From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 12 2020 - 09:52:36 CST

Did you try just using "chain A" as part of your selection rather
than having to use the atom indices? That should have worked...
You should also be able to color by "chain". Is there some reason
that isn't working for you?

Best,
  John

On Wed, Feb 12, 2020 at 11:19:01AM +0100, Francesco Pietra wrote:
> Hi John
> Answering again to remove confusion that I introduced.
> 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).
> At this point, with protein and nucleic as New Carton, in different
> colors, and residues near the traveling ligand highlighted as wdw, I
> opened the tk console, commanding
> set sel [atomselect top "index 1 to 67355"]
> in order to select chain A, which is nucleic. But found no way to assign a
> new color to this chain. Can selection by "Graphical Representation" be
> mixed with selection from the "tk console"?
> francesco
> On Tue, Feb 11, 2020 at 5:42 PM John Stone <[1]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
> [2]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][3]chiendarret_at_gmail.com>
> > Date: Tue, Feb 11, 2020 at 4:11 PM
> > Subject: Visulizing subunits
> > To: VMD Mailing List <[2][4]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:[5]chiendarret_at_gmail.com
> > 2. mailto:[6]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
> [7]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [8]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. mailto:vmd_at_ks.uiuc.edu
> 3. mailto:chiendarret_at_gmail.com
> 4. mailto:vmd-l_at_ks.uiuc.edu
> 5. mailto:chiendarret_at_gmail.com
> 6. mailto:vmd-l_at_ks.uiuc.edu
> 7. http://www.ks.uiuc.edu/~johns/
> 8. http://www.ks.uiuc.edu/Research/vmd/

-- 
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/