VMD-L Mailing List

From: Simon Dürr (simon.duerr_at_uni-konstanz.de)
Date: Tue Aug 02 2016 - 09:53:50 CDT

I have now renamed the atoms in vmd and after mol reanalyze the structure
gets (somewhat) recognized as nucleic
I can use atomselect "nucleic" to select the segment and "backbonetype
nucleicback" results only in the backbone of my segment.

However I can't use the NewCartoon representation and mol reanalyze says
there are 2 nucleic segments but there should be 3.
What else do I have to change ? Atom types?

The atom names in my segment now are:
C4' O4' H4' C1' C2' H1' H2'' O2' H2' C3' O3' H3' P O5' O2P O1P C5' C4' H5'
H5'' H4' O4' C1' H1' C2' O2' H2'' H2' C3' O3' H3' H3T N1 C2 O2 N3 C4 H3 O4
C5 C6 H5 H6 N1 C6 H6 C5 C4 H5 N3 C2 O2 N4 H42 H41 C5' O5' H5'' H5' P O3'
O2P O1P C3' C2' H3' H2'' C1' O4' H1' C4' C5' H4' H5'' H5' O5' P O1P O2P O5T
N9 C8 H8 N7 C5 C4 N3 C2 N1 H2 C6 N6 H61 H62 O2' H2'

and the residues are Ade - Cyt - Ura

Cheers,
Simon

2016-08-02 13:01 GMT+01:00 Simon Dürr <simon.duerr_at_uni-konstanz.de>:

> Hi list,
>
> I have added an extra segment to my system which is a part of nucleic acid
> double helix but with different atom names and VMD therefore does not
> recognize it as nucleic when loading the structure.
> Before I create a script to rename all the atoms with vmd and then
> reanalyzing the structure is there an easier way to tell vmd that this is
> nucleic acid and should be rendered with cartoon?
>
> If I did it with a script: Do I only have to change the atom name or also
> the atom type for VMD to recognize it as nucleic ?
> $sel set name NucleicAtomName
> mol reanalyze $mol
>
> Cheers,
> Simon
>