VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 11 2020 - 10:41:58 CST

I'm curious why you can't use segname or chain? The PDB file format
is obviously quite limited when it comes to modeling very large
complexes, so you've often just got "chain", possibly "segname",
and/or combinations with residue indices or residue names/types
to work with, depending on if your structure is entirely experimental
vs. something you built from multiple pieces. That, and of course
you can try and apply "protein" and "nucleic" if they work okay for
your structure.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 11, 2020 at 05:10:07PM +0100, Francesco Pietra wrote:
> Anything quicker that using selectio of index?
> fp
> ---------- Forwarded message ---------
> From: Francesco Pietra <[1]chiendarret_at_gmail.com>
> Date: Tue, Feb 11, 2020 at 4:11 PM
> Subject: Visulizing subunits
> To: VMD Mailing List <[2]vmd-l_at_ks.uiuc.edu>
>
> Hello
> I would appreciate advice as to visualize subunits having only the .pdb
> file for a very large RNA-protein complex (i.e., I cannot rely on segname)
> thanks
> francesco pietra
>
> References
>
> Visible links
> 1. mailto:chiendarret_at_gmail.com
> 2. mailto:vmd-l_at_ks.uiuc.edu 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
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