>Message: 2 >Date: Thu, 22 Mar 2012 13:26:35 +0800 (SGT) >From: rjayashree13-science@yahoo.co.in >To: modeller_usage@salilab.org >Subject: [modeller_usage] loop refinement >Message-ID: > 1332393995.15170.YahooMailClassic@web193505.mail.sg3.yahoo.com >Content-Type: text/plain; charset="utf-8" > >There is a script (loop.py) for the refinement of an existing model which requires the user to specify the residues to be optimized. > >How can one decide which residues need refinement? > > >Dr. Jayashree Ramana

You will find a nice example in the modeller tutorial. Hoping you may better grasp the general idea, I am attempting to rephrase the gist: The residues that need to be refined usually have a high energy. Probably because your alignment was not optimal in this position, or because you do not have any information from the template(s) because of missing residues in the templates PDB or because of an insertion in the target sequence. So when you align your template and your modeller structure in a molecular imaging program you will probably see that some residues in your model do not have a corresponding template residue (naturally, this is obvious from sequence alignment as well). When there is no information from the template, modeller cannot do comparative modeling and therefore these residues will probably not be modeled well. These residues (along with residues that have been poorly modeled for other reasons) are easily spotted by the assessment-methods within modeller. I recommend looking at an energy profile such as the DOPE profile. Comparing the graphs of template and model, you will see residues that need optimization (residues whose DOPE-pseudoenergy is much higher for the model than for the template). Be careful though – because of different residue lengths of template and target the DOPE profiles are not always strictly superimposable – for corresponding residues may not have the same number (again because of insertions, missing residues, etc.). Summing up: You may already know the residues. Look at the alignment and identify regions where the template provides no information for your target. Try to identify these and possibly other problematic regions by using the assessment methods and obtain the DOPE profile. Actually, the answers you seek are in the end of tutorial 1 ("Basic Modeling") and at the beginning of tutorial 2 ("Advanced Modeling) along with code examples to assess your model at http://salilab.org/modeller/tutorial/.

That should do the trick.

Cheers Jan

Jan H. Löhr Univ. Hamburg, Germany

-----Original Message----- From: modeller_usage-bounces@salilab.org [mailto:modeller_usage-bounces@salilab.org] On Behalf Of modeller_usage-request@salilab.org Sent: Thursday, March 22, 2012 3:55 PM To: modeller_usage@salilab.org Subject: modeller_usage Digest, Vol 11, Issue 32

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Message: 2 Date: Thu, 22 Mar 2012 13:26:35 +0800 (SGT) From: rjayashree13-science@yahoo.co.in To: modeller_usage@salilab.org Subject: [modeller_usage] loop refinement Message-ID: 1332393995.15170.YahooMailClassic@web193505.mail.sg3.yahoo.com Content-Type: text/plain; charset="utf-8"

There is a script (loop.py) for the refinement of an existing model which requires the user to specify the residues to be optimized.

How can one decide which residues need refinement?

Dr. Jayashree Ramana