How to write biological assembly info in PDB or mmCIF?
Hello,
I have a cryoEM map that was generated with C7 symmetry enforced, with its symmetry axis parallel to the z axis in ChimeraX. I fetched a prediction from AlphaFoldDB and docked it in the map. So far, so good.
I can generate the other protomers with a command like this:
sym #1 C7 axis z center cofr
(assuming #1 is the single protomer from AlphaFoldDB, and the cofr is correctly lying on the symmetry axis, which I get sufficiently close if I center the view on the map)
Now, because symmetry was enforced for the map, it makes no sense to model, refine and store the entire heptamer. I should be able to do everything with a single protomer, and store relevant info as "biological assembly" so the heptamer can be regenerated from the protomer. At least if I am understanding this correctly.
I tried the above command, or this variant: sym #1 C7 axis z center cofr addMmcifAssembly true
And subsequently saving in PDB or mmCIF format, but none of this produces what I want, which is a file containing the single protomer + assembly info. I either get a file with the single protomer or a file with the heptamer, in both cases without any biological assembly info.
I looked up the options of the save command for PDB and mmCIF format, but found nothing that seemed relevant to this problem.
Is there a way to do this? Or am I misunderstanding something?
Related question: it might make sense to use the whole heptamer for refinement, so all interfaces between protomers "see" each other (probably important when using ISOLDE). What is the best way to deal with this? Build and refine the whole heptamer and save only a single protomer + assembly info at the very end? Or have the symmetry enforced from the beginning, throughout the whole refinement process, and really ever refine a single protomer? (7 times less work, so probably the preferred option).
Thank you in advance,
Guillaume
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Hi Guillaume,
Adding the C7 symmetry to an mmCIF file is working for me in ChimeraX 1.6. Here's an example with GroEL.
open 1080 from emdb open 1grl fit #2 in #1 delete ~/A sym #2 C7 addmmcifassembly true save test.cif # If I now open the test.cif file in a text editor I see it wrote the symmetry matrices. open test.cif # Now the ChimeraX log lists the assembly as author defined assembly 3. Apparently there were 2 previous assemblies in PDB 1grl. sym #4 assembly 3
Not sure why it doesn't work for you. Make sure to read the ChimeraX documentation so you understand what it is doing
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html#addMmcifAssemb...
Tristan Croll, the developer of ISOLDE, would probably have the best advice on how to refine a symmetric complex in ISOLDE.
Tom

On Nov 3, 2023, at 8:26 AM, Guillaume Gaullier via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello,
I have a cryoEM map that was generated with C7 symmetry enforced, with its symmetry axis parallel to the z axis in ChimeraX. I fetched a prediction from AlphaFoldDB and docked it in the map. So far, so good.
I can generate the other protomers with a command like this:
sym #1 C7 axis z center cofr
(assuming #1 is the single protomer from AlphaFoldDB, and the cofr is correctly lying on the symmetry axis, which I get sufficiently close if I center the view on the map)
Now, because symmetry was enforced for the map, it makes no sense to model, refine and store the entire heptamer. I should be able to do everything with a single protomer, and store relevant info as "biological assembly" so the heptamer can be regenerated from the protomer. At least if I am understanding this correctly.
I tried the above command, or this variant: sym #1 C7 axis z center cofr addMmcifAssembly true And subsequently saving in PDB or mmCIF format, but none of this produces what I want, which is a file containing the single protomer + assembly info. I either get a file with the single protomer or a file with the heptamer, in both cases without any biological assembly info. I looked up the options of the save command for PDB and mmCIF format, but found nothing that seemed relevant to this problem.
Is there a way to do this? Or am I misunderstanding something?
Related question: it might make sense to use the whole heptamer for refinement, so all interfaces between protomers "see" each other (probably important when using ISOLDE). What is the best way to deal with this? Build and refine the whole heptamer and save only a single protomer + assembly info at the very end? Or have the symmetry enforced from the beginning, throughout the whole refinement process, and really ever refine a single protomer? (7 times less work, so probably the preferred option).
