Hello Elaine, I have been trying to save a protein-ligand complex in pdb format with the command line,but i haven't successful doing so. I have tried using write, display, select command but nothing worked. Steps that i followed: Open the NoH.pdb file in chimera With command line: cd /home/Desktop/test/Cmd_Tango_Dock/OUT/1abe.pdb/tmpO9IqaJ viewdock rigid_ranked.mol2 "Dock 4, 5 or 6" combine #0,1.1 111_#name.pdb-I used this command to save my result. If you could tell me what mistake I am making in saving the file. Thank You Regards Preet ------------------------------------------------------------------------------------------------------------ [ C-DAC is on Social-Media too. Kindly follow us at: Facebook: https://www.facebook.com/CDACINDIA & Twitter: @cdacindia ] This e-mail is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies and the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email is strictly prohibited and appropriate legal action will be taken. ------------------------------------------------------------------------------------------------------------
Hello Preet, The "combine" command just makes a combined model in Chimera. It does not save a file. You can check for the new combined model in Chimera by looking in the Model Panel (menu: Favorites... Model Panel), and you can save that model to a PDB file by using either menu: File... Save PDB, or the command "write" Your combine command is wrong, you cannot just give an output file name because it does not create an output file. Instead you want something like this combine #0,1.1 name 111_combined model #2 write relative #0 #2 111_combined.pdb See the help for how to use the commands: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> Probably chimera-users@cgl.ucsf.edu is a better place to send "how to use" questions -- this chimera-dev@cgl.ucsf.edu is for programming questions -- but I will reply to chimera-dev since that is where you sent it. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 2, 2022, at 2:57 AM, preetj via Chimera-dev <chimera-dev@cgl.ucsf.edu> wrote:
Hello Elaine,
I have been trying to save a protein-ligand complex in pdb format with the command line,but i haven't successful doing so. I have tried using write, display, select command but nothing worked. Steps that i followed: Open the NoH.pdb file in chimera With command line: cd /home/Desktop/test/Cmd_Tango_Dock/OUT/1abe.pdb/tmpO9IqaJ viewdock rigid_ranked.mol2 "Dock 4, 5 or 6"
combine #0,1.1 111_#name.pdb-I used this command to save my result. If you could tell me what mistake I am making in saving the file.
Thank You Regards Preet
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Elaine Meng -
preetj