May 2010 - modeller_usage

add restype to and how to select ligand
by Knut J Bjuland 05 May '10

05 May '10

If wish to use acetyl-coa in model which use a polypetid as template. How can I specify to modeller to use the atom in hetatm since I often get other petids if I cut of the amino acid to get better alignment. Knut J _________________________________________________________________ Hotmail: Free, trusted and rich email service. https://signup.live.com/signup.aspx?id=60969

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weighting restraints
by meier＠lmb.uni-muenchen.de 04 May '10

04 May '10

Hi, having multiple templates, I want to weight template based restraints down with respect to other (stereochemical) restraints. Is it then more sensible to weight down the template based restraints (weight < 1, weight=1 for rest) or to weight up the other restraints (weight > 1, weight=1 for rest)? Does it make any difference for the (simulated annealing) optimization scheme (because the "scale" is changed)? Thanks a lot for any hint Armin Meier

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Modeling Circular Permutations
by Spencer Bliven 04 May '10

04 May '10

Hello, I have produced a number of circular permutations for IL-1b. There are several structures available for the wild type protein, so I would like to model how the circular permutation effects the structure. Is MODELLER able to process circular permutations? If so, how would I encode this in my alignment file? It doesn't seem like the PIR format is well suited to this. Thanks in advance for your advice to a new modeller user. -Spencer Bliven

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Opening files
by pbonar＠ualberta.ca 04 May '10

04 May '10

Hi, I am new to modeller, and very inexperienced in python. I am trying to complete the first tutorial and I keep getting this error: IOError: openf______E> Cannot open file pdb_95.pir: No such file or directory. I have downloaded and extracted the files needed for this tutorial, however from what I gather by this message, the program cannot find/or read these files. Is there somewhere special where I must save them, or some other name that I have to give them. Do I have to do something to the file in order for it to work. And if so what program do I download to read the file? Thank you for you help Pam

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