Thank you in advance,
Guillaume
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu mailto:chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Thank you Tom.
It works for me too (both your example, and what I was initially trying to do). I realize now that I had managed to do what I wanted already. I was simply puzzled that the newly generated files opened with the assembly automatically displayed. I was expecting a single chain to be displayed until I request the assembly with the sym command or by clicking on the assembly ID in the log.
Cheers,
Guillaume
________________________________ From: Tom Goddard goddard@sonic.net Sent: Saturday, November 4, 2023 3:08:21 AM To: Guillaume Gaullier Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] How to write biological assembly info in PDB or mmCIF?
Hi Guillaume,
Adding the C7 symmetry to an mmCIF file is working for me in ChimeraX 1.6. Here's an example with GroEL.
open 1080 from emdb open 1grl fit #2 in #1 delete ~/A sym #2 C7 addmmcifassembly true save test.cif # If I now open the test.cif file in a text editor I see it wrote the symmetry matrices. open test.cif # Now the ChimeraX log lists the assembly as author defined assembly 3. Apparently there were 2 previous assemblies in PDB 1grl. sym #4 assembly 3
Not sure why it doesn't work for you. Make sure to read the ChimeraX documentation so you understand what it is doing
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html#addMmcifAssemb...
Tristan Croll, the developer of ISOLDE, would probably have the best advice on how to refine a symmetric complex in ISOLDE.
Tom
[testC7.png] On Nov 3, 2023, at 8:26 AM, Guillaume Gaullier via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello,
I have a cryoEM map that was generated with C7 symmetry enforced, with its symmetry axis parallel to the z axis in ChimeraX. I fetched a prediction from AlphaFoldDB and docked it in the map. So far, so good.
I can generate the other protomers with a command like this:
sym #1 C7 axis z center cofr
(assuming #1 is the single protomer from AlphaFoldDB, and the cofr is correctly lying on the symmetry axis, which I get sufficiently close if I center the view on the map)
Now, because symmetry was enforced for the map, it makes no sense to model, refine and store the entire heptamer. I should be able to do everything with a single protomer, and store relevant info as "biological assembly" so the heptamer can be regenerated from the protomer. At least if I am understanding this correctly.
I tried the above command, or this variant: sym #1 C7 axis z center cofr addMmcifAssembly true And subsequently saving in PDB or mmCIF format, but none of this produces what I want, which is a file containing the single protomer + assembly info. I either get a file with the single protomer or a file with the heptamer, in both cases without any biological assembly info. I looked up the options of the save command for PDB and mmCIF format, but found nothing that seemed relevant to this problem.
Is there a way to do this? Or am I misunderstanding something?
Related question: it might make sense to use the whole heptamer for refinement, so all interfaces between protomers "see" each other (probably important when using ISOLDE). What is the best way to deal with this? Build and refine the whole heptamer and save only a single protomer + assembly info at the very end? Or have the symmetry enforced from the beginning, throughout the whole refinement process, and really ever refine a single protomer? (7 times less work, so probably the preferred option).
Thank you in advance,
Guillaume
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edumailto:chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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Hi Guillaume,
Opening the saved mmCIF file with an assembly will never automatically show the assembly in ChimeraX. Seeing the assembly when you open the file indicates that your file contains all the coordinates for all of the subunits. You should save the asymmetric unit (the original mmCIF file that symmetry was added to) in order to just include those atom coordinates.
Tom
On Nov 8, 2023, at 6:00 AM, Guillaume Gaullier guillaume.gaullier@kemi.uu.se wrote:
Thank you Tom.
It works for me too (both your example, and what I was initially trying to do). I realize now that I had managed to do what I wanted already. I was simply puzzled that the newly generated files opened with the assembly automatically displayed. I was expecting a single chain to be displayed until I request the assembly with the sym command or by clicking on the assembly ID in the log.
Cheers,
Guillaume
From: Tom Goddard goddard@sonic.net Sent: Saturday, November 4, 2023 3:08:21 AM To: Guillaume Gaullier Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] How to write biological assembly info in PDB or mmCIF?
