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: asim_debnath@nybc.org > > ************** > > > > ======================================================================== > > -- > , > Andras Fiser, PhD # phone: (212) 327 7216 > The Rockefeller University # fax: (212) 327 7540 > Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu > 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: wang.hailong@mayo.edu > Mayo Foundation receptor293@yahoo.com > Rochester, MN 55905 > **************************************************************************** > **