VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 31 2006 - 16:27:21 CST

Margaret,
  Does the structure you're loading have BIOMT records in it, or does
it only contain crystallographic symmetry records? The script I sent
only handles the BIOMT records and not the SMTRY records, though it could
likely be changed to read and process those as well.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Mar 31, 2006 at 05:19:20PM -0500, Margaret Shun Cheung wrote:
>
> Dear John,
> Thank you for the second script. The first one didn't work out for me.
> but when I use your pdb example 1c8e.pdb, it works.
> I'll try this one again.
> Thanks.
> Margaret
>
> On Fri, 31 Mar 2006, John Stone wrote:
>
> >Hi,
> > I've attached another version of the script which will auto-generate
> >chain ID codes if you don't provide a list of codes to go with each
> >monomer transformation matrix, this should be a bit easier to use than
> >the last one. (see attached script)
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Fri, Mar 31, 2006 at 03:52:08PM -0600, John Stone wrote:
> >>Hi,
> >> I've got a VMD script that Mashaojienuaa sent to me which
> >>reads the BIOMT records from a PDB file, applies the appropriate
> >>transformations to them, and writes out a new PDB file with the
> >>complete structure. I tested it on the the 1c8e virus structure
> >>and was able to get it to work after commenting out the line of code
> >>he's got that assigns a new chain ID to each of the transformed
> >>monomers (this could be fixed in a few minutes of work so that it
> >>auto-generates its own chain list when not specified explicitly..)
> >>If you want to assign the chains to the the transformed monomers, you'll
> >>want to enable that code again (it's marked with an XXX comment next
> >>to it) and you'll need to specify a chain list of the same length as
> >>the number of transformed monomers it's going to create.
> >>
> >>I used it like this:
> >> source mono2poly.tcl
> >> mol new 1c8e.pdb
> >> set sel [atomselect top all]
> >> set matrix [parsematrix 1c8e.pdb]
> >> mono2poly -o outname $sel $matrix
> >>
> >>
> >>The script is attached to this email.
> >>
> >>Enjoy,
> >> John Stone
> >> vmd_at_ks.uiuc.edu
> >>
> >>On Fri, Mar 31, 2006 at 03:33:51PM -0500, Margaret Shun Cheung wrote:
> >>>Dear VMD wizards,
> >>>
> >>>I downloaded a structure from PDB, but it only includes the monomeric
> >>>structure from its multimeric native structure (it's from X-ray).
> >>>Is there a script for VMD to reinstate its symmetry and give back its
> >>>multimeric coordinates?
> >>>Thanks!
> >>>Sincerely,
> >>>Margaret S. Cheung,
> >>>Ph. D. Postdoctoral Fellow,
> >>>
> >>>------------------------------------------------------------
> >>>Room 2117 Tel: (301) 405-4892
> >>>Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
> >>>University of Maryland http://glue.umd.edu/~mscheung
> >>>College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
> >>>------------------------------------------------------------
> >>
> >>--
> >>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/ Fax: 217-244-6078
> >
> >
> >
> >--
> >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/ Fax: 217-244-6078
> >
>
> Margaret S. Cheung,
> Ph. D. Postdoctoral Fellow,
>
> ------------------------------------------------------------
> Room 2117 Tel: (301) 405-4892
> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
> University of Maryland http://glue.umd.edu/~mscheung
> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
> ------------------------------------------------------------ 

-- 
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/      Fax: 217-244-6078