Hi Guillaume,
Adding the C7 symmetry to an mmCIF file is working for me in ChimeraX 1.6. Here's an example with GroEL.
open 1080 from emdb open 1grl fit #2 in #1 delete ~/A sym #2 C7 addmmcifassembly true save test.cif # If I now open the test.cif file in a text editor I see it wrote the symmetry matrices. open test.cif # Now the ChimeraX log lists the assembly as author defined assembly 3. Apparently there were 2 previous assemblies in PDB 1grl. sym #4 assembly 3
Not sure why it doesn't work for you. Make sure to read the ChimeraX documentation so you understand what it is doing
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html#addMmcifAssemblyTristan Croll, the developer of ISOLDE, would probably have the best advice on how to refine a symmetric complex in ISOLDE.
Tom
<testC7.png>
On Nov 3, 2023, at 8:26 AM, Guillaume Gaullier via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello,
I have a cryoEM map that was generated with C7 symmetry enforced, with its symmetry axis parallel to the z axis in ChimeraX. I fetched a prediction from AlphaFoldDB and docked it in the map. So far, so good.
I can generate the other protomers with a command like this:
sym #1 C7 axis z center cofr
(assuming #1 is the single protomer from AlphaFoldDB, and the cofr is correctly lying on the symmetry axis, which I get sufficiently close if I center the view on the map)
Now, because symmetry was enforced for the map, it makes no sense to model, refine and store the entire heptamer. I should be able to do everything with a single protomer, and store relevant info as "biological assembly" so the heptamer can be regenerated from the protomer. At least if I am understanding this correctly.
I tried the above command, or this variant: sym #1 C7 axis z center cofr addMmcifAssembly true And subsequently saving in PDB or mmCIF format, but none of this produces what I want, which is a file containing the single protomer + assembly info. I either get a file with the single protomer or a file with the heptamer, in both cases without any biological assembly info. I looked up the options of the save command for PDB and mmCIF format, but found nothing that seemed relevant to this problem.
Is there a way to do this? Or am I misunderstanding something?
Related question: it might make sense to use the whole heptamer for refinement, so all interfaces between protomers "see" each other (probably important when using ISOLDE). What is the best way to deal with this? Build and refine the whole heptamer and save only a single protomer + assembly info at the very end? Or have the symmetry enforced from the beginning, throughout the whole refinement process, and really ever refine a single protomer? (7 times less work, so probably the preferred option).
Thank you in advance,
Guillaume
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu mailto:chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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Hi Tom,
Ah, this is precisely what I was trying to do: save an mmCIF file containing a single chain and assembly info. But I still can’t figure this out. When I run your example using ChimeraX 1.6.1 on macOS 12.6.7, from a new session, here is what I get. What happens is explained in comments (# marks your original comments, ## marks my comments, ### marks the log output I see):
open 1080 from emdb open 1grl fit #2 in #1 delete ~/A sym #2 C7 addmmcifassembly true ## At this stage, I get model #3 with seven sub-models #3.1-7. save test.cif # If I now open the test.cif file in a text editor I see it wrote the symmetry matrices. ## Agreed, I see assembly and symmetry info in this file too, when opening with a text editor. open test.cif # Now the ChimeraX log lists the assembly as author defined assembly 3. Apparently there were 2 previous assemblies in PDB 1grl. ## I see this too in the log, but I also see 7 additional grey boxes with the two original assemblies. ## And in the model panel, test.cif shows up as model #4 with 8 sub-models #4.1-8, with #4.1 and #4.2 being on top of each other, at the location where chain A was at the delete ~/A stage. sym #4 assembly 3 ## At this stage, the log reports: ### Made 7 copies for test.cif assembly 3 ### Assembly "3" not found, have 1, 2 ## I still get a new model #5 with sub-models #5.1-7, which is the correct outcome I think.
The part that puzzles me in this example is the result of opening test.cif: I would expect a model with a single chain and no sub-models. Is this what you expect too? If so, is the observed behavior a bug?
