Hi Hailong,
I include a recent message about the inadequacy of modeller scores when
comparing models generated with different sets of restraints.
If you want to evaluate your model you can use a wide variety of external
programs:
http://salilab.org/modeller/methenz/
best
Andras
Andras Fiser wrote:
>
> Hi Asim,
>
> The energy scores in modeller are not comparable if you use different sets of
> restraints i.e. including/excluing disulfide restrainst in your case.
>
> Scores only from the same run i.e. by generating several models, can be
> compared.
>
> otherwise the overall energy score is included in the header of the coordinate
> file as "REMARK MODELLER OBJECTIVE FUNCTION: "
>
> Best,
>
> Andras
>
> please take advantage (so others can benefit too) of our modeller user list if
> you have other questions.
> http://salilab.org/cgi-bin/lwgate/lwgate/MODELLER_USAGE/
>
> Asim Kumar Debnath wrote:
> >
> > Hi Andras:
> > I have modeled a protein using your program Modeler. The target
> > sequence has two cystine residues which may form a disulfide bond but
> > there is no experimental evidence on that. I have modeled both without a
> > disulfide bond and with a disulfide bond (by using special_patches
> > subroutine). Now I want to compare which one is the energetically best
> > probable structure between these two.
> > I would greatly appreciate if you could give some advise how to
> > proceed in Modeler to find out which one is the most likely model. How
> > do I get the overall energy of the 3D-model in your program?
> > Thank you in advance for your help.
> > Regards,
> >
> > Asim
> >
> > =======================================================================
> >
> > ***
> > *** Asim K. Debnath, Ph.D.
> > **** Associate Member
> > **** Lindsley F. Kimball Research Institute
> > **** *** The New York Blood Center
> > **** **** 310 E 67 Th Street
> > **** ** **** New York, NY 10021
> > **** **** **** Tel. (212) 570-3373
> > **** ** **** Fax. (212) 570-3299
> > **************** E-mail:
> > **************
> >
> > ========================================================================
>
> --
> ,
> Andras Fiser, PhD # phone: (212) 327 7216
> The Rockefeller University # fax: (212) 327 7540
> Box 270, 1230 York Avenue # e-mail:
> New York, NY 10021-6399, USA # http://salilab.org/~andras
Hai-Long Wang wrote:
>
> At 02:20 PM 6/22/2001 -0400, you wrote:
> Hi, Andras
>
> My protein has several disulf bonds. I had tried modeller to built model
> protein both with patch and without patch command. When the patch command
> not include, the disuf bonds are not there, but it has overall higher
> score. Is there any way in modeller to rebuilt the disuf bonds and keep the
> rest unchange?
>
> Thank you.
>
> Hailong
> ******************************************************************************
> Hai-Long Wang Ph.D. Tel: (507)284-5297
> Receptor Biology Laboratory Fax: (507)284-9420
> 1-149, Medical Science Building email:
> Mayo Foundation
> Rochester, MN 55905
> ****************************************************************************
> **
--
,
Andras Fiser, PhD # phone: (212) 327 7216
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras