March 2001 - modeller_usage

Error using MALIGN3D
by Michael Buck 24 Jan '02

24 Jan '02

MALIGN3D Top files which worked well using Modeler 4 are giving me this error : fndatmi_284E> Beginning atom index for a residue out of bounds: 0 0 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I am using the following script # MALIGN3D READ_ALIGNMENT FILE = 'pair.aa' SET ATOM_FILES = '1.pdb' '2.pdb' SET FIT_ATOMS = 'CA' MALIGN3D GAP_PENALTIES_3D= 0 2.0, WRITE_FIT = on, WRITE_WHOLE_PDB = off If anybody has seen this problem, please help. Thank you … [View More]

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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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TRITON version 2
by Jiri Damborsky 22 Mar '01

22 Mar '01

Dear MODELLERs: We would like to inform you about the release of a new version of the program TRITON (version 2). The program serves for modelling of protein mutants and estimation of their activities. The mutant proteins are constructed by the external program MODELLER using the modelling protocol specifically adjusted for this purpose (new in this version). Mutant activities are estimated from the calculation of reaction pathways using external programs MOPAC and DRIVER. Extensive changes in … [View More]

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constraining an serine triade
by MarcoBocola 15 Mar '01

15 Mar '01

Hello from Marburg, I want to do homology modelling on serine hydrolases with highly conserved fold and reasonable AA-identity. So the difficulty is to model the active site correctly with respect to the catalytic triade and the backbone nitrogens in the oxyanion hole. These few amino acids should be overlayed as exact as possible. Is there a straightforward way to contstrain modeller only for these higly conserved topology of the catalytic residues within one Angstroem, thus remaining the … [View More]

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