Unless I really don’t understand what is supposed to happen, this seems like a bug to me. And it is possible I really don’t understand this (I have never worked with symmetric assemblies before), but if we agree that the desired output is an mmCIF file containing a single chain, no sub-models and an assembly that re-creates the heptamer on-demand, then your example does not produce this in my hands.
Thank you!
Guillaume
On 8 Nov 2023, at 19:05, Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> wrote:
Hi Guillaume,
Opening the saved mmCIF file with an assembly will never automatically show the assembly in ChimeraX. Seeing the assembly when you open the file indicates that your file contains all the coordinates for all of the subunits. You should save the asymmetric unit (the original mmCIF file that symmetry was added to) in order to just include those atom coordinates.
Tom
On Nov 8, 2023, at 6:00 AM, Guillaume Gaullier <guillaume.gaullier@kemi.uu.semailto:guillaume.gaullier@kemi.uu.se> wrote:
Thank you Tom.
It works for me too (both your example, and what I was initially trying to do). I realize now that I had managed to do what I wanted already. I was simply puzzled that the newly generated files opened with the assembly automatically displayed. I was expecting a single chain to be displayed until I request the assembly with the sym command or by clicking on the assembly ID in the log.
Cheers,
Guillaume
________________________________ From: Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> Sent: Saturday, November 4, 2023 3:08:21 AM To: Guillaume Gaullier Cc: chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] How to write biological assembly info in PDB or mmCIF?
Hi Guillaume,
Adding the C7 symmetry to an mmCIF file is working for me in ChimeraX 1.6. Here's an example with GroEL.
open 1080 from emdb open 1grl fit #2 in #1 delete ~/A sym #2 C7 addmmcifassembly true save test.cif # If I now open the test.cif file in a text editor I see it wrote the symmetry matrices. open test.cif # Now the ChimeraX log lists the assembly as author defined assembly 3. Apparently there were 2 previous assemblies in PDB 1grl. sym #4 assembly 3
Not sure why it doesn't work for you. Make sure to read the ChimeraX documentation so you understand what it is doing
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html#addMmcifAssemb...
Tristan Croll, the developer of ISOLDE, would probably have the best advice on how to refine a symmetric complex in ISOLDE.
Tom
<testC7.png> On Nov 3, 2023, at 8:26 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I have a cryoEM map that was generated with C7 symmetry enforced, with its symmetry axis parallel to the z axis in ChimeraX. I fetched a prediction from AlphaFoldDB and docked it in the map. So far, so good.
I can generate the other protomers with a command like this:
sym #1 C7 axis z center cofr
(assuming #1 is the single protomer from AlphaFoldDB, and the cofr is correctly lying on the symmetry axis, which I get sufficiently close if I center the view on the map)
Now, because symmetry was enforced for the map, it makes no sense to model, refine and store the entire heptamer. I should be able to do everything with a single protomer, and store relevant info as "biological assembly" so the heptamer can be regenerated from the protomer. At least if I am understanding this correctly.
I tried the above command, or this variant: sym #1 C7 axis z center cofr addMmcifAssembly true And subsequently saving in PDB or mmCIF format, but none of this produces what I want, which is a file containing the single protomer + assembly info. I either get a file with the single protomer or a file with the heptamer, in both cases without any biological assembly info. I looked up the options of the save command for PDB and mmCIF format, but found nothing that seemed relevant to this problem.
Is there a way to do this? Or am I misunderstanding something?
Related question: it might make sense to use the whole heptamer for refinement, so all interfaces between protomers "see" each other (probably important when using ISOLDE). What is the best way to deal with this? Build and refine the whole heptamer and save only a single protomer + assembly info at the very end? Or have the symmetry enforced from the beginning, throughout the whole refinement process, and really ever refine a single protomer? (7 times less work, so probably the preferred option).
Thank you in advance,
Guillaume
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edumailto:chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.
