VMD-L Mailing List

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Tue Feb 20 2007 - 14:52:36 CST

The point was in using the correct tool for each kind of job. The
suggestion was to look for and homology modelling program, not
neccesarily MODELLER. If you like you can use DeepView (formerly
SwissPDBViewer) with acceptable results. Surely there are also many
servers that might help on building an homology models for proteins.
Regards
Cesar

Brian Bennion escribió:
> Hello,
>
> It might be wiser to use another program, but modeller is very
> expensive for non academics. If one only needed to fill in missing
> loops (small) or atoms from residues VMD can help. Just make the
> atomselections appropriately, "move'" the template, and then save the
> resulting coordinates for the missing density.
>
> Then you would have to do some hand editing of a pdb file to include
> the appropriate atoms (residues).
> Granted it takes a few more steps than modeller, but for a situation
> like this it is worth the money.
>
> A more flashy way to do this is use the following website (unpaid
> promotion ;) )
> http://as2ts.llnl.gov/AS2TS/LGA/lga.html
>
> Brian
>
>
>
> At 10:56 AM 2/20/2007, John Stone wrote:
>> Hi,
>> Yes, I don't think there's a good way of doing this without the
>> use of other packages, and it certainly sounds like homology modeling
>> is what he's actually after.
>>
>> John
>>
>> On Tue, Feb 20, 2007 at 03:43:52PM -0300, Cesar Luis Avila wrote:
>> > May be you would prefer to use some homology modelling program like
>> > MODELLER for that task.
>> > Regards
>> > Cesar
>> >
>> > bertrand russell escribió:
>> > >
>> > >Dear VMD users,
>> > >
>> > >I want to superimpose two structures and trying to get the
>> coordinates
>> > >of missing atoms in one structure with that of the reference. Is it
>> > >possible to do with VMD. It would be of great help if somone could
>> > >help me to do this. Many thanks in advance.
>> > >--
>> > >Live Life; Don't pass it
>> > >Bertrand.P.S.Russell
>> > >+91-9894398441
>>
>> --
>> 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
>