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You can also give it a shot with CaspR
http://igs-server.cnrs-mrs.fr/Caspr/index.cgi
It will also generate some homology models similar to what you gave it
as input coordinates.
Alternatively run a molrep script in a foreach loop.
Good luck,
Juergen
something like this:
#!/bin/tcsh -f
# usage brute_MR. [RFree dataset] [resolution] [expected monomers]
[expected solvent]
set data = ${1}
set reso = ${2}
set mono = ${3}
set solvent = ${4}
set models = `ls *pdb`
foreach sim_in ( 0.8 0.5 )
foreach compl_in ( 0.8 0.5 )
foreach model ( ${models} )
set sim=${sim_in}
set compl=${compl_in}
molrep hklin ${1}.mtz \
MODEL ${model} <<stopmr > ${model}_${sim}_${compl}.log
DOC Y
LABIN F=F SIGF=SIGF
SURF Y
NMON ${mono}
COMPL ${compl}
SIM ${sim}
RESMAX ${reso}
RES_R 30.0
NP 10
NPT 10
MODE M
STICK Y
END
stopmr
mv molrep.pdb Results/${model}_${sim}_${compl}.pdb
mv molrep.doc Results/${model}_${sim}_${compl}.doc
end
end
Jiamu Du wrote:
Thanks.
I will contact Fitzgerrald soon.
My purpose is to use Merlot for screening about 100 potential
model against my data and then determine the best model for molecular
replacement. But I can not find other program or webserver to do this.
Does anyone know any other program can do this?
On 8/17/06, *Fred. Vellieux* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
On Thu, 17 Aug 2006, Jiamu Du wrote:
> Dear All:
> I want to download an old program Merlot, which is a program for
determine
> the best search model for molecular replacement.(see ref. *J. Appl.
> Cryst.*(1988). 21, 273-278 ).
> But I can not find the homepage or the download site for this
program.
> Is there anyone can help me download this program, or tell me
some other
> program or webserver have the same function?
> Thanks.
You could try contacting the author(ess) of the program suite, Paula
Fitzgerald who is at Merck. BTW Merlot is a molecular replacement
suite of
programs, perhaps there are alternative approaches to generate a
suitable
molecular replacement model. I don't know if Merlot has survived the
disappearance of the Digital Equipment Corporation computers and
associated VMS OS (which survives in a few places though).
Anyway the e-mail address is:
Paula_Fitzgerald at Merck.com <http://Merck.com>
As usual replace the ' at ' by the correct sign.
Fred.
--
s-mail: F.M.D. Vellieux (B.Sc., Ph.D.)
Institut de Biologie Structurale J.-P. Ebel CEA CNRS UJF
41 rue Jules Horowitz
38027 Grenoble Cedex 01
France
Tel: (+33) (0) 438789605
Fax: (+33) (0) 438785494
e-mail: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
--
Jiamu Du
Key Laboratory of Proteomics
Institute of Biochemistry and Cell Biology Shanghai Institutes for
Biological Sciences
Chinese Academy of Sciences (CAS)
--
Jürgen Bosch
Howard Hughes Medical Institute and
University of Washington
Dept. of Biochemistry, K-418
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4542
FAX: +1-206-685-7002
