VMD-L Mailing List

From: Davide Provasi (davide.provasi_at_gmail.com)
Date: Thu Aug 18 2011 - 13:00:15 CDT

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
>>
>
>