation Matrix by entering reflection transformation
>  h=l k=h l=k
> 
> 
>Ethan
> 
> 
> > I have a script file that
> > runs with scalepack but was wondering if there is an easier way to do it
> > with HKL2000 gui mode.
> > thanks,
> > Shya
> >
> 
> --
> Ethan A Merritt
> Biomolecular Structure Center,  K-428 Health Sciences Bldg
> University of Washington, Seattle 98195-7742
> 
> 
> 
> -- 
> ***
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> email: j-kell...@northwestern.edu
> ***

Re: [ccp4bb] P21221 to P21212 conversion

[Felix Frolow]

HKL or most probably SCALEPACK know nothing above point group if you do not 
tell it.
But even in GUI one can use "hkl matrix" with the needed transformation matrix 
:-\  
What is nice about it that it will never let you to change the handedness of 
the data, so anomalous signal is safe…
FF
Dr Felix Frolow   
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfro...@post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On May 7, 2012, at 23:48 , Jacob Keller wrote:

> Is it true that HKL adopts the naming convention of putting the screw axes 
> first and then naming a a automatically be p21212?
> 
> JPK
> 
> On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt  
> wrote:
> On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote:
> > Hi all,
> > I was wondering if anyone knows how to convert the P21221 to P21212
> > spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I
> > got a correct MR solution in P21221 spacegroup.
> 
> Shya:
> 
> Scaling is done in a point group, not a space group.
> 
> The point group P222 contains both space groups P2(1)22(1) and P2(1)2(1)2,
> so your original scaling is correct in either case.
> 
> It is not clear from your query which of two things happened:
> 
> 1) The MR solution kept the same a, b, and c axis assignments but made a
> different call on whether each axis did or did not correspond to a 2(1) screw.
> In this case you don't need to do anything to your files.  Just make sure
> that you keep the new space group as you go forward into refinement.
> 
> 2) The MR solution kept the orginal screw-axis identifications but
> permuted the axes to the standard setting (non-screw axis is labelled "c").
> In this case you will need to construct a file containing the permuted
> indices.  For example, the reflection originally labeled  (h=1 k=2 l=3) is now
> (h=3 k=1 l=2).  There are several programs that can help you do this,
> including the HKL2000 GUI.   But you do not need to go back into HKL
> if you don't want to.  You could, for example, use the ccp4i GUI to
> select
> -> Reflection Data Utilities
>   -> Reindex Reflections
>  Define Transformation Matrix by entering reflection transformation
>  h=l k=h l=k
> 
> 
>Ethan
> 
> 
> > I have a script file that
> > runs with scalepack but was wondering if there is an easier way to do it
> > with HKL2000 gui mode.
> > thanks,
> > Shya
> >
> 
> --
> Ethan A Merritt
> Biomolecular Structure Center,  K-428 Health Sciences Bldg
> University of Washington, Seattle 98195-7742
> 
> 
> 
> -- 
> ***
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> email: j-kell...@northwestern.edu
> ***

Re: [ccp4bb] P21221 to P21212 conversion

[Jacob Keller]

Is it true that HKL adopts the naming convention of putting the screw axes
first and then naming awrote:

> On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote:
> > Hi all,
> > I was wondering if anyone knows how to convert the P21221 to P21212
> > spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I
> > got a correct MR solution in P21221 spacegroup.
>
> Shya:
>
> Scaling is done in a point group, not a space group.
>
> The point group P222 contains both space groups P2(1)22(1) and P2(1)2(1)2,
> so your original scaling is correct in either case.
>
> It is not clear from your query which of two things happened:
>
> 1) The MR solution kept the same a, b, and c axis assignments but made a
> different call on whether each axis did or did not correspond to a 2(1)
> screw.
> In this case you don't need to do anything to your files.  Just make sure
> that you keep the new space group as you go forward into refinement.
>
> 2) The MR solution kept the orginal screw-axis identifications but
> permuted the axes to the standard setting (non-screw axis is labelled "c").
> In this case you will need to construct a file containing the permuted
> indices.  For example, the reflection originally labeled  (h=1 k=2 l=3) is
> now
> (h=3 k=1 l=2).  There are several programs that can help you do this,
> including the HKL2000 GUI.   But you do not need to go back into HKL
> if you don't want to.  You could, for example, use the ccp4i GUI to
> select
> -> Reflection Data Utilities
>   -> Reindex Reflections
>  Define Transformation Matrix by entering reflection transformation
>  h=l k=h l=k
>
>
>Ethan
>
>
> > I have a script file that
> > runs with scalepack but was wondering if there is an easier way to do it
> > with HKL2000 gui mode.
> > thanks,
> > Shya
> >
>
> --
> Ethan A Merritt
> Biomolecular Structure Center,  K-428 Health Sciences Bldg
> University of Washington, Seattle 98195-7742
>



