This is not a python solution, perhaps there is one, but what I did was to write a bash shell script to modify the python script changing the name of the model consecutively (might have to be modified for other shells):

# DOPE for c in 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15; do sed 's/NAME/Model_'${c}'/g' model-DOPE.py > tmp.py; mod9v4 tmp.py ; echo "Model "${c}": ";grep 'DOPE' tmp.log >> Models_DOPE.dat; done

In the python script (model-DOPE.py in my case) replace the line mdl = complete_pdb(env, '1acb.pdb') with mdl = complete_pdb(env, 'NAME.pdb')

your previously built models should be named sequentially Model_01 to Model_15 (or the last one in your case), or change the regexp in the sed command above according to your file naming. At the end you'll have a list of DOPE values in the file Models_DOPE.dat.

Hope this helps...

Message: 1 > Date: Thu, 27 Nov 2008 10:03:30 +0800 > From: "jinlian" jinlian05@lzu.cn > Subject: [modeller_usage] dope batch processing > To: modeller_usage@salilab.org > Message-ID: 427750030.20199@lzu.cn > Content-Type: text/plain; charset="us-ascii" > > Hi all > > I want to use the 'DOPE' to do the filtering the docking structure of > thousands of proteins, and I want to do batch possessing, but the script > can > only calculate one structure: > > > from modeller import * > from modeller.scripts import complete_pdb > > env = environ() > env.libs.topology.read(file='$(LIB)/top_heav.lib') > env.libs.parameters.read(file='$(LIB)/par.lib') > > # Read a model previously generated by Modeller's automodel class > mdl = complete_pdb(env, '1acb.pdb') > > # Select all atoms in the first chain > atmsel = selection(mdl.chains[0]) > > score = atmsel.assess_dope() > > I am not familiar with python, Could you tell me how to do the batch > processing in the above script? > Thank you very much! >