Re: [ccp4bb] Generating rotation/translation matrices for biological assemblies
But you know that each rotation matrix still only fits one semi-tetramer to
its symmetry partner?
Eleanor
On Sun, 3 Feb 2019 at 16:54, Klontz, Erik
wrote:
> Thank you all for your feedback. I received many helpful responses. To
> summarize them, users might find the following resources helpful:
>
> http://img.chem.ucl.ac.uk/sgp/LARGE/sgp.htm
> http://achesym.ibch.poznan.pl
> http://eppic-web.org
> http://www.ruppweb.org/new_comp/spacegroup_decoder.htm
> http://www.ebi.ac.uk/msd-srv/prot_int/cgi-bin/piserver
>
> In my own example, my crystal was C 2 2 21 with unit cell 89.30, 137.12,
> 264.71, 90, 90, 90
>
>
> The easiest solution I found to generate the 3x4 translation/rotation
> matrix was to open the structure in Coot, turn on symmetry mates
> (Draw-->Cell & Symmetry) and then middle mouse click on the correct chain
> that completes the biological assembly (or alternatively, File-->Save
> Symmetry Coordinates-->left click chain). The symmetry operator shows in
> the bottom left of the window in Coot. In my case, this gave an output of
> "(X, -Y, -Z) + (0 0 0)" for one, and "(-X, Y, -Z + 1/2) + (-1 0 -1)" for
> the other. In the 3x4 translation/rotation matrix format required for PDB
> deposition, these correspond to:
>
>
> Format:
> R1-1 R1-2 R1-3 T1
> R2-1 R2-2 R2-3 T2
> R3-1 R3-2 R3-3 T3
>
>
> Solutions:
>
> 1 0 0 0
>
> 0 -1 0 0
>
> 0 0 -1 0
>
>
> -1 0 0 -89.3
>
> 0 1 0 0
>
> 0 0 -1 -132.35
>
>
> To check your work, you can save the symmetry coordinates and then load
> them into the ccp4 program "superpose". Superimpose your original PDB onto
> the symmetry mate. The output contains a rotation matrix and a translation
> vector that should correspond to the same solution.
>
>
> Thanks everyone!
>
> Erik
>
> ------
> *From:* CCP4 bulletin board on behalf of Eleanor
> Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
> *Sent:* Sunday, February 3, 2019 6:21:41 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Generating rotation/translation matrices for
> biological assemblies
>
> Well - you have one of many examples where your 4 chains do not form the
> biological tetramer, but as you say there are two half tetramers in the
> asymmetric unit, I would expect that Pisa has already told you there is an
> interface between AC and it’s summetry equivalent and told you the symmetry
> operator that generates this? Look st interfaced output
> And the same for the BD interface . Lots of haemoobin examples of this.
>
> On Sun, 3 Feb 2019 at 22:42, Bernhard Rupp
> wrote:
>
> The most trivial procedure is probably to generate the symmetry mates in
> Coot
>
> (color by symop makes selection easier), pick the ones completing your
> known biological
>
> assembly, and saving those using File/Save Symmetry Coordinates.
>
>
>
> Once you have the correct model you can superimpose the dimers in Coot and
> read the DCM and
>
> the translation vector – if that is what you want. If you click any of the
> atoms in a symop-ed
>
> molecule, you get the crystallographic operator and translation.
>
>
>
> If you want the crystallographic symops in symbolic and matrix format, you
> can use
>
> http://www.ruppweb.org/new_comp/spacegroup_decoder.htm
>
> Standard settings only.
>
>
>
> Best, BR
>
>
>
> *From:* CCP4 bulletin board *On Behalf Of *Klontz,
> Erik
> *Sent:* Saturday, February 2, 2019 22:05
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Generating rotation/translation matrices for
> biological assemblies
>
>
>
> Hi all,
>
>
>
> I'm working on a protein that I believe is tetrameric based on AUC, gel
> filtration, and crystallography. However, although my asymmetric unit has 4
> chains, I cannot form the tetramer within the asymmetric unit. Instead, the
> asymmetric unit has two half-tetramers ('dimers'), and each full tetramer
> is completed by pairing up with another half-tetramer from a symmetry mate.
