[chimera-dev] Issue regrading saving the protein-ligand complex

[Elaine Meng]

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 at cgl.ucsf.edu is a better place to send "how to use" questions -- this chimera-dev at 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 at 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