June 2014 - modeller_usage

'environ' is not defined error
by Sajeewa Pemasinghe 30 Jun '14

30 Jun '14

Hi everyone, I am working on the tutorial http://salilab.org/modeller/wiki/Missing%20residues I am trying to run the script 1qg8_getseq.py which has # Get the sequence of the 1qg8 PDB file, and write to an alignment file code = '1qg8' e = environ() m = model(e, file=code) aln = alignment(e) aln.append_model(m, align_codes=code) aln.write(file=code+'.seq') I get the following error. File "1qg8_getseq.py", line 4, in <module> e = environ() NameError: name 'environ' is not defined Looks like python is not reading the modeller libraries. Could you please advise how to solve this error? Thank you Sajeewa Dewage

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Heme out in space
by Joel Tyndall 16 Jun '14

16 Jun '14

Hey Ben, I've been generating some models of some cytochrome proteins with heme. I have generated ~6 structures that are all fine but the next two have the heme placed out in space relative to the protein. I have seen this before but have put it down to user error. Now I'm not so sure its me as I have been simply replicating the input files. Any suggestions? (I don't what to post files to bulletin board but can send direct (if needed)). J _________________________________ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293

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Reading density files
by chris.wood＠stfc.ac.uk 09 Jun '14

09 Jun '14

I'm trying to read a density file. The docs (http://salilab.org/modeller/manual/node414.html) suggest that this should work >>> m = modeller.density(modeller.environ(), "file.mrc", 10) Traceback (most recent call last): File "<stdin>", line 1, in <module> TypeError: __init__() takes exactly 2 arguments (4 given) Instead, I've tried: >>> m = modeller.density(modeller.environ()) >>> m.read("file.mrc",10) read_data> Reading electron density of the main map readlinef__W> File: file.mrc, Line: 1 Modeller will only read the first 400 characters of this line. readlinef__W> File: file.mrc, Line: 3 Modeller will only read the first 400 characters of this line. forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read Any suggestions what I'm doing wrong? Chris -- Scanned by iCritical.

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