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: modeller_usage-bounces@salilab.org [mailto:modeller_usage-bounces@salilab.org] Im Auftrag von modeller_usage-request@salilab.org Gesendet: Montag, 12. April 2010 09:09 An: modeller_usage@salilab.org Betreff: modeller_usage Digest, Vol 9, Issue 52

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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)

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Message: 1 Date: Fri, 9 Apr 2010 14:31:35 +0100 From: Thomas Evangelidis tevang3@gmail.com Subject: [modeller_usage] evaluation of a region with DOPE z-score To: modeller_usage@salilab.org Message-ID: r2p833e1faf1004090631n974f1e63j3c927a306ca71ebd@mail.gmail.com 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]