Re: [modeller_usage] scoring function and optimization
To: sdimicco <>
Subject: Re: [modeller_usage] scoring function and optimization
From: Modeller Caretaker <>
Date: Tue, 11 Dec 2012 13:01:20 -0800
Cc:
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.