Re: issues with writing models as pdb files
Hi everyone, I noticed that sometimes when i write pdb of one model or a selection , it does not open in other programs.( MOE,Pymol). One of the errors i noticed recently was that th pdb file was written as a multi model pdb file ( each of the 70 residues in the protein were separate models) , i cleaned it using notepad++ by removing the model lines and it was opening correctly. i was told that it might be related to using split command. i use split often and it might be the case. can some one please explain how using split can lead to this? and if so what is best way to fix it? should i perhaps run some version of combine command on the model prior to writing it out as pdb file. thanks again, best amith
Hi Amith, If you are writing multiple models you can either write them to a multimodel PDB file (which is valid format, just not the one that you may want for other programs) or multiple individual PDB files. See the explanation of [NAME] and [ID] in the first sentence under the usage of the PDB save command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> If you want all of the atomic coordinates in a single model you would need to use "combine" -- if it was originally a single model and you used "split," that is the reason you have multiple models. That is the whole purpose of split, to make multiple models out of a single model. I don't know why you were using it if you didn't want multiple models. You can specify parts within a single model by chain ID, residue numbers, etc. without having to split it. See: combine, split, rename, ... <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rename.html> Just look in the Models list, including expanding any disclosure triangles, to see what models and submodels you have. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelpanel.html> I hope this helps, 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 Apr 8, 2025, at 4:22 AM, amith via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi everyone,
I noticed that sometimes when i write pdb of one model or a selection , it does not open in other programs.( MOE,Pymol). One of the errors i noticed recently was that th pdb file was written as a multi model pdb file ( each of the 70 residues in the protein were separate models) , i cleaned it using notepad++ by removing the model lines and it was opening correctly. i was told that it might be related to using split command. i use split often and it might be the case. can some one please explain how using split can lead to this? and if so what is best way to fix it? should i perhaps run some version of combine command on the model prior to writing it out as pdb file.
thanks again, best amith
Hi elaine, Dear Meng, Thanks for the response. I guess these are my doubts: 1. if I run split without specifying the target spec will it split the existing models into sub models? If a chain was already existing as a model, will running split command split each residue into a sub-model?. I had used split on a pdb file and I got each chain as a model ( #1.1, #1.2, etc..) upon trying to write one of such model out I was getting a multimodel pdb as an output, each residue of the chain was getting written as a model . I was adding several structures into the session and had used split several times so I wanted to know if it was the reason for my multimodel pdb output. 2. How to check if a model has submodels in them using command line.( not sure if info will work) thanks a lot , Best -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, April 8, 2025 8:16 AM To: Amith Rangarajan <arangarajan@initialtx.com> Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] issues with writing models as pdb files Hi Amith, If you are writing multiple models you can either write them to a multimodel PDB file (which is valid format, just not the one that you may want for other programs) or multiple individual PDB files. See the explanation of [NAME] and [ID] in the first sentence under the usage of the PDB save command: <https://url.avanan.click/v2/r01/___https://rbvi.ucsf.edu/chimerax/docs/user/...> If you want all of the atomic coordinates in a single model you would need to use "combine" -- if it was originally a single model and you used "split," that is the reason you have multiple models. That is the whole purpose of split, to make multiple models out of a single model. I don't know why you were using it if you didn't want multiple models. You can specify parts within a single model by chain ID, residue numbers, etc. without having to split it. See: combine, split, rename, ... <https://url.avanan.click/v2/r01/___https://rbvi.ucsf.edu/chimerax/docs/user/...> <https://url.avanan.click/v2/r01/___https://rbvi.ucsf.edu/chimerax/docs/user/...> <https://url.avanan.click/v2/r01/___https://rbvi.ucsf.edu/chimerax/docs/user/...> Just look in the Models list, including expanding any disclosure triangles, to see what models and submodels you have. <https://url.avanan.click/v2/r01/___https://rbvi.ucsf.edu/chimerax/docs/user/...> I hope this helps, 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 Apr 8, 2025, at 4:22 AM, amith via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi everyone,
I noticed that sometimes when i write pdb of one model or a selection , it does not open in other programs.( MOE,Pymol). One of the errors i noticed recently was that th pdb file was written as a multi model pdb file ( each of the 70 residues in the protein were separate models) , i cleaned it using notepad++ by removing the model lines and it was opening correctly. i was told that it might be related to using split command. i use split often and it might be the case. can some one please explain how using split can lead to this? and if so what is best way to fix it? should i perhaps run some version of combine command on the model prior to writing it out as pdb file.