Hi Guillaume,
Somehow I didn't copy the commands to the email right. You need
save test.cif model #2
while I had in the previous email
save test.cif
If you don't specify which model to save (the original #2 or the new copies #3) then you get all of them saved in the cif file (so it ends up with 8 copies). Sorry I left out the most critical detail in the original email!
Tom
On Nov 8, 2023, at 11:56 AM, Guillaume Gaullier guillaume.gaullier@kemi.uu.se wrote:
Hi Tom,
Ah, this is precisely what I was trying to do: save an mmCIF file containing a single chain and assembly info. But I still can’t figure this out. When I run your example using ChimeraX 1.6.1 on macOS 12.6.7, from a new session, here is what I get. What happens is explained in comments (# marks your original comments, ## marks my comments, ### marks the log output I see):
open 1080 from emdb open 1grl fit #2 in #1 delete ~/A sym #2 C7 addmmcifassembly true ## At this stage, I get model #3 with seven sub-models #3.1-7. save test.cif # If I now open the test.cif file in a text editor I see it wrote the symmetry matrices. ## Agreed, I see assembly and symmetry info in this file too, when opening with a text editor. open test.cif # Now the ChimeraX log lists the assembly as author defined assembly 3. Apparently there were 2 previous assemblies in PDB 1grl. ## I see this too in the log, but I also see 7 additional grey boxes with the two original assemblies. ## And in the model panel, test.cif shows up as model #4 with 8 sub-models #4.1-8, with #4.1 and #4.2 being on top of each other, at the location where chain A was at the delete ~/A stage. sym #4 assembly 3 ## At this stage, the log reports: ### Made 7 copies for test.cif assembly 3 ### Assembly "3" not found, have 1, 2 ## I still get a new model #5 with sub-models #5.1-7, which is the correct outcome I think.
The part that puzzles me in this example is the result of opening test.cif: I would expect a model with a single chain and no sub-models. Is this what you expect too? If so, is the observed behavior a bug?
Unless I really don’t understand what is supposed to happen, this seems like a bug to me. And it is possible I really don’t understand this (I have never worked with symmetric assemblies before), but if we agree that the desired output is an mmCIF file containing a single chain, no sub-models and an assembly that re-creates the heptamer on-demand, then your example does not produce this in my hands.
Thank you!
Guillaume
On 8 Nov 2023, at 19:05, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:
Hi Guillaume,
Opening the saved mmCIF file with an assembly will never automatically show the assembly in ChimeraX. Seeing the assembly when you open the file indicates that your file contains all the coordinates for all of the subunits. You should save the asymmetric unit (the original mmCIF file that symmetry was added to) in order to just include those atom coordinates.
Tom
On Nov 8, 2023, at 6:00 AM, Guillaume Gaullier <guillaume.gaullier@kemi.uu.se mailto:guillaume.gaullier@kemi.uu.se> wrote:
Thank you Tom.
It works for me too (both your example, and what I was initially trying to do). I realize now that I had managed to do what I wanted already. I was simply puzzled that the newly generated files opened with the assembly automatically displayed. I was expecting a single chain to be displayed until I request the assembly with the sym command or by clicking on the assembly ID in the log.
Cheers,
Guillaume
From: Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> Sent: Saturday, November 4, 2023 3:08:21 AM To: Guillaume Gaullier Cc: chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] How to write biological assembly info in PDB or mmCIF?
Hi Guillaume,
Adding the C7 symmetry to an mmCIF file is working for me in ChimeraX 1.6. Here's an example with GroEL.
open 1080 from emdb open 1grl fit #2 in #1 delete ~/A sym #2 C7 addmmcifassembly true save test.cif # If I now open the test.cif file in a text editor I see it wrote the symmetry matrices. open test.cif # Now the ChimeraX log lists the assembly as author defined assembly 3. Apparently there were 2 previous assemblies in PDB 1grl. sym #4 assembly 3
Not sure why it doesn't work for you. Make sure to read the ChimeraX documentation so you understand what it is doing
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html#addMmcifAssemblyTristan Croll, the developer of ISOLDE, would probably have the best advice on how to refine a symmetric complex in ISOLDE.
