Hi there, I'm using Rosetta using comparative modeling of protein, and I get 1000 new PDBs. I wanted to upload all of them together and average them into one structure and to see if the average one is the better then the last one the software creates, which needs to be the best. Thanks, Yehuda
Hi Yehuda, To average the structures in Chimera, you need to open them as a trajectory with the MD Movie tool (in menu under Tools… MD/Ensemble Analysis). This can be done even if they are separate PDB files but they would have to meet certain naming conventions; see the multiple-files PDB option in the “Startup and Input” section of the MD Movie manual page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> So you might need to rename your files. Also I believe they would need to each contain the same set of atoms. Once they are loaded as a trajectory, then see the “Structure Averaging” section of the manual page linked above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 11, 2016, at 4:35 PM, Yehuda Halfon <yehuda.halfon@weizmann.ac.il> wrote:
Hi there, I'm using Rosetta using comparative modeling of protein, and I get 1000 new PDBs. I wanted to upload all of them together and average them into one structure and to see if the average one is the better then the last one the software creates, which needs to be the best. Thanks, Yehuda
Hi Elaine, Thanks, it works fine. Now I just need to remove all the hydrogens from the PDBs and make sure the files ends with TER and not END. Yehuda ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Thursday, May 12, 2016 2:43 AM To: Yehuda Halfon Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Averaging multiple structures Hi Yehuda, To average the structures in Chimera, you need to open them as a trajectory with the MD Movie tool (in menu under Tools… MD/Ensemble Analysis). This can be done even if they are separate PDB files but they would have to meet certain naming conventions; see the multiple-files PDB option in the “Startup and Input” section of the MD Movie manual page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> So you might need to rename your files. Also I believe they would need to each contain the same set of atoms. Once they are loaded as a trajectory, then see the “Structure Averaging” section of the manual page linked above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 11, 2016, at 4:35 PM, Yehuda Halfon <yehuda.halfon@weizmann.ac.il> wrote:
Hi there, I'm using Rosetta using comparative modeling of protein, and I get 1000 new PDBs. I wanted to upload all of them together and average them into one structure and to see if the average one is the better then the last one the software creates, which needs to be the best. Thanks, Yehuda
Is that a question? :-) Deleting hydrogens is easy (e.g. command “delete H”) but I believe the other thing requires editing the file(s) outside of Chimera… should be pretty easy to script in whatever is your favorite scripting approach, though. Elaine On May 11, 2016, at 5:05 PM, Yehuda Halfon <yehuda.halfon@weizmann.ac.il> wrote:
Hi Elaine,
Thanks, it works fine. Now I just need to remove all the hydrogens from the PDBs and make sure the files ends with TER and not END.
Yehuda ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Thursday, May 12, 2016 2:43 AM To: Yehuda Halfon Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Averaging multiple structures
Hi Yehuda, To average the structures in Chimera, you need to open them as a trajectory with the MD Movie tool (in menu under Tools… MD/Ensemble Analysis). This can be done even if they are separate PDB files but they would have to meet certain naming conventions; see the multiple-files PDB option in the “Startup and Input” section of the MD Movie manual page:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
So you might need to rename your files. Also I believe they would need to each contain the same set of atoms.
Once they are loaded as a trajectory, then see the “Structure Averaging” section of the manual page linked above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 11, 2016, at 4:35 PM, Yehuda Halfon <yehuda.halfon@weizmann.ac.il> wrote:
Hi there, I'm using Rosetta using comparative modeling of protein, and I get 1000 new PDBs. I wanted to upload all of them together and average them into one structure and to see if the average one is the better then the last one the software creates, which needs to be the best. Thanks, Yehuda
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I found how to do it. I load all the files. Remove the hydrogens and save them together as one PDB. Load it in MD Movie tool and run the average on it (since it has all the PDBs in it). Then I save the new PDB. Thanks a lot, Yehdua ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Thursday, May 12, 2016 3:10 AM To: Yehuda Halfon Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Averaging multiple structures Is that a question? :-) Deleting hydrogens is easy (e.g. command “delete H”) but I believe the other thing requires editing the file(s) outside of Chimera… should be pretty easy to script in whatever is your favorite scripting approach, though. Elaine On May 11, 2016, at 5:05 PM, Yehuda Halfon <yehuda.halfon@weizmann.ac.il> wrote:
Hi Elaine,
Thanks, it works fine. Now I just need to remove all the hydrogens from the PDBs and make sure the files ends with TER and not END.
Yehuda ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Thursday, May 12, 2016 2:43 AM To: Yehuda Halfon Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Averaging multiple structures
Hi Yehuda, To average the structures in Chimera, you need to open them as a trajectory with the MD Movie tool (in menu under Tools… MD/Ensemble Analysis). This can be done even if they are separate PDB files but they would have to meet certain naming conventions; see the multiple-files PDB option in the “Startup and Input” section of the MD Movie manual page:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
So you might need to rename your files. Also I believe they would need to each contain the same set of atoms.
Once they are loaded as a trajectory, then see the “Structure Averaging” section of the manual page linked above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 11, 2016, at 4:35 PM, Yehuda Halfon <yehuda.halfon@weizmann.ac.il> wrote:
Hi there, I'm using Rosetta using comparative modeling of protein, and I get 1000 new PDBs. I wanted to upload all of them together and average them into one structure and to see if the average one is the better then the last one the software creates, which needs to be the best. Thanks, Yehuda
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Elaine Meng -
Yehuda Halfon