-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] P21221 to P21212 conversion

[Ethan Merritt]

On Monday, May 07, 2012 01:42:58 pm Shya Biswas wrote:
> Hi,
> My case is old b is changed to c (scenario 2 as you explained) or hkl is
> changed to hlk. Thanks for the help

hkl -> hkl  gives an inverted coordinate system.  You don't want that.

Ethan


> 
> Shya
> 
> On Mon, May 7, 2012 at 4:33 PM, Ethan Merritt wrote:
> 
> > On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote:
> > > Hi all,
> > > I was wondering if anyone knows how to convert the P21221 to P21212
> > > spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I
> > > got a correct MR solution in P21221 spacegroup.
> >
> > Shya:
> >
> > Scaling is done in a point group, not a space group.
> >
> > The point group P222 contains both space groups P2(1)22(1) and P2(1)2(1)2,
> > so your original scaling is correct in either case.
> >
> > It is not clear from your query which of two things happened:
> >
> > 1) The MR solution kept the same a, b, and c axis assignments but made a
> > different call on whether each axis did or did not correspond to a 2(1)
> > screw.
> > In this case you don't need to do anything to your files.  Just make sure
> > that you keep the new space group as you go forward into refinement.
> >
> > 2) The MR solution kept the orginal screw-axis identifications but
> > permuted the axes to the standard setting (non-screw axis is labelled "c").
> > In this case you will need to construct a file containing the permuted
> > indices.  For example, the reflection originally labeled  (h=1 k=2 l=3) is
> > now
> > (h=3 k=1 l=2).  There are several programs that can help you do this,
> > including the HKL2000 GUI.   But you do not need to go back into HKL
> > if you don't want to.  You could, for example, use the ccp4i GUI to
> > select
> > -> Reflection Data Utilities
> >   -> Reindex Reflections
> >  Define Transformation Matrix by entering reflection transformation
> >  h=l k=h l=k
> >
> >
> >Ethan
> >
> >
> > > I have a script file that
> > > runs with scalepack but was wondering if there is an easier way to do it
> > > with HKL2000 gui mode.
> > > thanks,
> > > Shya
> > >
> >
> > --
> > Ethan A Merritt
> > Biomolecular Structure Center,  K-428 Health Sciences Bldg
> > University of Washington, Seattle 98195-7742
> >
> 

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

Re: [ccp4bb] P21221 to P21212 conversion

[Matthew Franklin]

On 5/7/12 4:09 PM, Shya Biswas wrote:

Hi all,
I was wondering if anyone knows how to convert the P21221 to P21212 
spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but 
I got a correct MR solution in P21221 spacegroup. I have a script file 
that runs with scalepack but was wondering if there is an easier way 
to do it with HKL2000 gui mode.

thanks,
Shya

Hi Shya -

Under the Scale tab of HKL2000, you'll see a button near the bottom 
labeled "Reindex".  Clicking this brings up a dialog box with the 
reindexing conventions appropriate to your spacegroup.  For P 
orthorhombic, there are only two choices: hkl -> klh, or hkl -> lhk.  If 
you have P21221, and want to go to P21212, you want hkl ->lhk.


HOWEVER, there seems to be a bug in this particular reindexing (or maybe 
the options are written confusingly).  You want to choose the "wrong" 
option (number 2 in the list presented), as the two options seem to be 
reversed.  You'll know that you got it right by inspection of the 
scaling log file - look at the systematic absence table at the bottom.  
Also check that the unit cell axes were permuted in the correct way - 
you want your old b axis to be your new c axis.


