Re: [modeller_usage] Question about Make_restraints

[Mensur Dlakic <>]

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.


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