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Re: [modeller_usage] scoring function and optimization



On 11/21/2012 08:08 AM, sdimicco wrote:
1) As I changed the optimization protocol, I woul dlike to check if my
set up has been done. Where could I check it?

I'm not sure what you mean here. Look in the log file?

2) I am building a multimeric protein. The DOPE and GA341 scores are
developed for single chain models. How can I asses the quality of my
models? The sole molpdf is sufficient?

molpdf just shows you how closely the model satisfies the restraints. It doesn't tell you whether the restraints themselves encode for a good model. We don't have any assessment scores that are tested on multimeric proteins.

3) I found thie messagge in the log file:

               Treating residue type  GSH as a BLK (rigid body)
               even though topology information appears to be at least
               partially available. To treat this residue flexibly
               instead, remove the corresponding 'MODELLER BLK RESIDUE'
               REMARK from the input PDB file.

I have understood that the input PDB file is the .ini, which is written
during the calculation. Thus, how can I "remove the corresponding
'MODELLER BLK RESIDUE" to treat the residue flexible? Have I to define
it as my own residue?

If you want to treat the residue flexibly, add its one-letter code to your alignment rather than using the '.' code. For most ligands, '.' (BLK) is quite sufficient, however.

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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