Hello, I am adding hydrogen atoms by entering addh#1 to the command line, and it works but when I export the pdb and import it into houdini, things are messed up. Sometimes it just doesn't show up and other times, just part of the structure shows up. Am I missing something? Thank you, Daniel.
Hello Daniel, No idea why Houdini (a program I have never used) would or would not show atoms . We haven't had problems with saved PDB files after adding hydrogens, and ChimeraX PDB saving is careful about using the correct format. If you are saving using the dialog opened from the menu with File... Save, just make sure you specified the correct file type to save (PDB) and did NOT turn on any options to save the displayed or selected atoms only. As you might expect, those options would only save the atoms that are displayed or selected instead of all atoms. 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 25, 2022, at 4:47 PM, Daniel VillanuevaAvalos via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am adding hydrogen atoms by entering addh#1 to the command line, and it works but when I export the pdb and import it into houdini, things are messed up. Sometimes it just doesn't show up and other times, just part of the structure shows up. Am I missing something?
Thank you, Daniel.
Thank you. I simply will not display hydrogen atoms in my animation. One thing that I am trying to do but cannot figure out how to do is to save all the chains as separate pdb files. I am looking into the command:save documentation but cannot find if it is possible. Thank you, Daniel. El lun, 25 jul 2022 a la(s) 17:56, Elaine Meng (meng@cgl.ucsf.edu) escribió:
Hello Daniel, No idea why Houdini (a program I have never used) would or would not show atoms . We haven't had problems with saved PDB files after adding hydrogens, and ChimeraX PDB saving is careful about using the correct format. If you are saving using the dialog opened from the menu with File... Save, just make sure you specified the correct file type to save (PDB) and did NOT turn on any options to save the displayed or selected atoms only. As you might expect, those options would only save the atoms that are displayed or selected instead of all atoms. 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 25, 2022, at 4:47 PM, Daniel VillanuevaAvalos via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am adding hydrogen atoms by entering addh#1 to the command line, and it works but when I export the pdb and import it into houdini, things are messed up. Sometimes it just doesn't show up and other times, just part of the structure shows up. Am I missing something?
Thank you, Daniel.
Hi Daniel, One way to do that is to select only the chain of interest, then use the dialog (menu: File... Save) to save PDB file type with the option to save only selected atoms. Then repeat the process with each of the other chains that you want to save. There are several ways to select, including the menu (Select... Chains...[depends on what chains are in your structure]) or a command (for example "select /A" to select chain A). <https://rbvi.ucsf.edu/chimerax/docs/user/selection.html> <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#select> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/select.html#new> 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 25, 2022, at 6:21 PM, Daniel VillanuevaAvalos via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thank you. I simply will not display hydrogen atoms in my animation. One thing that I am trying to do but cannot figure out how to do is to save all the chains as separate pdb files. I am looking into the command:save documentation but cannot find if it is possible.
Thank you, Daniel.
For saving a separate PDB file for each chain when you have many chains, the split and save command can do the job split #1 save [NAME].pdb model #1 The split command makes separate models for each chain and the [NAME] in the save command saves each using the model names which include the chain identifier. Tom
On Jul 25, 2022, at 6:38 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Daniel, One way to do that is to select only the chain of interest, then use the dialog (menu: File... Save) to save PDB file type with the option to save only selected atoms. Then repeat the process with each of the other chains that you want to save.
There are several ways to select, including the menu (Select... Chains...[depends on what chains are in your structure]) or a command (for example "select /A" to select chain A).
<https://rbvi.ucsf.edu/chimerax/docs/user/selection.html> <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#select> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/select.html#new>
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 25, 2022, at 6:21 PM, Daniel VillanuevaAvalos via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thank you. I simply will not display hydrogen atoms in my animation. One thing that I am trying to do but cannot figure out how to do is to save all the chains as separate pdb files. I am looking into the command:save documentation but cannot find if it is possible.
Thank you, Daniel.
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participants (3)
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Daniel VillanuevaAvalos -
Elaine Meng -
Tom Goddard