August 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 Michael Buck ************************************************ Michael Buck NCSU Genetics mjbuck(a)unity.ncsu.edu Phone (919)515-5759 Fax (919)515-3355 http://www4.ncsu.edu/~mjbuck *************************************************

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Modelling a loop repeat
by Troy Wymore 29 Aug '01

29 Aug '01

Hello Modellers, I would like to restrain a loop that is repeated throughout my TARGET to have the same conformation as the first loop conformation where the alignment to the TEMPLATE is good. What is the easiest way to go about this? DEFINE_SYMMETRY? Any help would be much appreciated, Troy Wymore Biomedical Initiative Group Pittsburgh Supercomputing Center

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[Fwd: Problems with heteroatoms (Zn)]
by Sirisha sunkara 27 Aug '01

27 Aug '01

Hi, I have this problem solved. I had a wrong representation of the Zn heteroatoms in my PDB file. It had to be annotated as ZN2 and not ZN, because that's how it's represented in the top_heav.lib file. Thanks to one of the modeller users who pointed this out to me - I'm sorry I forget his name. Regards, Sirisha Sunkara

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Problems with heteroatoms (Zn)
by Sirisha sunkara 17 Aug '01

17 Aug '01

Hi, I'm trying to model a 283 aa long protein using Modeller4 with Zn heteroatom. The problem is Zn heteroatom does not show up in my output file. My template structure has a Zn Heteroatom in it. At this point I'm not interested in a model with hydrogens or water. I know people have had similar problems earlier and I also tried all the methods suggested in the archives of the mailing lists from 1998 and 1999. It still doesn't work. Has there been any update in the library files in Modeller5 for this? My model-segment.top file looks like this: INCLUDE # Include the predefined TOP routines SET ALNFILE = 'file.ali' SET KNOWNS = 'abc' SET SEQUENCE = 'gi_xxxxxxxx' SET ATOM_FILES_DIRECTORY = './:../atomfiles' SET TOPOLOGY_MODEL =3, HYDROGEN_IO = off, WATER_IO = off, HETATM_IO = on READ_PARAMETERS FILE = '$(LIB)/par.lib' READ_TOPOLOGY FILE= '$(LIB)/top_heav.lib' SET STARTING_MODEL= 4 SET ENDING_MODEL = 4 SET DYNAMIC_FLAG = 0 CALL ROUTINE = 'model' SUBROUTINE ROUTINE = 'select_atoms' PICK_ATOMS SELECTION_SEGMENT='1:' '283:', SELECTION_SEARCH='segment', ; PICK_ATOMS_SET=1, RES_TYPES='all', ATOM_TYPES='all', ; SELECTION_FROM='all', SELECTION_STATUS='initialize', SELECTION_STEP=1 RETURN END_SUBROUTINE I have Zn in my alignment files set up as XXX/z* in both template and query sequences. My template PDB file also has "only ZN" heteroatoms - I stripped out all other heteroatoms in my template PDB file just to make sure. What am I doing wrong? I appreciate all your help, Sirisha Sunkara

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Modelling a loop repeat
by Troy Wymore 10 Aug '01

10 Aug '01

Hello Modellers, I would like to restrain a loop that is repeated throughout my TARGET to have the same conformation as the first loop conformation where the alignment to the TEMPLATE is good. What is the easiest way to go about this? DEFINE_SYMMETRY? Any help would be much appreciated, Troy Wymore Biomedical Initiative Group Pittsburgh Supercomputing Center

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