VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Feb 12 2020 - 02:21:55 CST

Hi John
It is an experimental .pdb and has lablels for subunits (chains A, B, C,
etc) but no segname.
I find now, on your suggestion, that <protein> and <nucleic> are useful to
visualize the pathway of ligands (obtained from a smaller model of this
RNA-protein, projecting MD data onto the unabridged RAN-protein, which is
much to big for MD, and also problematic for AutoPSF).

I am no aware of any command, from either "Graphical Representations" or
the "tk Console" for chains A, B, C, D. I can only think to the general ID

thans
francesco

On Tue, Feb 11, 2020 at 5:42 PM John Stone <johns_at_ks.uiuc.edu> wrote:

> 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
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>