Hi Asim,
The energy scores in modeller are not comparable if you use different sets of restraints i.e. including/excluing disulfide restraints 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 > ************** > > ========================================================================