> If I load this structure into PISA, it recognizes that each of the 'dimers'
> forms a stable assembly, but cannot seem to assemble the tetramer. However,
> if I the generate symmetry mates in pymol to create a new PDB for the
> biological tetramer and give this to PISA, it recognizes a stable tetramer.
>
>
>
> Specifically, chains A and C in the original PDB pair with chains A and C
> of the second symmetry mate generated in pymol, while chains B and D in the
> original pair with chains B and D of the third symmetry mate. How do I use
> this knowledge to generate a 3x4 rotation with translation matrix for PDB
> deposition?
&
Re: [ccp4bb] Generating rotation/translation matrices for biological assemblies
Thank you all for your feedback. I received many helpful responses. To
summarize them, users might find the following resources helpful:
http://img.chem.ucl.ac.uk/sgp/LARGE/sgp.htm
http://achesym.ibch.poznan.pl
http://eppic-web.org
http://www.ruppweb.org/new_comp/spacegroup_decoder.htm
http://www.ebi.ac.uk/msd-srv/prot_int/cgi-bin/piserver
In my own example, my crystal was C 2 2 21 with unit cell 89.30, 137.12,
264.71, 90, 90, 90
The easiest solution I found to generate the 3x4 translation/rotation matrix
was to open the structure in Coot, turn on symmetry mates (Draw-->Cell &
Symmetry) and then middle mouse click on the correct chain that completes the
biological assembly (or alternatively, File-->Save Symmetry Coordinates-->left
click chain). The symmetry operator shows in the bottom left of the window in
Coot. In my case, this gave an output of "(X, -Y, -Z) + (0 0 0)" for one, and
"(-X, Y, -Z + 1/2) + (-1 0 -1)" for the other. In the 3x4 translation/rotation
matrix format required for PDB deposition, these correspond to:
Format:
R1-1 R1-2 R1-3 T1
R2-1 R2-2 R2-3 T2
R3-1 R3-2 R3-3 T3
Solutions:
1 0 0 0
0 -1 0 0
0 0 -1 0
-1 0 0 -89.3
0 1 0 0
0 0 -1 -132.35
To check your work, you can save the symmetry coordinates and then load them
into the ccp4 program "superpose". Superimpose your original PDB onto the
symmetry mate. The output contains a rotation matrix and a translation vector
that should correspond to the same solution.
Thanks everyone!
Erik
From: CCP4 bulletin board on behalf of Eleanor Dodson
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Sent: Sunday, February 3, 2019 6:21:41 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Generating rotation/translation matrices for biological
assemblies
Well - you have one of many examples where your 4 chains do not form the
biological tetramer, but as you say there are two half tetramers in the
asymmetric unit, I would expect that Pisa has already told you there is an
interface between AC and it’s summetry equivalent and told you the symmetry
operator that generates this? Look st interfaced output
And the same for the BD interface . Lots of haemoobin examples of this.
On Sun, 3 Feb 2019 at 22:42, Bernhard Rupp
mailto:hofkristall...@gmail.com>> wrote:
The most trivial procedure is probably to generate the symmetry mates in Coot
(color by symop makes selection easier), pick the ones completing your known
biological
assembly, and saving those using File/Save Symmetry Coordinates.
Once you have the correct model you can superimpose the dimers in Coot and read
the DCM and
the translation vector – if that is what you want. If you click any of the
atoms in a symop-ed
molecule, you get the crystallographic operator and translation.
If you want the crystallographic symops in symbolic and matrix format, you can
use
http://www.ruppweb.org/new_comp/spacegroup_decoder.htm
Standard settings only.
Best, BR
From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>>
On Behalf Of Klontz, Erik
Sent: Saturday, February 2, 2019 22:05
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] Generating rotation/translation matrices for biological
assemblies
Hi all,
I'm working on a protein that I believe is tetrameric based on AUC, gel
filtration, and crystallography. However, although my asymmetric unit has 4
chains, I cannot form the tetramer within the asymmetric unit. Instead, the
asymmetric unit has two half-tetramers ('dimers'), and each full tetramer is
completed by pairing up with another half-tetramer from a symmetry mate. If I
load this structure into PISA, it recognizes that each of the 'dimers' forms a
stable assembly, but cannot seem to assemble the tetramer. However, if I the
generate symmetry mates in pymol to create a new PDB for the biological
tetramer and give this to PISA, it recognizes a stable tetramer.
