[Chimera-users] Writing a SINGLE pose (with ligand and protein) to a PDB file

[Elaine Meng]

Hi Edmund,
Your first mistake if you only want one output file is that in the save dialog, you chose to save multiple models "in multiple files". That is the reason for the name error, instead of "Test.pdb" you would need to give something like "Test$number.pdb" because there will be more than one output file, and that would specify filenames something like Test0.1.pdb and Test1.pdb (including the model number).  So the error message means exactly what it says.

Save PDB help:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>

It has a choice to save multiple models in "a single file" instead.  However, my advice is NOT to save the file yet, but instead first combine your receptor and ligand models into one model.  To combine them, open Model Panel, choose those two models on the left, and on the right use the "copy/combine" function.

Model Panel copy/combine
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine>

Then save only the single new combined model to a PDB file.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 21, 2020, at 10:26 PM, Edmund Marinelli <edmundmarinelli at gmail.com> wrote:
> 
> Hello:  I used ViewDock to open a pdbqt file generated by use of AutoDock Vina.  The ligand was shown in the graphics window.  Then I opened the protein pdb file that was used in the docking experiment.  The ViewDock dialog lists the poses obtained and I can select each and view the resulting pose in the graphics window fine.  I opened the Model Pane.  I selected from the list of models the first pose (#0.1) and the protein (#1) in the list.  I assumed that saving these two into a file would give a file that contained only the protein and the ligand bound as in the best pose .  I want to save the best pose as a pdb file wherein the protein and ligand are present.  I gave a filename Test.pdb  .  Chimera returned the following error message:  "You must provide a filename that contains either $name or $number , which will be changed to the model name or model number (respectively) in the final saved file name."  I do not understand what this means.  I tried using the pose number and also the protein name but it gave the same error. I don't understand what is meant by $name and $number - what do they refer to ? What do I need to do to save a single pose containing protein and the ligand to a unique file not containing other poses?   
> 
> The screenshot below is what I see:  Note that in the models list I selected the best pose #0.1 and also the protein, which is at the bottom of the list, hence it is not visible in the picture.  What is the filename syntax that I need to use to save a pose with protein to a single PDB file?  Stated more plainly: Can you give a viable example of what I need to enter as a filename that will allow saving of the file?  Or am I going about this all wrong?  Sorry for the verbose email.    
> 
> <image.png>