thanks again, best amith
Hi Amith, As mentioned in the previous message, the whole purpose of "split" is to create submodels (= more models). If you don't want more models, don't use "split"! - your questions to how it works are all answered in the help page for "split": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html> As it says in that help page, blank specification means all atomic models, and default is by chain. If you don't want to look in the Models panel, you can use command "info models" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#models> Example commands: open 4hhb split info models Log says (see the lines for AtomicStructure): model id #1 type Model name 4hhb model id #1.1 type AtomicStructure name "4hhb A" model id #1.1.1 type PseudobondGroup name "metal coordination bonds" model id #1.2 type AtomicStructure name "4hhb B" model id #1.2.1 type PseudobondGroup name "metal coordination bonds" model id #1.3 type AtomicStructure name "4hhb C" model id #1.3.1 type PseudobondGroup name "metal coordination bonds" model id #1.4 type AtomicStructure name "4hhb D" model id #1.4.1 type PseudobondGroup name "metal coordination bonds" Or you can use a specific number, e.g. command: info models #1 I hope this helps, 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 Apr 8, 2025, at 8:58 AM, Amith Rangarajan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi elaine,
Dear Meng,
Thanks for the response.
I guess these are my doubts:
1. if I run split without specifying the target spec will it split the existing models into sub models? If a chain was already existing as a model, will running split command split each residue into a sub-model?. I had used split on a pdb file and I got each chain as a model ( #1.1, #1.2, etc..) upon trying to write one of such model out I was getting a multimodel pdb as an output, each residue of the chain was getting written as a model . I was adding several structures into the session and had used split several times so I wanted to know if it was the reason for my multimodel pdb output.
2. How to check if a model has submodels in them using command line.( not sure if info will work)
thanks a lot ,
Best
-----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, April 8, 2025 8:16 AM To: Amith Rangarajan <arangarajan@initialtx.com> Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] issues with writing models as pdb files
Hi Amith, If you are writing multiple models you can either write them to a multimodel PDB file (which is valid format, just not the one that you may want for other programs) or multiple individual PDB files. See the explanation of [NAME] and [ID] in the first sentence under the usage of the PDB save command: <https://url.avanan.click/v2/r01/___https://rbvi.ucsf.edu/chimerax/docs/user/...>
If you want all of the atomic coordinates in a single model you would need to use "combine" -- if it was originally a single model and you used "split," that is the reason you have multiple models. That is the whole purpose of split, to make multiple models out of a single model. I don't know why you were using it if you didn't want multiple models. You can specify parts within a single model by chain ID, residue numbers, etc. without having to split it. See: combine, split, rename, ... <https://url.avanan.click/v2/r01/___https://rbvi.ucsf.edu/chimerax/docs/user/...> <https://url.avanan.click/v2/r01/___https://rbvi.ucsf.edu/chimerax/docs/user/...> <https://url.avanan.click/v2/r01/___https://rbvi.ucsf.edu/chimerax/docs/user/...>
Just look in the Models list, including expanding any disclosure triangles, to see what models and submodels you have. <https://url.avanan.click/v2/r01/___https://rbvi.ucsf.edu/chimerax/docs/user/...>
I hope this helps, 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 Apr 8, 2025, at 4:22 AM, amith via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi everyone,
I noticed that sometimes when i write pdb of one model or a selection , it does not open in other programs.( MOE,Pymol). One of the errors i noticed recently was that th pdb file was written as a multi model pdb file ( each of the 70 residues in the protein were separate models) , i cleaned it using notepad++ by removing the model lines and it was opening correctly. i was told that it might be related to using split command. i use split often and it might be the case. can some one please explain how using split can lead to this? and if so what is best way to fix it? should i perhaps run some version of combine command on the model prior to writing it out as pdb file.
