Hi,
In my experience, Modeller is not the best program for what you are trying to do. What worked for me before is reconstructing all coordinates from the C-alpha trace (using, say, MaxSprout at http://www.ebi.ac.uk/maxsprout/) and then optimizing side-chains with SCWRL (http://dunbrack.fccc.edu/SCWRL3.php). This procedure will not move C-alpha atoms and is much faster. I have read a paper not too long ago (can't remember the exact reference, sorry) making a convincing claim that SCWRL is currently the best program for side-chain optimization - somebody on the list please correct me if that's not the case.
Cheers,
Mensur
On Tue, 8 Jun 2004, Alejandra Leo wrote:
|>Hi all, |> |>I have a problem using Modeller and maybe someone could give a hand. |> |>I have my alignment (ecoli-FINAL.pir), my query sequence |>(Nei1Ecoli_exp), and as structural template I have a trace of |>C-alpha atoms (E_Coli_Test85) that is very important that do not move from their |>initial positions. The only thing I want to do is to add the other atoms needed to |>complete the backbone to my C-alpha trace.
========================================================================== | Mensur Dlakic, Ph.D. | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | http://www.umich.edu/~mensur/ | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic@montana.edu | ==========================================================================