Assigning id to a chain with no id
Hi, I need help with chimera. In my pdb I have a chain with no id and I want to assign it a new id. I tried using 'changechain' command but I am getting error messages because I don't have any specific from-chain id. I don't know what exactly to give as from-chain id or is there any other command that could help me? Thanks, Aleena.
HI Aleena, You can do it with the "Change Chain IDs" graphical interface, open from menu: Tools... Structure Editing... Change Chain IDs. That dialog will list the chain with no ID separately (something like "principal chain") and you can click to choose it in that interface, then enter a new ID. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechai...> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 4, 2020, at 2:41 PM, Aleena Jose <aleena.jose@students.iiserpune.ac.in> wrote:
Hi, I need help with chimera. In my pdb I have a chain with no id and I want to assign it a new id. I tried using 'changechain' command but I am getting error messages because I don't have any specific from-chain id. I don't know what exactly to give as from-chain id or is there any other command that could help me? Thanks, Aleena.
Hi Elaine, Thanks a lot for your reply. The problem is that I have got hundreds of such pdbs with no id chains after random scanning mutagenesis. I wish I could solve it using a python script. Regards Aleena. On Mon, Jul 6, 2020, 9:32 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
HI Aleena, You can do it with the "Change Chain IDs" graphical interface, open from menu: Tools... Structure Editing... Change Chain IDs. That dialog will list the chain with no ID separately (something like "principal chain") and you can click to choose it in that interface, then enter a new ID.
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechai...
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 4, 2020, at 2:41 PM, Aleena Jose < aleena.jose@students.iiserpune.ac.in> wrote:
Hi, I need help with chimera. In my pdb I have a chain with no id and I want to assign it a new id. I tried using 'changechain' command but I am getting error messages because I don't have any specific from-chain id. I don't know what exactly to give as from-chain id or is there any other command that could help me? Thanks, Aleena.
Hi Aleena, Seems like it would be easier just to write your own script to add a chain ID to the PDB files than to do it with a python script in Chimera. All you have to do is replace the blank character at position 22 of ATOM and HETATM lines with A (or whatever you want the chain ID to be). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.htm...> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#coo...> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 7, 2020, at 5:48 AM, Aleena Jose <aleena.jose@students.iiserpune.ac.in> wrote:
Hi Elaine,
Thanks a lot for your reply. The problem is that I have got hundreds of such pdbs with no id chains after random scanning mutagenesis. I wish I could solve it using a python script.
Regards Aleena.
On Mon, Jul 6, 2020, 9:32 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: HI Aleena, You can do it with the "Change Chain IDs" graphical interface, open from menu: Tools... Structure Editing... Change Chain IDs. That dialog will list the chain with no ID separately (something like "principal chain") and you can click to choose it in that interface, then enter a new ID.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechai...>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 4, 2020, at 2:41 PM, Aleena Jose <aleena.jose@students.iiserpune.ac.in> wrote:
Hi, I need help with chimera. In my pdb I have a chain with no id and I want to assign it a new id. I tried using 'changechain' command but I am getting error messages because I don't have any specific from-chain id. I don't know what exactly to give as from-chain id or is there any other command that could help me? Thanks, Aleena.
Thanks for the tip! On Tue, Jul 7, 2020, 9:09 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Aleena, Seems like it would be easier just to write your own script to add a chain ID to the PDB files than to do it with a python script in Chimera. All you have to do is replace the blank character at position 22 of ATOM and HETATM lines with A (or whatever you want the chain ID to be).
< http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.htm...
< http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#coo...
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 7, 2020, at 5:48 AM, Aleena Jose < aleena.jose@students.iiserpune.ac.in> wrote:
Hi Elaine,
Thanks a lot for your reply. The problem is that I have got hundreds of such pdbs with no id chains after random scanning mutagenesis. I wish I could solve it using a python script.
Regards Aleena.
On Mon, Jul 6, 2020, 9:32 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: HI Aleena, You can do it with the "Change Chain IDs" graphical interface, open from menu: Tools... Structure Editing... Change Chain IDs. That dialog will list the chain with no ID separately (something like "principal chain") and you can click to choose it in that interface, then enter a new ID.
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechai...
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 4, 2020, at 2:41 PM, Aleena Jose < aleena.jose@students.iiserpune.ac.in> wrote:
Hi, I need help with chimera. In my pdb I have a chain with no id and I want to assign it a new id. I tried using 'changechain' command but I am getting error messages because I don't have any specific from-chain id. I don't know what exactly to give as from-chain id or is there any other command that could help me? Thanks, Aleena.
Hi Aleena, If you have some structures open with blank IDs that you want to change to 'A', I believe the Python code is: from ChangeChainIDs import changeChains from chimera import openModels, Molecule changeChains(openModels.list(modelTypes=[Molecule]), [(' ', 'A')]) --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jul 7, 2020, at 5:48 AM, Aleena Jose <aleena.jose@students.iiserpune.ac.in> wrote:
Hi Elaine,
Thanks a lot for your reply. The problem is that I have got hundreds of such pdbs with no id chains after random scanning mutagenesis. I wish I could solve it using a python script.
Regards Aleena.
On Mon, Jul 6, 2020, 9:32 PM Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: HI Aleena, You can do it with the "Change Chain IDs" graphical interface, open from menu: Tools... Structure Editing... Change Chain IDs. That dialog will list the chain with no ID separately (something like "principal chain") and you can click to choose it in that interface, then enter a new ID.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechai... <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechains.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 Jul 4, 2020, at 2:41 PM, Aleena Jose <aleena.jose@students.iiserpune.ac.in <mailto:aleena.jose@students.iiserpune.ac.in>> wrote:
Hi, I need help with chimera. In my pdb I have a chain with no id and I want to assign it a new id. I tried using 'changechain' command but I am getting error messages because I don't have any specific from-chain id. I don't know what exactly to give as from-chain id or is there any other command that could help me? Thanks, Aleena.
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks a lot! On Tue, Jul 7, 2020, 11:28 PM Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Aleena, If you have some structures open with blank IDs that you want to change to 'A', I believe the Python code is:
from ChangeChainIDs import changeChains from chimera import openModels, Molecule changeChains(openModels.list(modelTypes=[Molecule]), [(' ', 'A')])
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jul 7, 2020, at 5:48 AM, Aleena Jose < aleena.jose@students.iiserpune.ac.in> wrote:
Hi Elaine,
Thanks a lot for your reply. The problem is that I have got hundreds of such pdbs with no id chains after random scanning mutagenesis. I wish I could solve it using a python script.
Regards Aleena.
On Mon, Jul 6, 2020, 9:32 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
HI Aleena, You can do it with the "Change Chain IDs" graphical interface, open from menu: Tools... Structure Editing... Change Chain IDs. That dialog will list the chain with no ID separately (something like "principal chain") and you can click to choose it in that interface, then enter a new ID.
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechai...
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 4, 2020, at 2:41 PM, Aleena Jose < aleena.jose@students.iiserpune.ac.in> wrote:
Hi, I need help with chimera. In my pdb I have a chain with no id and I want to assign it a new id. I tried using 'changechain' command but I am getting error messages because I don't have any specific from-chain id. I don't know what exactly to give as from-chain id or is there any other command that could help me? Thanks, Aleena.
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Aleena Jose -
Elaine Meng -
Eric Pettersen