thanks again, best amith
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Got it ! Thanks elaine -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, April 8, 2025 9:39 AM To: Amith Rangarajan <arangarajan@initialtx.com> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] issues with writing models as pdb files Hi Amith, As mentioned in the previous message, the whole purpose of "split" is to create submodels (= more models). If you don't want more models, don't use "split"! - your questions to how it works are all answered in the help page for "split": <https://url.avanan.click/v2/r01/___https://rbvi.ucsf.edu/chimerax/docs/user/...> As it says in that help page, blank specification means all atomic models, and default is by chain. If you don't want to look in the Models panel, you can use command "info models" <https://url.avanan.click/v2/r01/___https://rbvi.ucsf.edu/chimerax/docs/user/...> Example commands: open 4hhb split info models Log says (see the lines for AtomicStructure): model id #1 type Model name 4hhb model id #1.1 type AtomicStructure name "4hhb A" model id #1.1.1 type PseudobondGroup name "metal coordination bonds" model id #1.2 type AtomicStructure name "4hhb B" model id #1.2.1 type PseudobondGroup name "metal coordination bonds" model id #1.3 type AtomicStructure name "4hhb C" model id #1.3.1 type PseudobondGroup name "metal coordination bonds" model id #1.4 type AtomicStructure name "4hhb D" model id #1.4.1 type PseudobondGroup name "metal coordination bonds" Or you can use a specific number, e.g. command: info models #1 I hope this helps, 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 Apr 8, 2025, at 8:58 AM, Amith Rangarajan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi elaine,
Dear Meng,
Thanks for the response.
I guess these are my doubts:
1. if I run split without specifying the target spec will it split the existing models into sub models? If a chain was already existing as a model, will running split command split each residue into a sub-model?. I had used split on a pdb file and I got each chain as a model ( #1.1, #1.2, etc..) upon trying to write one of such model out I was getting a multimodel pdb as an output, each residue of the chain was getting written as a model . I was adding several structures into the session and had used split several times so I wanted to know if it was the reason for my multimodel pdb output.
2. How to check if a model has submodels in them using command line.( not sure if info will work)
thanks a lot ,
Best
-----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, April 8, 2025 8:16 AM To: Amith Rangarajan <arangarajan@initialtx.com> Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] issues with writing models as pdb files
Hi Amith, If you are writing multiple models you can either write them to a multimodel PDB file (which is valid format, just not the one that you may want for other programs) or multiple individual PDB files. See the explanation of [NAME] and [ID] in the first sentence under the usage of the PDB save command: <https://url.avanan.click/v2/r01/___https://rbvi.ucsf.edu/chimerax/docs/user/...>
If you want all of the atomic coordinates in a single model you would need to use "combine" -- if it was originally a single model and you used "split," that is the reason you have multiple models. That is the whole purpose of split, to make multiple models out of a single model. I don't know why you were using it if you didn't want multiple models. You can specify parts within a single model by chain ID, residue numbers, etc. without having to split it. See: combine, split, rename, ... <https://url.avanan.click/v2/r01/___https://rbvi.ucsf.edu/chimerax/docs/user/...> <https://url.avanan.click/v2/r01/___https://rbvi.ucsf.edu/chimerax/docs/user/...> <https://url.avanan.click/v2/r01/___https://rbvi.ucsf.edu/chimerax/docs/user/...>
Just look in the Models list, including expanding any disclosure triangles, to see what models and submodels you have. <https://url.avanan.click/v2/r01/___https://rbvi.ucsf.edu/chimerax/docs/user/...>
I hope this helps, 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 Apr 8, 2025, at 4:22 AM, amith via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi everyone,
I noticed that sometimes when i write pdb of one model or a selection , it does not open in other programs.( MOE,Pymol). One of the errors i noticed recently was that th pdb file was written as a multi model pdb file ( each of the 70 residues in the protein were separate models) , i cleaned it using notepad++ by removing the model lines and it was opening correctly. i was told that it might be related to using split command. i use split often and it might be the case. can some one please explain how using split can lead to this? and if so what is best way to fix it? should i perhaps run some version of combine command on the model prior to writing it out as pdb file.
thanks again, best amith
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://url.avanan.click/v2/r01/___https://mail.cgl.ucsf.edu/mailman/archive...>
participants (3)
-
Amith Rangarajan -
arangarajan＠initialtx.com
-
Elaine Meng