The interpretation below makes all the sense. The aligned parts of the template structures need to be similar to each other.
Regards, Andrej
-- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4258 Email sali@salilab.org; Web http://salilab.org
> -----Original Message----- > From: Guittet, Muriel [mailto:Guittet@vegmail.ucdavis.edu] > Sent: Wednesday, May 21, 2003 9:15 AM > To: Ben.Tehan@vcp.monash.edu.au > Cc: sali@salilab.org > Subject: RE: error STDEV < 0: > > > Hi, > This is not a huge help, but I encountered that problem too > when using different templates which do not belong to the > same family. Their structures were too far from each other in > some parts of the sequence. Actually, they were kinases and > the alignment of the kinase domain was not so bad but the > beginning of the sequence was very different in each > template. I could run modeller with these different templates > by using all the templates I wanted for the kinase domain but > just that with the best alignment for the beginning of the > sequence. Anyway, even if it ran, the log file pointed out > many problems (in the check alignment command, in the > restraints violations..) as well as the Procheck report... I > decided , but maybe I am wrong, to use only one template (or > all those of the same family) for the major part of the model > and if necessary, some parts of other templates if I had > important gaps with the major template. Best regards Muriel > > -----Original Message----- > From: Andrej Sali [mailto:sali@salilab.org] > Sent: Tue 5/20/2003 1:40 PM > To: 'Benjamin Tehan' > Cc: modeller_usage@salilab.org > Subject: RE: error STDEV < 0: > > > > Hi, > > I hope you do not mind I cc-ed modeller_usage here. > > I am guessing you are using more than one template > structure. If so, the > problem probably arises because the input alignment > aligns a distance in the > target sequence with two or more distances in the > template structures that > are very different from each other. I suggest that you > use the output of > CHECK_ALIGNMENT to follow up on this suggestion and, if > appropriate, edit > the alignment of the structures with each other so that > pairs of aligned > residues in known structures do not span very different > distances. > > Best regards, Andrej > > -- > Andrej Sali, Professor > Departments of Biopharmaceutical Sciences and > Pharmaceutical Chemistry, and > California Institute for Quantitative Biomedical Research > Mission Bay Genentech Hall > 600 16th Street, Suite N472D > University of California, San Francisco > San Francisco, CA 94143-2240 (CA 94107 for direct > delivery by courier) > Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 > Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, > 4233, 4258 > Email sali@salilab.org; Web http://salilab.org > > > > -----Original Message----- > > From: Benjamin Tehan [mailto:Ben.Tehan@vcp.monash.edu.au] > > Sent: Tuesday, May 20, 2003 1:19 AM > > To: sali@salilab.org > > Subject: error STDEV < 0: > > > > > > Dear Professor Sali, > > > > I am having a problem in regards to > > > > Two basis restraints have means too far apart: > > error STDEV < 0: > > > > I noted on the mailing list that someone else had encountered > > this problem and you advised them to modify file > > $MODINSTALL6v2/modlib/messages.lib > > by adding @S1 to the end of > > M 644 3 1 > > etc... > > > > I have not been able to find a response to this this problem > > and thus have attached the log file that I recieved as output. > > > > I would appreciate any advice that you are able to give me in > > regards to this matter. > > > > yours sincerely, > > Ben Tehan. > > > > PhD student > > Monash University > > Australia. > > > > > > >