VMD-L Mailing List

From: Cojocaru, Vlad (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Thu Aug 18 2011 - 14:46:45 CDT

You can write connect records to the pdb file to indicate which residue is
connected with which.
Then you can use bonds or dynamic bonds to visualize.
You can color the residues by secondary structure.

It's not exact cartoon or ribbons but it's good to see secondary structures.

A script to add connect records to coarse grained pubs can be found in the
manuscript "Structure and dynamics of cytochrome p450 2c9" just published
last week in plos computational biology (see protocol S2 in supporting
information)

Greetings
Vlad

Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]mpi-muenster.mpg.de

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu on behalf of Davide Provasi
Sent: Thu 18/08/2011 20:00
To: Mert Gür
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: How can I draw secondary structures if I only have the
carbon alpha coordinates
 
Hi-
one possible solution is to rebuild the backbone from the calpha positions.
a number of tools are available to do that.
for example http://www.pirx.com/pulchra/index.shtml

hope this helps,
Davide 

-- 
Davide Provasi
Dept. of Structural and Chemical Biology
Mount Sinai School of Medicine
Icahn Medical Institute Building
1425 Madison Avenue, Box 1677
New York, NY 10029-6574
Tel.:212-659-8618
Fax: 212-849-2456
On Thu, Aug 18, 2011 at 7:20 PM, Mert Gür <gurmert_at_gmail.com> wrote:
> Dear John,
>
> Is there no way to trick VMD so that it can do it ?
>
> Best,
>
> Mert
>
>
>
> On Thu, Aug 18, 2011 at 12:48 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>>
>> Hi,
>>  VMD needs more than just the C-alpha atoms in order to draw
>> either Cartoon or Ribbons representations, because it looks for
>> oxygen atoms to determine the orientation of the ribbon cross section.
>> Without this information, VMD can only draw a tube representation.
>>
>> Cheers,
>>  John Stone
>>  vmd_at_ks.uiuc.edu
>>
>> On Thu, Aug 18, 2011 at 11:01:00AM -0400, Mert Gür wrote:
>> >    Dear all,
>> >    I only have  the carbon alpha coordinates of an  adenylate kinase MD
>> >    trajectory.
>> >    I would like to draw/depict the trajectory in VMD with New Ribbons or
>> New
>> >    Carton  representation so that I can see the secondary structures
>> >    visually.
>> >    However, this seems not to be possible. The closest I get to what I
>> want
>> >    is to select the tube representation.
>> >    Does anyone have a solution for this?
>> >    I have the starting full atomistic pdb and psf files of the
>> trajectory.
>> >    Best,
>> >    Mert
>>
>> --
>> NIH Resource 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/       Fax: 217-244-6078
>>
>
>