Specifically, chains A and C in the original PDB pair with chains A and C of
the second symmetry mate generated in pymol, while chains B and D in the
original pair with chains B and D of the third symmetry mate. How do I use this
knowledge to generate a 3x4 rotation with translation matrix for PDB deposition?
Thanks,
Erik Klontz
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Re: [ccp4bb] Generating rotation/translation matrices for biological assemblies
Well - you have one of many examples where your 4 chains do not form the
biological tetramer, but as you say there are two half tetramers in the
asymmetric unit, I would expect that Pisa has already told you there is an
interface between AC and it’s summetry equivalent and told you the symmetry
operator that generates this? Look st interfaced output
And the same for the BD interface . Lots of haemoobin examples of this.
On Sun, 3 Feb 2019 at 22:42, Bernhard Rupp wrote:
> The most trivial procedure is probably to generate the symmetry mates in
> Coot
>
> (color by symop makes selection easier), pick the ones completing your
> known biological
>
> assembly, and saving those using File/Save Symmetry Coordinates.
>
>
>
> Once you have the correct model you can superimpose the dimers in Coot and
> read the DCM and
>
> the translation vector – if that is what you want. If you click any of the
> atoms in a symop-ed
>
> molecule, you get the crystallographic operator and translation.
>
>
>
> If you want the crystallographic symops in symbolic and matrix format, you
> can use
>
> http://www.ruppweb.org/new_comp/spacegroup_decoder.htm
>
> Standard settings only.
>
>
>
> Best, BR
>
>
>
> *From:* CCP4 bulletin board *On Behalf Of *Klontz,
> Erik
> *Sent:* Saturday, February 2, 2019 22:05
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Generating rotation/translation matrices for
> biological assemblies
>
>
>
> Hi all,
>
>
>
> I'm working on a protein that I believe is tetrameric based on AUC, gel
> filtration, and crystallography. However, although my asymmetric unit has 4
> chains, I cannot form the tetramer within the asymmetric unit. Instead, the
> asymmetric unit has two half-tetramers ('dimers'), and each full tetramer
> is completed by pairing up with another half-tetramer from a symmetry mate.
> If I load this structure into PISA, it recognizes that each of the 'dimers'
> forms a stable assembly, but cannot seem to assemble the tetramer. However,
> if I the generate symmetry mates in pymol to create a new PDB for the
> biological tetramer and give this to PISA, it recognizes a stable tetramer.
>
>
>
> Specifically, chains A and C in the original PDB pair with chains A and C
> of the second symmetry mate generated in pymol, while chains B and D in the
> original pair with chains B and D of the third symmetry mate. How do I use
> this knowledge to generate a 3x4 rotation with translation matrix for PDB
> deposition?
>
>
>
> Thanks,
> Erik Klontz
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
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Re: [ccp4bb] Generating rotation/translation matrices for biological assemblies
The most trivial procedure is probably to generate the symmetry mates in
Coot
(color by symop makes selection easier), pick the ones completing your known
biological
assembly, and saving those using File/Save Symmetry Coordinates.
Once you have the correct model you can superimpose the dimers in Coot and
read the DCM and
the translation vector - if that is what you want. If you click any of the
atoms in a symop-ed
molecule, you get the crystallographic operator and translation.
If you want the crystallographic symops in symbolic and matrix format, you
can use
http://www.ruppweb.org/new_comp/spacegroup_decoder.htm
Standard settings only.
