modeller_usage

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modeller_usage@salilab.org

August 1998

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2 discussions

problem!
by Paola D'Alessio 15 Jun '01

15 Jun '01

Dear users, I am trying to produce a chimeric model for my protein. The first thing I want to do is to check the alignment I have. When I tell Modeller to execute the "check_alignment" command, I get the following message: rdpir___E> alignment sequence not found in PDB file: 1 ./pXXXX.pdb ####################################################################################################################################### The alignment I have is: >P1;pXXXX structureX:… [View More]

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Re: Modeling a loop
by Robert Jorissen 05 Aug '98

05 Aug '98

Dear fellow MODELLERs I have found that the problem mentioned by Tom Lee about modelling loops only occurs for the MSI version of MODELLER and not the academic version. I get around the problem by putting the following in the TOP file.: INCLUDE DEFINE_STRING VARIABLES = LOOP_CSRFILE LOOP_INI_MODEL SET SEQUENCE = 'aaa' SET MODEL = 'aaa.pdb' # initial model of the target : : The define_string... line is the only line to be added. I can't remember how … [View More]

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