VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Feb 12 2020 - 03:54:49 CST

Please forget about that. Save Visualiation State works well also with the
huge RNA-protein once my mistakes were corrected.
francesco

---------- Forwarded message ---------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Wed, Feb 12, 2020 at 9:31 AM
Subject: Fwd: vmd-l: Fwd: Visulizing subunits
To: John Stone <johns_at_ks.uiuc.edu>, VMD Mailing List <vmd-l_at_ks.uiuc.edu>

I forgot to mention that, with the unabridged RNA-protein, the ligand
pathways (highlighted by coloring vivinal residues in various forms -
bonds, wdw, etc - onto the RNA-protein as new carton) could not be saved
with "Save Visualization State", i.e. all that highlighted was not saved.
In contrast, all that worked well with the smaller model of RNA-protein.
Saving as image.tga worked well in all cases.
francesco

---------- Forwarded message ---------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Wed, Feb 12, 2020 at 9:21 AM
Subject: Re: vmd-l: Fwd: Visulizing subunits
To: John Stone <johns_at_ks.uiuc.edu>, Francesco Pietra <chiendarret_at_gmail.com>,
VMD Mailing List <vmd-l_at_ks.uiuc.edu>
Cc: VMD Mailing List <vmd-l_at_ks.uiuc.edu>

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/
>