Best, BR
From: CCP4 bulletin board On Behalf Of Klontz, Erik
Sent: Saturday, February 2, 2019 22:05
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Generating rotation/translation matrices for biological
assemblies
Hi all,
I'm working on a protein that I believe is tetrameric based on AUC, gel
filtration, and crystallography. However, although my asymmetric unit has 4
chains, I cannot form the tetramer within the asymmetric unit. Instead, the
asymmetric unit has two half-tetramers ('dimers'), and each full tetramer is
completed by pairing up with another half-tetramer from a symmetry mate. If
I load this structure into PISA, it recognizes that each of the 'dimers'
forms a stable assembly, but cannot seem to assemble the tetramer. However,
if I the generate symmetry mates in pymol to create a new PDB for the
biological tetramer and give this to PISA, it recognizes a stable tetramer.
Specifically, chains A and C in the original PDB pair with chains A and C of
the second symmetry mate generated in pymol, while chains B and D in the
original pair with chains B and D of the third symmetry mate. How do I use
this knowledge to generate a 3x4 rotation with translation matrix for PDB
deposition?
Thanks,
Erik Klontz
_
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Re: [ccp4bb] Generating rotation/translation matrices for biological assemblies
Try EPPIC (http://eppic-web.org), it will give you all possible symmetric
assemblies in your crystal and their constituent interfaces, listing the
symmetry operators too. See some help here http://eppic-web.org/ewui/#help
Jose
On Sat, 2 Feb 2019 at 16:42, Ricardo Padua wrote:
> Hi Erik,
>
> Have you tried Achesym?
>
> http://achesym.ibch.poznan.pl
>
> Kowiel, M., Jaskolski, M. & Dauter, Z. (2014). ACHESYM: an algorithm and
> server for standardized placement of macromolecular models in the unit cell.
> Acta Cryst. D70, doi:10.1107/S1399004714024572.
>
> Best
>
> Ricardo Padua
>
> On Sat, Feb 2, 2019 at 4:06 PM Klontz, Erik
> wrote:
>
>> Hi all,
>>
>>
>> I'm working on a protein that I believe is tetrameric based on AUC, gel
>> filtration, and crystallography. However, although my asymmetric unit has 4
>> chains, I cannot form the tetramer within the asymmetric unit. Instead, the
>> asymmetric unit has two half-tetramers ('dimers'), and each full tetramer
>> is completed by pairing up with another half-tetramer from a symmetry mate.
>> If I load this structure into PISA, it recognizes that each of the 'dimers'
>> forms a stable assembly, but cannot seem to assemble the tetramer. However,
>> if I the generate symmetry mates in pymol to create a new PDB for the
>> biological tetramer and give this to PISA, it recognizes a stable tetramer.
>>
>>
>> Specifically, chains A and C in the original PDB pair with chains A and C
>> of the second symmetry mate generated in pymol, while chains B and D in the
>> original pair with chains B and D of the third symmetry mate. How do I use
>> this knowledge to generate a 3x4 rotation with translation matrix for
>> PDB deposition?
>>
>>
>> Thanks,
>> Erik Klontz
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
> --
> Ricardo Padua
> HHMI Research Associate
> Kern Lab
> Dept. of Biochemistry, MS009
> Brandeis University
> Waltham, MA 02454, USA
>
> E-mail: rpa...@brandeis.edu
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
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Re: [ccp4bb] Generating rotation/translation matrices for biological assemblies
Hi Erik,
Have you tried Achesym?
http://achesym.ibch.poznan.pl
Kowiel, M., Jaskolski, M. & Dauter, Z. (2014). ACHESYM: an algorithm and
server for standardized placement of macromolecular models in the unit cell.
Acta Cryst. D70, doi:10.1107/S1399004714024572.
Best
Ricardo Padua
On Sat, Feb 2, 2019 at 4:06 PM Klontz, Erik
wrote:
> Hi all,
>
>
> I'm working on a protein that I believe is tetrameric based on AUC, gel
> filtration, and crystallography. However, although my asymmetric unit has 4
> chains, I cannot form the tetramer within the asymmetric unit. Instead, the
> asymmetric unit has two half-tetramers ('dimers'), and each full tetramer
> is completed by pairing up with another half-tetramer from a symmetry mate.
