Re: [modeller_usage] evaluation of a region with DOPE z-score

["Jan H. Löhr" <>]

Dear Tom,

I am not sure if I understood your problem correctly, but I guess what you
are referring to is the smoothing option (s.assess_dopehr (...
smoothing_window=15)).
I would try turning it off, so the displayed DOPEHR-value of a specific
residue is not "affected by neighboring atoms".

Hope this helps,

Jan


-----Ursprüngliche Nachricht-----
Von: 
[">mailto:] Im Auftrag von

Gesendet: Montag, 12. April 2010 09:09
An: 
Betreff: modeller_usage Digest, Vol 9, Issue 52

Send modeller_usage mailing list submissions to
	

To subscribe or unsubscribe via the World Wide Web, visit
	https://salilab.org/mailman/listinfo/modeller_usage
or, via email, send a message with subject or body 'help' to
	

You can reach the person managing the list at
	

When replying, please edit your Subject line so it is more specific
than "Re: Contents of modeller_usage digest..."


Today's Topics:

   1. evaluation of a region with DOPE z-score (Thomas Evangelidis)
   2. .aln files. (Daniel Fernandez)
   3. Error when reading the alignment PIR file. (Daniel Fernandez)


----------------------------------------------------------------------

Message: 1
Date: Fri, 9 Apr 2010 14:31:35 +0100
From: Thomas Evangelidis <>
Subject: [modeller_usage] evaluation of a region with DOPE z-score
To: 
Message-ID:
	<>
Content-Type: text/plain; charset="iso-8859-1"

Dear Modeller Caretaker,

I have generated several models with different template combinations and
want select the best with regard to some regions of interest (i.e. the ATP
binding site).
 In the case of the binding site my residue selection is not contiguous
(roughly all residues within 10 A. from the ATP). Does the resulting score
make sense? Also if you look into the profile plot you will notice that the
line is also curved in regions outside the binding cavity, and that happens
even if the residue selection is conti. I think DOPE score is affected by
neighboring atoms. If that's true what's the best way to assess a model
region?

thanks,
Tom

PS: the class to evaluate the cavity is pasted below.



from modeller import *
from modeller.parallel import task
from modeller.scripts import complete_pdb
import os

class Evaluate_Cavity(task):
    """A task to evaluate a model with the DOPEHR method"""
    def run(self, template_combination, i):
        log.minimal()    # request minimal output
        env = environ()
        env.libs.topology.read(file='$(LIB)/top_heav.lib') # read topology
        env.libs.parameters.read(file='$(LIB)/par.lib') # read parameters
        # read model file
        mdl = complete_pdb(env,
"/home/thomas2/Documents/PfMDR1_AAA1/new_alignment_"+template_combination+"/
modeller/target.B999900"+str(i)+".pdb")
        # Select all residues except for the loop
        s = selection(mdl.residue_range('8', '20'), mdl.residue_range('34',
'53'), mdl.residue_range('210', '212'), mdl.residue_range('242', '244'),
mdl.residue_range('258', '261'))
        # Assess with DOPE:

os.chdir("/home/thomas2/Documents/PfMDR1_AAA1/new_alignment_"+template_combi
nation+"/modeller/")
        score = s.assess_dopehr(output='ENERGY_PROFILE NO_REPORT',
file="model_"+str(i)+"_"+template_combination+".profile",
                      normalize_profile=True, smoothing_window=15)
        return [str(i), score]