Tom
<testC7.png>
On Nov 3, 2023, at 8:26 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I have a cryoEM map that was generated with C7 symmetry enforced, with its symmetry axis parallel to the z axis in ChimeraX. I fetched a prediction from AlphaFoldDB and docked it in the map. So far, so good.
I can generate the other protomers with a command like this:
sym #1 C7 axis z center cofr
(assuming #1 is the single protomer from AlphaFoldDB, and the cofr is correctly lying on the symmetry axis, which I get sufficiently close if I center the view on the map)
Now, because symmetry was enforced for the map, it makes no sense to model, refine and store the entire heptamer. I should be able to do everything with a single protomer, and store relevant info as "biological assembly" so the heptamer can be regenerated from the protomer. At least if I am understanding this correctly.
I tried the above command, or this variant: sym #1 C7 axis z center cofr addMmcifAssembly true And subsequently saving in PDB or mmCIF format, but none of this produces what I want, which is a file containing the single protomer + assembly info. I either get a file with the single protomer or a file with the heptamer, in both cases without any biological assembly info. I looked up the options of the save command for PDB and mmCIF format, but found nothing that seemed relevant to this problem.
Is there a way to do this? Or am I misunderstanding something?
Related question: it might make sense to use the whole heptamer for refinement, so all interfaces between protomers "see" each other (probably important when using ISOLDE). What is the best way to deal with this? Build and refine the whole heptamer and save only a single protomer + assembly info at the very end? Or have the symmetry enforced from the beginning, throughout the whole refinement process, and really ever refine a single protomer? (7 times less work, so probably the preferred option).
Thank you in advance,
Guillaume
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Ah, now it all makes sense, thank you!
I just understood now that the command
sym #2 C7 addmmcifassembly true
adds the assembly info to model #2. I didn’t understand until now that it modifies its input model, in addition to generating a new model with sub-models.
Thank you for the clarification. :-)
Guillaume
On 8 Nov 2023, at 21:15, Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> wrote:
Hi Guillaume,
Somehow I didn't copy the commands to the email right. You need
save test.cif model #2
while I had in the previous email
save test.cif
If you don't specify which model to save (the original #2 or the new copies #3) then you get all of them saved in the cif file (so it ends up with 8 copies). Sorry I left out the most critical detail in the original email!
Tom
On Nov 8, 2023, at 11:56 AM, Guillaume Gaullier <guillaume.gaullier@kemi.uu.semailto:guillaume.gaullier@kemi.uu.se> wrote:
Hi Tom,
Ah, this is precisely what I was trying to do: save an mmCIF file containing a single chain and assembly info. But I still can’t figure this out. When I run your example using ChimeraX 1.6.1 on macOS 12.6.7, from a new session, here is what I get. What happens is explained in comments (# marks your original comments, ## marks my comments, ### marks the log output I see):
open 1080 from emdb open 1grl fit #2 in #1 delete ~/A sym #2 C7 addmmcifassembly true ## At this stage, I get model #3 with seven sub-models #3.1-7. save test.cif # If I now open the test.cif file in a text editor I see it wrote the symmetry matrices. ## Agreed, I see assembly and symmetry info in this file too, when opening with a text editor. open test.cif # Now the ChimeraX log lists the assembly as author defined assembly 3. Apparently there were 2 previous assemblies in PDB 1grl. ## I see this too in the log, but I also see 7 additional grey boxes with the two original assemblies. ## And in the model panel, test.cif shows up as model #4 with 8 sub-models #4.1-8, with #4.1 and #4.2 being on top of each other, at the location where chain A was at the delete ~/A stage. sym #4 assembly 3 ## At this stage, the log reports: ### Made 7 copies for test.cif assembly 3 ### Assembly "3" not found, have 1, 2 ## I still get a new model #5 with sub-models #5.1-7, which is the correct outcome I think.