Once you select the correct reindexing (make sure you apply it to all 
datasets being scaled at the same time), you click "Reindex" in the 
popup dialog, and this triggers another round of scaling with the 
reindexing included.  This reindexing is "sticky" - you don't need to 
select it again for subsequent rounds of scaling.


Hope that helps - feel free to contact me if you want more explanation.

- Matt


--
Matthew Franklin, Ph. D.
Senior Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(212) 939-0660 ext. 9374

Re: [ccp4bb] P21221 to P21212 conversion

[Shya Biswas]

Hi,
My case is old b is changed to c (scenario 2 as you explained) or hkl is
changed to hlk. Thanks for the help

Shya

On Mon, May 7, 2012 at 4:33 PM, Ethan Merritt wrote:

> On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote:
> > Hi all,
> > I was wondering if anyone knows how to convert the P21221 to P21212
> > spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I
> > got a correct MR solution in P21221 spacegroup.
>
> Shya:
>
> Scaling is done in a point group, not a space group.
>
> The point group P222 contains both space groups P2(1)22(1) and P2(1)2(1)2,
> so your original scaling is correct in either case.
>
> It is not clear from your query which of two things happened:
>
> 1) The MR solution kept the same a, b, and c axis assignments but made a
> different call on whether each axis did or did not correspond to a 2(1)
> screw.
> In this case you don't need to do anything to your files.  Just make sure
> that you keep the new space group as you go forward into refinement.
>
> 2) The MR solution kept the orginal screw-axis identifications but
> permuted the axes to the standard setting (non-screw axis is labelled "c").
> In this case you will need to construct a file containing the permuted
> indices.  For example, the reflection originally labeled  (h=1 k=2 l=3) is
> now
> (h=3 k=1 l=2).  There are several programs that can help you do this,
> including the HKL2000 GUI.   But you do not need to go back into HKL
> if you don't want to.  You could, for example, use the ccp4i GUI to
> select
> -> Reflection Data Utilities
>   -> Reindex Reflections
>  Define Transformation Matrix by entering reflection transformation
>  h=l k=h l=k
>
>
>Ethan
>
>
> > I have a script file that
> > runs with scalepack but was wondering if there is an easier way to do it
> > with HKL2000 gui mode.
> > thanks,
> > Shya
> >
>
> --
> Ethan A Merritt
> Biomolecular Structure Center,  K-428 Health Sciences Bldg
> University of Washington, Seattle 98195-7742
>

Re: [ccp4bb] P21221 to P21212 conversion

[Ethan Merritt]

On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote:
> Hi all,
> I was wondering if anyone knows how to convert the P21221 to P21212
> spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I
> got a correct MR solution in P21221 spacegroup. 

Shya:

Scaling is done in a point group, not a space group.

The point group P222 contains both space groups P2(1)22(1) and P2(1)2(1)2,
so your original scaling is correct in either case.

It is not clear from your query which of two things happened: 

1) The MR solution kept the same a, b, and c axis assignments but made a 
different call on whether each axis did or did not correspond to a 2(1) screw.
In this case you don't need to do anything to your files.  Just make sure
that you keep the new space group as you go forward into refinement.

2) The MR solution kept the orginal screw-axis identifications but 
permuted the axes to the standard setting (non-screw axis is labelled "c").
In this case you will need to construct a file containing the permuted
indices.  For example, the reflection originally labeled  (h=1 k=2 l=3) is now
(h=3 k=1 l=2).  There are several programs that can help you do this,
including the HKL2000 GUI.   But you do not need to go back into HKL
if you don't want to.  You could, for example, use the ccp4i GUI to
select
-> Reflection Data Utilities
   -> Reindex Reflections
  Define Transformation Matrix by entering reflection transformation
  h=l k=h l=k


Ethan


> I have a script file that
> runs with scalepack but was wondering if there is an easier way to do it
> with HKL2000 gui mode.
> thanks,
> Shya
> 

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

[ccp4bb] P21221 to P21212 conversion

[Shya Biswas]

Hi all,
I was wondering if anyone knows how to convert the P21221 to P21212
spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I
got a correct MR solution in P21221 spacegroup. I have a script file that
runs with scalepack but was wondering if there is an easier way to do it
with HKL2000 gui mode.
thanks,
Shya