Edition of the pdb/trajectories via Chimera
Dear Chimera Users! I have a pdb file for the 16 monomers of the coarse-grained GPCRs and its corresponded trajectory in dcd. In both files all the monomers are defined as the same letter of the chain (X). My question: are there an easy way to assign a unique letter to each of the monomers in the both files via Chimera to facilitate the further analysis ? Thanks so much! James
Hi James, If the PDB file or trajectory is already open in Chimera and the monomers are not bonded to each other, you could try using Change Chain IDs (in menu under Tools… Structure Editing). Since they all have the same ID to start with, you would have to use the workaround given in the page for “Handling multiple chains with the same ID” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechains.html> To open the dcd file in Chimera as a trajectory, you'd also need either a psf file or an AMBER-style prmtop file for the system. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 30, 2017, at 10:22 AM, James Starlight <jmsstarlight@gmail.com> wrote:
Dear Chimera Users!
I have a pdb file for the 16 monomers of the coarse-grained GPCRs and its corresponded trajectory in dcd. In both files all the monomers are defined as the same letter of the chain (X). My question: are there an easy way to assign a unique letter to each of the monomers in the both files via Chimera to facilitate the further analysis ?
Thanks so much! James
Hi Elaine, I thank you very much for the help! Indeed "Change Chain IDs" has recognized correctly each of the monomers and proposed an assignment of the unique ID for it ( I checked initial pdb - actually there were no chain assigments within it). One question- is it possible to perform the same assignment automatically using batch-chimera, providing as an input some script file and the initial pdb ? E.g. to assign unique chain name automatically for each protein entities w/o identified chains. Thank you! James 2017-12-01 1:02 GMT+01:00 Elaine Meng <meng@cgl.ucsf.edu>:
Hi James, If the PDB file or trajectory is already open in Chimera and the monomers are not bonded to each other, you could try using Change Chain IDs (in menu under Tools… Structure Editing). Since they all have the same ID to start with, you would have to use the workaround given in the page for “Handling multiple chains with the same ID” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechains.html>
To open the dcd file in Chimera as a trajectory, you'd also need either a psf file or an AMBER-style prmtop file for the system. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 30, 2017, at 10:22 AM, James Starlight <jmsstarlight@gmail.com> wrote:
Dear Chimera Users!
I have a pdb file for the 16 monomers of the coarse-grained GPCRs and its corresponded trajectory in dcd. In both files all the monomers are defined as the same letter of the chain (X). My question: are there an easy way to assign a unique letter to each of the monomers in the both files via Chimera to facilitate the further analysis ?
Thanks so much! James
Hi James, Although there is a “changechains” command, <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/changechains.html> ... it does not handle the case of multiple chains having the same ID to start with. To handle that, you would have to use the GUI (Change Chain IDs dialog). Thus I don’t think you would be able to batch process this situation with Chimera…. it may be necessary to write your own script to edit chain IDs in your files without using Chimera, or find some other program to do it. I don’t know what other program(s) have this capability, though — sorry. Elaine
On Dec 1, 2017, at 1:42 AM, James Starlight <jmsstarlight@gmail.com> wrote:
Hi Elaine,
I thank you very much for the help!
Indeed "Change Chain IDs" has recognized correctly each of the monomers and proposed an assignment of the unique ID for it ( I checked initial pdb - actually there were no chain assigments within it).
One question- is it possible to perform the same assignment automatically using batch-chimera, providing as an input some script file and the initial pdb ? E.g. to assign unique chain name automatically for each protein entities w/o identified chains.
Thank you!
James
2017-12-01 1:02 GMT+01:00 Elaine Meng <meng@cgl.ucsf.edu>:
Hi James, If the PDB file or trajectory is already open in Chimera and the monomers are not bonded to each other, you could try using Change Chain IDs (in menu under Tools… Structure Editing). Since they all have the same ID to start with, you would have to use the workaround given in the page for “Handling multiple chains with the same ID” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechains.html>
To open the dcd file in Chimera as a trajectory, you'd also need either a psf file or an AMBER-style prmtop file for the system. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 30, 2017, at 10:22 AM, James Starlight <jmsstarlight@gmail.com> wrote:
Dear Chimera Users!
I have a pdb file for the 16 monomers of the coarse-grained GPCRs and its corresponded trajectory in dcd. In both files all the monomers are defined as the same letter of the chain (X). My question: are there an easy way to assign a unique letter to each of the monomers in the both files via Chimera to facilitate the further analysis ?
Thanks so much! James
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Thanks, Elaine!! James 2017-12-01 18:19 GMT+01:00 Elaine Meng <meng@cgl.ucsf.edu>:
Hi James, Although there is a “changechains” command, <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/changechains.html>
... it does not handle the case of multiple chains having the same ID to start with. To handle that, you would have to use the GUI (Change Chain IDs dialog). Thus I don’t think you would be able to batch process this situation with Chimera…. it may be necessary to write your own script to edit chain IDs in your files without using Chimera, or find some other program to do it. I don’t know what other program(s) have this capability, though — sorry. Elaine
On Dec 1, 2017, at 1:42 AM, James Starlight <jmsstarlight@gmail.com> wrote:
Hi Elaine,
I thank you very much for the help!
Indeed "Change Chain IDs" has recognized correctly each of the monomers and proposed an assignment of the unique ID for it ( I checked initial pdb - actually there were no chain assigments within it).
One question- is it possible to perform the same assignment automatically using batch-chimera, providing as an input some script file and the initial pdb ? E.g. to assign unique chain name automatically for each protein entities w/o identified chains.
Thank you!
James
2017-12-01 1:02 GMT+01:00 Elaine Meng <meng@cgl.ucsf.edu>:
Hi James, If the PDB file or trajectory is already open in Chimera and the monomers are not bonded to each other, you could try using Change Chain IDs (in menu under Tools… Structure Editing). Since they all have the same ID to start with, you would have to use the workaround given in the page for “Handling multiple chains with the same ID” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechains.html>
To open the dcd file in Chimera as a trajectory, you'd also need either a psf file or an AMBER-style prmtop file for the system. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 30, 2017, at 10:22 AM, James Starlight <jmsstarlight@gmail.com> wrote:
Dear Chimera Users!
I have a pdb file for the 16 monomers of the coarse-grained GPCRs and its corresponded trajectory in dcd. In both files all the monomers are defined as the same letter of the chain (X). My question: are there an easy way to assign a unique letter to each of the monomers in the both files via Chimera to facilitate the further analysis ?
Thanks so much! James
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Elaine Meng -
James Starlight