The part that puzzles me in this example is the result of opening test.cif: I would expect a model with a single chain and no sub-models. Is this what you expect too? If so, is the observed behavior a bug?
Unless I really don’t understand what is supposed to happen, this seems like a bug to me. And it is possible I really don’t understand this (I have never worked with symmetric assemblies before), but if we agree that the desired output is an mmCIF file containing a single chain, no sub-models and an assembly that re-creates the heptamer on-demand, then your example does not produce this in my hands.
Thank you!
Guillaume
On 8 Nov 2023, at 19:05, Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> wrote:
Hi Guillaume,
Opening the saved mmCIF file with an assembly will never automatically show the assembly in ChimeraX. Seeing the assembly when you open the file indicates that your file contains all the coordinates for all of the subunits. You should save the asymmetric unit (the original mmCIF file that symmetry was added to) in order to just include those atom coordinates.
Tom
On Nov 8, 2023, at 6:00 AM, Guillaume Gaullier <guillaume.gaullier@kemi.uu.semailto:guillaume.gaullier@kemi.uu.se> wrote:
Thank you Tom.
It works for me too (both your example, and what I was initially trying to do). I realize now that I had managed to do what I wanted already. I was simply puzzled that the newly generated files opened with the assembly automatically displayed. I was expecting a single chain to be displayed until I request the assembly with the sym command or by clicking on the assembly ID in the log.
Cheers,
Guillaume
________________________________ From: Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> Sent: Saturday, November 4, 2023 3:08:21 AM To: Guillaume Gaullier Cc: chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] How to write biological assembly info in PDB or mmCIF?
Hi Guillaume,
Adding the C7 symmetry to an mmCIF file is working for me in ChimeraX 1.6. Here's an example with GroEL.
open 1080 from emdb open 1grl fit #2 in #1 delete ~/A sym #2 C7 addmmcifassembly true save test.cif # If I now open the test.cif file in a text editor I see it wrote the symmetry matrices. open test.cif # Now the ChimeraX log lists the assembly as author defined assembly 3. Apparently there were 2 previous assemblies in PDB 1grl. sym #4 assembly 3
Not sure why it doesn't work for you. Make sure to read the ChimeraX documentation so you understand what it is doing
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html#addMmcifAssemb...
Tristan Croll, the developer of ISOLDE, would probably have the best advice on how to refine a symmetric complex in ISOLDE.
Tom
<testC7.png> On Nov 3, 2023, at 8:26 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I have a cryoEM map that was generated with C7 symmetry enforced, with its symmetry axis parallel to the z axis in ChimeraX. I fetched a prediction from AlphaFoldDB and docked it in the map. So far, so good.
I can generate the other protomers with a command like this:
sym #1 C7 axis z center cofr
(assuming #1 is the single protomer from AlphaFoldDB, and the cofr is correctly lying on the symmetry axis, which I get sufficiently close if I center the view on the map)
Now, because symmetry was enforced for the map, it makes no sense to model, refine and store the entire heptamer. I should be able to do everything with a single protomer, and store relevant info as "biological assembly" so the heptamer can be regenerated from the protomer. At least if I am understanding this correctly.
I tried the above command, or this variant: sym #1 C7 axis z center cofr addMmcifAssembly true And subsequently saving in PDB or mmCIF format, but none of this produces what I want, which is a file containing the single protomer + assembly info. I either get a file with the single protomer or a file with the heptamer, in both cases without any biological assembly info. I looked up the options of the save command for PDB and mmCIF format, but found nothing that seemed relevant to this problem.
Is there a way to do this? Or am I misunderstanding something?
Related question: it might make sense to use the whole heptamer for refinement, so all interfaces between protomers "see" each other (probably important when using ISOLDE). What is the best way to deal with this? Build and refine the whole heptamer and save only a single protomer + assembly info at the very end? Or have the symmetry enforced from the beginning, throughout the whole refinement process, and really ever refine a single protomer? (7 times less work, so probably the preferred option).
Thank you in advance,
Guillaume
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participants (2)
-
Guillaume Gaullier -
Tom Goddard