Hi Dmitry, You sent this to the chimera-users list but chimerax-users@cgl.ucsf.edu (CC'd here) is the better address for ChimeraX questions. We try not confuse Chimera users with ChimeraX answers and vice versa. Since your text said "Chimerax" I will answer for ChimeraX. Not sure what you mean by "multiple" ... of course you can fetch structures from the PDB using their IDs, e.g. commands: open 1zik open 2gbp 2fw0 1plx 1plz <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch> If by "multiple" you mean a huge number that is not practical to put in a single command, that is a different matter. Also, a single "save" command only saves one file and it does not have option to automatically figure out filename from model name. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> However, ChimeraX does allow writing a single command script (.cxc file) and applying it to multiple input files when the .cxc file is opened with the "open" command and "forEachFile" option: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile> It also allows substituting part of the input file name as the output file name. However, it was intended for the case where all the input files are local files. So as far as I know you would have to first fetch all the files from the PDB so that they are in your local cache (~/Downloads/ChimeraX/PDB/ ) and then in a separate step, use your .cxc file with this forEachFile mechanism. To do so, you would probably also need to segragate these files into their own directory since you don't also want to run the script on all of the other structures you've previously fetched from the PDB using ChimeraX. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 26, 2023, at 9:39 AM, Dmitry Semchonok via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear colleagues,
Is there a way to
• download the multiple pdb/mmcif using Chimerax knowing their ID entry? • save multiple opened pdbs using their corresponding original names in Chimerax? Thank you in advance.
Kind regards, Dmitry