Dear BIN ZHANG, MODELLER based on your constructed alignment file parsing the reliable template residues mapped against the target ones, constructs and fixes the average alpha carbon backbone (if you choose a single template) or an average backbone topology (for Multiple templates' local aligned chunks). Then it fits in the side chains and backbone atoms to make the model complete. However, easy saying but really a vicious circle problem, the alignment could have actually been wrong to incorrectly fit target against parsed template residues. Regardless of the earlier problems, On increased sampling, MODELLER tries best to satisfy the Lennard Jones and all the energetic equations composing its DOPE energy function. The non-physical local atomic clashes are thus minimized with every such iteration. So only you see, Restraints earlier, now with end of every such iterative step. That in fact, is the trial to leap the energetic landscape, precisely focusing on the probably erroneous regions encompassing the higher local steric clashes.

The story continues until the number of iterations are over.

Ashish

Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

Message: 1 Date: Sun, 8 Apr 2012 23:58:13 -0700 From: BIN ZHANG zhngbn@gmail.com To: modeller_usage@salilab.org Subject: [modeller_usage] In what are the initial structures different? Message-ID: 602A5241-132A-4319-81BA-94C238A459AF@gmail.com Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

Dear All:

I have a question about the differences of the initial structure built for homology modeling. Can anyone tell me how exactly are these initial structures different? Do they differ in the secondary structures in uncertain regions? I cannot find this information in the manual.

For example, by using

a = automodel() a.starting_model = 1 a.ending_model = 50

I can built 50 different homology models starting from different initial structures, but I have want to know how these different initial structures are constructed.

Thanks very much for help.

Best, Bin