Hey there, I have a specific pdf file (3BMP.pdb) and I would like to "clean" it from the chemical compounds which are in the file. I would like to know if there is anyway in ChimeraX to "clean" the file programmatically? Greetings from Germany - Martin
Hi Martin, If by programatically you mean by python code, that is beyond my area of expertise and someone else will have to advise. Of course you can open the structure and use commands like "delete solvent" or "delete ligand" whatever else you decide needs deleting, and then save a PDB file... however, ChimeraX does not yet have a Dock Prep tool like Chimera does. The Chimera Dock Prep tool does several things like fixing up truncated side chains, adding hydrogens and charges, etc. ChimeraX has "addh" and "delete" so you can use it for those now, but not all of the other dock-prep steps. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 16, 2022, at 2:23 AM, Martin Urban via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hey there,
I have a specific pdf file (3BMP.pdb) and I would like to "clean" it from the chemical compounds which are in the file.
I would like to know if there is anyway in ChimeraX to "clean" the file programmatically?
Greetings from Germany
- Martin
Hi Elaine thanks for your quick response. With programmatically I meant how to use the program ChimeraX to clean the .pdb file. I will try out your described steps. You helped me out, Martin On 1/16/2022 7:38 PM, Elaine Meng wrote:
Hi Martin, If by programatically you mean by python code, that is beyond my area of expertise and someone else will have to advise.
Of course you can open the structure and use commands like "delete solvent" or "delete ligand" whatever else you decide needs deleting, and then save a PDB file... however, ChimeraX does not yet have a Dock Prep tool like Chimera does. The Chimera Dock Prep tool does several things like fixing up truncated side chains, adding hydrogens and charges, etc. ChimeraX has "addh" and "delete" so you can use it for those now, but not all of the other dock-prep steps.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 16, 2022, at 2:23 AM, Martin Urban via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hey there,
I have a specific pdf file (3BMP.pdb) and I would like to "clean" it from the chemical compounds which are in the file.
I would like to know if there is anyway in ChimeraX to "clean" the file programmatically?
Greetings from Germany
- Martin
participants (2)
-
Elaine Meng -
Martin Urban