VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Feb 12 2020 - 11:14:57 CST

Sometimes one makes the matter more complicate than it is, and this
happened to me.

Yes, "chain A" in Graphical Representation/Selected Atom works nicely and
takes the color that one wants.

I have a long list of possible selections with VMD, clearly is not long
enough.

thanks a lot
francesco

On Wed, Feb 12, 2020 at 4:53 PM John Stone <johns_at_ks.uiuc.edu> wrote:

> 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,
> > Â John Stone
> > Â [2]vmd_at_ks.uiuc.edu
> >
> > On Tue, Feb 11, 2020 at 05:10:07PM +0100, Francesco Pietra wrote:
> > >Â Â Anything quicker that using selectio of index?
> > >Â Â fp
> > >Â Â ---------- Forwarded message ---------
> > >Â Â From: Francesco Pietra <[1][3]chiendarret_at_gmail.com>
> > >Â Â Date: Tue, Feb 11, 2020 at 4:11 PM
> > >Â Â Subject: Visulizing subunits
> > >Â Â To: VMD Mailing List <[2][4]vmd-l_at_ks.uiuc.edu>
> > >
> > >Â Â Hello
> > >Â Â I would appreciate advice as to visualize subunits having
> only
> > the .pdb
> > >Â Â file for a very large RNA-protein complex (i.e., I cannot
> rely on
> > segname)
> > >Â Â thanks
> > >Â Â francesco pietra
> > >
> > > References
> > >
> > >Â Â Visible links
> > >Â Â 1. mailto:[5]chiendarret_at_gmail.com
> > >Â Â 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/Â Â Â Â Â Â Phone:
> 217-244-3349
> > [8]http://www.ks.uiuc.edu/Research/vmd/Â Â Â
> >
> > 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/
>