VMD-L Mailing List

From: Michael Robinson (michael.robinson1_at_monash.edu)
Date: Mon Sep 26 2022 - 08:53:11 CDT

Hi Amanda,

Josh has provided an alternative way to get what you need, but for the sake
of completeness I'll provide my answer as well. When it comes to deleting
selected chains, I think the easiest way would be just to create a
selection that doesn't include the chains you want deleted, and then use
writepdb and writepsf to create files without them present. If you just
want the analysis to only run on your chain of interest, we should just be
able to tweak the analysis script to only run on that chain. In either
case, we need to be able to tell VMD what areas you're interested in and
what areas you aren't. If the chains are identical in amino acid sequence,
but aren't connected to each other with a covalent linkage when you view it
in VMD with the .psf file loaded, we can do that pretty easily. Instead of
using resid or resname to select the chain of interest, we can use the atom
index - simply go to the chain you want to run analysis on in VMD, select
one of the atoms, and look in the console you opened VMD from. It'll list
some information about the atom there, including the index of the atom - a
unique number for any given atom in your .pdb file.

Then, the selection "same fragment as index [number here]" should be able
to select only your chain of interest. You can either write out a file with
only that chain and the water and ions (set sel [atomselect top "(same
fragment as index xyz) or water or ions"), or just change the protein
selection in your script to "same fragment as index xyz". If your system
has covalent bonds between the chains, a different approach will be needed.

Regards,
Michael Robinson

On Mon, 26 Sept 2022 at 22:36, Amanda Jenkins <
amanda.jenkins1379_at_outlook.com> wrote:

> Hi Michael,
>
> Thanks for your input. On the topic of the three distinct chains,
> unfortunately the three chains are identical in amino acid sequence so
> there is no unique amino acid or sequence of amino acids in my chain of
> interest to distinguish it from the other chains. Would you have any
> advice on how to outright delete selected chains when one is in VMD? I'm
> hoping that if I delete the other chains, but leave my chain of interest
> along with the solvent and solute molecules (which appear to be necessary
> in order to properly calculate the Ramachandran angles), then maybe I can
> calculate the dihedral angles I need without mixing them with the
> Ramachandran angles of the chains I don't need. Thanks.
>
> Amanda J.
> ------------------------------
> *From:* Michael Robinson <michael.robinson1_at_monash.edu>
> *Sent:* Sunday, September 25, 2022 11:58 PM
> *To:* Amanda Jenkins <amanda.jenkins1379_at_outlook.com>
> *Cc:* vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
> *Subject:* Re: vmd-l: Ramachandran Dihedral Angles Suspiciously Constant
>
> Hi Amanda,
>
> Just quickly jumping in here, as I suspect I can help with these questions:
> - If you have three distinct, unconnected chains and only wish to perform
> analysis on one of them, but the chain naming has them as the same chain,
> you can use some of the more advanced selection language. Setting a
> selection of something like "same fragment as [a unique identifier that
> only occurs in chain C, perhaps a specific resid + resname combination]"
> will select the continuous set of connected atoms from that unique
> identifier. You can even use this to fix the chain naming, if you want to
> do it that way - create that selection in the TCL console and then set the
> chain name back to chain C and write updated .psf and .pdb files.
> - When it comes to the selection for GLY311 also showing water and ion
> atoms, it might be worth double checking how you're selecting the residue--000000000000e2776605e994d980--