[chimerax-users] How to batch process structures?

[Elaine Meng]

Hi Jacky,
It was not clear from your messages whether you are trying to save image files in a completely automated process or viewing interactively.  My answer before was about scripting an automated process.

If viewing interactively:  for molecular docking results, there is a ViewDockX tool for easily clicking through the list of docked ligands and seeing them one at a time.  It can also show the H-bonds between ligand and receptor.  To see more information on this tool, use menu: Help… Users Guide and then in the Tools section click the ViewDockX link.

Also, there are icons in the top toolbar “Molecule Display” tab that you can use on any atomic structures, for showing and hiding H-Bonds and showing the molecular surface colored by lipophilicity potential.
<http://rbvi.ucsf.edu/chimerax/docs/user/tools/moldisplay.html>

For writing command scripts, see commands: hbonds, clashes, contacts, mlp, show/hide, color, …
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files>
<http://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands>

Elaine

> On Jan 20, 2020, at 2:46 PM, jacky zhao <jackyzhao010 at gmail.com> wrote:
> 
> Hi Elaine,
>   Thank you for your reply. I always generated more than thousands of pdbs in one folder and will analysis the interaction of the complexes. In pymol, we can easy to show the interaction one by one. So I just wonder how to show the interaction of the complexes one by one instantly.
> 
> Thanks,
> 
> Jacky
> 
>> 2020年1月20日 上午8:12，Elaine Meng <meng at cgl.ucsf.edu> 写道：
>> 
>> Hi Jacky,
>> I can’t answer about the batching specifically (maybe others can help on that part), but here are some thoughts about this type of processing.
>> 
>> First, you have to figure out if ChimeraX is the right program  —  if you open an example structure, can you manually (by trial and error) figure out a set a commands that will do what you want?
>> 
>> If your goal is to save an image for each structure, consider:
>> 
>> (A) Type of display: figure out the commands that will generate the display that you want, including which atoms are shown and which are hidden, their display style, as well as any ribbons and/or molecular surface, and other things like coloring, showing h-bonds, etc..  That is probably the easiest part.
>> 
>> (B) Orientation and view: in general, it is very difficult to get good views of a variety of structures in an automated process.  Without interactive positioning by a human looking at the screen, many times a bunch of atoms are stacked on top of each other, or some piece of ribbon or another protein subunit is  in the front blocking everything else.
>> 
>> (C) Different chain IDs, ligand names, etc. in different structures.  If all of your interfaces are between chain A and chain B, or between the whole protein and a ligand that always has the same residue name, then it is easier.  If you are processing a whole bunch of structures where you don’t know ahead of time which chain(s) or ligand(s) are forming the interface, it becomes nearly impossible.
>> 
>> Only if it is possible to come up with a set of commands that works for most of your structures, would you then consider how to make this a batch process.
>> 
>> I speak from experience trying to do this with Chimera, to make active-site images for the enzyme families in the Structure-Function Linkage Database.  
>> <http://sfld.rbvi.ucsf.edu/archive/django/index.html>
>> I had an extremely elaborate process with a lot of manual work per structure, including entering the specific chain IDs and active-site residue numbers for each structure.  For each set of related structures (superfamily), I had a different session with an invisible reference structure, to which I would match the current structure (superimpose with matchmaker) before saving the image.  Creating the reference sessions also required manual work.  This was the only way I could think of to get a consistent view of a set of related structures.
>> 
>> 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 18, 2020, at 1:48 PM, jacky zhao <jackyzhao010 at gmail.com> wrote:
>>> 
>>> Hi everyone,
>>> I have tried to use chimeraX yesterday. It is vey cool! I just wonder how to batch process the structures?
>>> 
>>> We will generate more than thousands of structures and will analysis the binding interface. Can I use chimeraX to instantly show the interface interactions one by one?
>>> 
>>> Thank you for your time.
>>> Jacky
>>