March 2014 - modeller_usage

Modeller Parallel work
by Yao, Jianzhuang 21 Apr '14

21 Apr '14

?Dear Sir/Madam, I am running Modeller to build 500 homology models for a methyltransferase. Now I am running serial job. Do you think I can run parallel job? Or do you think I can submit the same script for 500 times and I can get the same results with serial job? Thanks a lot! Jianzhuang

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PYTHONPATH on Windows 7
by chris.wood＠stfc.ac.uk 01 Apr '14

01 Apr '14

Hello, I’ve got Python 2.7.3 on Windows 7: Python 2.7.3 |EPD 7.3-2 (64-bit)| (default, Apr 12 2012, 15:20:16) [MSC v.1500 64 bit (AMD64)] on win32 Type "copyright", "credits" or "license()" for more information. I’ve installed Modeller 9.12; but typing from modeller import * results in the “ImportError: No module named modeller” error, even though I've got modeller in my python path: >>> sys.path ['', 'C:\\Python27\\Lib\\idlelib', 'C:\\Program Files (x86)\\Modeller9.12\\modlib\\modeller', 'C:\\Program Files (x86)\\Modeller9.12\\modlib\\python2.7', 'C:\\Python27\\python27.zip', 'C:\\Python27\\DLLs', 'C:\\Python27\\lib', 'C:\\Python27\\lib\\plat-win', 'C:\\Python27\\lib\\lib-tk', 'C:\\Python27', 'C:\\Python27\\lib\\site-packages', 'C:\\Python27\\lib\\site-packages\\PIL', 'C:\\Python27\\lib\\site-packages\\win32', 'C:\\Python27\\lib\\site-packages\\win32\\lib', 'C:\\Python27\\lib\\site-packages\\Pythonwin'] >>> import modeller Traceback (most recent call last): File "<pyshell#5>", line 1, in <module> import modeller ImportError: No module named modeller I'm sure I've missed something obvious, but can't see it! Cheers, Chris ------------------- Dr Chris Wood STFC Rutherford Appleton Laboratory Didcot OX11 0QX chris.wood(a)stfc.ac.uk www.ccpem.ac.uk Tel: +44(0)1235 567864 Tel: +44(0)7909 586624 Fax: +44(0)1235 567801 Skype: chris_c_wood<callto://chris_c_wood/> -- Scanned by iCritical.

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How to override the build_seq() command in loopmodel class
by Abhijit Muley 21 Mar '14

21 Mar '14

I am having knots in my structure, same problem as this person had- http://salilab.org/archives/modeller_usage/2005/msg00394.html I went through the manual but could not find any specific part where such instructions have been mentioned (althought they could have been in some section I have missed). Can anyone please direct me to the appropriate resources to solve this problem?

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(no subject)
by Ankita Nagpal 17 Mar '14

17 Mar '14

hi I have just started using modeller with the help of tutorial example.In the aligning step when iam aligning 1bdm with TvLDH IAM getting error only 317 residue out of 318 contain atom of type CA .Can you plz help me out what is going wro <http://wrong.it/>ng

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Use some local alignments
by fakharian 15 Mar '14

15 Mar '14

Hi I want to build a model for my target protein base on a known template structure. And I have some target-template local alignments. I want to use(and force) these local alignments on known regions; and align other regions of target by MODELLER alignment functions such as align2d or salign. Can anyone suggest a method to perform this? Thank you.

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Select and remove atoms from automodel
by Ignacio Ibarra 04 Mar '14

04 Mar '14

Hello, Currently I am generating nucleic acid models using the MODELLER suite. I would like to remove the initial phosphate group declared in the first residue of each nucleic acid chain. Those atoms should not be present in real structures. I would like to do it without writing new text in the .lib files that are into the modlib folder I read about a pick_atoms() method in an older version of MODELLER, but it is not commented in the 9v11 manual ( http://binf.gmu.edu/software/MODELLER/node131.html) Is there something similar currently available for removing atoms from the model in the automodel or another class? Regards, Ignacio

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