> If I load this structure into PISA, it recognizes that each of the 'dimers'
> forms a stable assembly, but cannot seem to assemble the tetramer. However,
> if I the generate symmetry mates in pymol to create a new PDB for the
> biological tetramer and give this to PISA, it recognizes a stable tetramer.
>
>
> Specifically, chains A and C in the original PDB pair with chains A and C
> of the second symmetry mate generated in pymol, while chains B and D in the
> original pair with chains B and D of the third symmetry mate. How do I use
> this knowledge to generate a 3x4 rotation with translation matrix for PDB
> deposition?
>
>
> Thanks,
> Erik Klontz
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
--
Ricardo Padua
HHMI Research Associate
Kern Lab
Dept. of Biochemistry, MS009
Brandeis University
Waltham, MA 02454, USA
E-mail: rpa...@brandeis.edu
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Re: [ccp4bb] Generating rotation/translation matrices for biological assemblies
Hi Eric,
You can lookup the symmetry operator in the International Tables
(http://img.chem.ucl.ac.uk/sgp/LARGE/sgp.htm).
Alternatively, you can use coot to find the crystallographic symmetry operator
that generates the second half of your tetramer.
Draw/Cell & Symmetry and then generate the symmetry mates.
Select File/Save Symmetry Coordinates
Click on the right symmetry mate.
Coot will display the symmetry operator in the panel below the viewport of the
GUI.
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
office: (405) 271-8300 lab: (405) 271-8313
e-mail: blaine-moo...@ouhsc.edu <mailto:blaine-moo...@ouhsc.edu>
Faculty webpage: https://tinyurl.com/BMBmooers
Google Scholar: https://tinyurl.com/GSbmooers
X-ray lab (LBSF): https://tinyurl.com/ouhsclbsf
SSRL-LCLS User Meeting: https://conf.slac.stanford.edu/ssrl-lcls-2018/
EasyPyMOL: https://github.com/MooersLab
Molecular Graphics Course Links: https://tinyurl.com/molgr
Small Angle Scattering Links: https://tinyurl.com/ouhscsaxs
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Klontz, Erik
[erik.klo...@som.umaryland.edu]
Sent: Saturday, February 02, 2019 3:04 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] [ccp4bb] Generating rotation/translation matrices for
biological assemblies
Hi all,
I'm working on a protein that I believe is tetrameric based on AUC, gel
filtration, and crystallography. However, although my asymmetric unit has 4
chains, I cannot form the tetramer within the asymmetric unit. Instead, the
asymmetric unit has two half-tetramers ('dimers'), and each full tetramer is
completed by pairing up with another half-tetramer from a symmetry mate. If I
load this structure into PISA, it recognizes that each of the 'dimers' forms a
stable assembly, but cannot seem to assemble the tetramer. However, if I the
generate symmetry mates in pymol to create a new PDB for the biological
tetramer and give this to PISA, it recognizes a stable tetramer.
Specifically, chains A and C in the original PDB pair with chains A and C of
the second symmetry mate generated in pymol, while chains B and D in the
original pair with chains B and D of the third symmetry mate. How do I use this
knowledge to generate a 3x4 rotation with translation matrix for PDB deposition?
Thanks,
Erik Klontz
To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] Generating rotation/translation matrices for biological assemblies
Hi all,
I'm working on a protein that I believe is tetrameric based on AUC, gel
filtration, and crystallography. However, although my asymmetric unit has 4
chains, I cannot form the tetramer within the asymmetric unit. Instead, the
asymmetric unit has two half-tetramers ('dimers'), and each full tetramer is
completed by pairing up with another half-tetramer from a symmetry mate. If I
load this structure into PISA, it recognizes that each of the 'dimers' forms a
stable assembly, but cannot seem to assemble the tetramer. However, if I the
generate symmetry mates in pymol to create a new PDB for the biological
tetramer and give this to PISA, it recognizes a stable tetramer.
Specifically, chains A and C in the original PDB pair with chains A and C of
the second symmetry mate generated in pymol, while chains B and D in the
original pair with chains B and D of the third symmetry mate. How do I use this
knowledge to generate a 3x4 rotation with translation matrix for PDB deposition?
Thanks,
Erik Klontz
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
