VMD-L Mailing List
From: Bernardo Sosa Padilla Araujo (bernardospa_at_gmail.com)
Date: Mon Mar 22 2010 - 13:25:35 CDT
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Thanks for the suggestions!
That was really helpful.
Best
Bernardo
2010/3/22 Axel Kohlmeyer <akohlmey_at_gmail.com>
> alternate suggestion (you may need to get v1.1 of the topotools package):
>
> set sel1 [atomselect $mol1 {<enzyme selection>}]
> set sel2 [atomselect $mol2 {<substrate selection text>}]
>
> package require topotools
>
> set mol3 [::TopoTools::selections2mol "$sel1 $sel2"]
>
> animate write psf merged.psf $mol3
> animate write pdb merged.pdb $mol3
>
> this works for an arbitrary number of selections (unless you run out of
> memory).
>
> please note that neither approach checks for atom overlaps.
> therefore you have to choose your selections carefully.
>
> cheers,
> axel.
>
> On Mon, Mar 22, 2010 at 12:05 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > Hi,
> > You may find it easier to first write out the structure that you move
> > to a new file, and then simply use the "mergestructs" plugin, or merge
> them
> > then move and write a new file, whichever works best for your intended
> purpose:
> > http://www.ks.uiuc.edu/Research/vmd/plugins/mergestructs/
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Fri, Mar 19, 2010 at 09:29:56PM -0700, Bernardo Sosa Padilla Araujo
> wrote:
> >> Hi All,
> >>
> >> I have two pdb files:
> >>
> >> -one of them with an enzyme and its substrate
> >> -the second one only has a very similar substrate( no enzyme)
> >>
> >> I want to load both pdbs, align the substrate from the second pdb to
> the
> >> substrate in the first pdb, and finally write a pdb file containing
> the
> >> enzyme (from the first pdb) and the substrate from the second pdb
> but in
> >> the same position(with respect to the enzyme) as the substrate in the
> >> first pdb.
> >> I have in mind this script :
> >>
> >> #molecule 0 is the enzyme +substrate
> >> #molecule 1 is the other substrate
> >> #BAS is the resname of the substrate
> >>
> >> # Create a reference structure
> >> set ref [atomselect 0 "resname BAS"]
> >>
> >> # Create a selection to align
> >> set sel [atomselect 1 "resname BAS"]
> >>
> >> # Move molecule 1 onto molecule 0
> >> set all [atomselect 1 all]
> >> $all move [measure fit $sel $ref]
> >>
> >> In order to use writepdb I need to have everything in one selection,
> but I
> >> don't know how to put structures form different pdb in one vmd
> slection.
> >> Does anyone know how to do/circunvent this ?
> >> Thanks a lot in advance,
> >>
> >> Bernardo
> >>
> >>
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/> Fax: 217-244-6078
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
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