Question about processing of multi-model PDB
Dear Chimera-X users ! I am working on the processing of a multi-model pdb file containing biological assembly of the dimeric protein. Precisely, every monomer is in a separate model with the same chain ID (A). I need to rename the chain A to chain B in the second model and then fuse the both models, so that the entire construction will be in the same model. What commands could be used to such modifications? Many thanks in advance Enrico
That is exactly what the "combine" command does. It combines two or models into one, and it can change the chain ID so that there are not two of the same ID. Something like combine #1,2 modelId #3 See command help for the various options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 23, 2024, at 2:50 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users !
I am working on the processing of a multi-model pdb file containing biological assembly of the dimeric protein. Precisely, every monomer is in a separate model with the same chain ID (A). I need to rename the chain A to chain B in the second model and then fuse the both models, so that the entire construction will be in the same model. What commands could be used to such modifications?
Many thanks in advance
Enrico
Fantastic, actually it renames chains automatically, thank you very much! One question: assuming that in both parts there are two ligands with the same ID. is it possible using the same command to rename the both ligands and change at the same time their change ID and residue number. E.g. Having two ligands in chain A and B defined as CUP I need to rename them to :lig (chain C, residue number 888) and :lih (chain D, residues number 999) respectively. I could only rename the chain ID using the commands like : changechains #3/A:CUP C changechains #3/B:CUP D but I did not find a possibility to make at the same moment the others modifications .. Many thanks in advance Enrico Il giorno lun 23 set 2024 alle ore 17:38 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
That is exactly what the "combine" command does. It combines two or models into one, and it can change the chain ID so that there are not two of the same ID. Something like
combine #1,2 modelId #3
See command help for the various options: < https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html>
Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 23, 2024, at 2:50 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users !
I am working on the processing of a multi-model pdb file containing biological assembly of the dimeric protein. Precisely, every monomer is in a separate model with the same chain ID (A). I need to rename the chain A to chain B in the second model and then fuse the both models, so that the entire construction will be in the same model. What commands could be used to such modifications?
Many thanks in advance
Enrico
To do more complicated things like that, you will have to use multiple commands (combine, changechain, renumber, etc.). Elaine
On Sep 23, 2024, at 8:54 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Fantastic, actually it renames chains automatically, thank you very much!
One question: assuming that in both parts there are two ligands with the same ID. is it possible using the same command to rename the both ligands and change at the same time their change ID and residue number. E.g. Having two ligands in chain A and B defined as CUP I need to rename them to :lig (chain C, residue number 888) and :lih (chain D, residues number 999) respectively.
I could only rename the chain ID using the commands like :
changechains #3/A:CUP C changechains #3/B:CUP D
but I did not find a possibility to make at the same moment the others modifications ..
Many thanks in advance
Enrico
Il giorno lun 23 set 2024 alle ore 17:38 Elaine Meng <meng@cgl.ucsf.edu> ha scritto: That is exactly what the "combine" command does. It combines two or models into one, and it can change the chain ID so that there are not two of the same ID. Something like
combine #1,2 modelId #3
See command help for the various options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html>
Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 23, 2024, at 2:50 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users !
I am working on the processing of a multi-model pdb file containing biological assembly of the dimeric protein. Precisely, every monomer is in a separate model with the same chain ID (A). I need to rename the chain A to chain B in the second model and then fuse the both models, so that the entire construction will be in the same model. What commands could be used to such modifications?
Many thanks in advance
Enrico
participants (2)
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Elaine Meng -
Enrico Martinez