- modeller_usage - salilab.org

symmetry problems
by Gail Bartlett 07 Oct '99

07 Oct '99

Dear Modellers, Help! I am trying to generate a homology model of a dimer using a known structure which is tetrameric. I want to impose tetrameric symmetry on the model, but cannot do this on the whole chain as the two halves which correspond to each tetramer in the known structure are different in length. I have selected four segments, two from each dimer, which should be symmetrical, and have set them to be symmetrical using the 'defsym' subroutine. This works fine, but if I try to repeat this using another set of four segments which should also be identical, the program seems to lock up. The top file that I used is below: # Symmetry # Define the segments (chains in this case) to be identical: DEFINE_STRING VARIABLES = SEG1 SEG2 SEG3 SEG4 CALL ROUTINE = 'defsym', SEG1 = '5:' '29:', SEG2 = '157:' '181:', SEG3 = '249:' '273:', SEG4 = '401:' '425:' DEFINE_STRING VARIABLES = SEG5 SEG6 SEG7 SEG8 CALL ROUTINE = 'defsym', SEG5 = '79:' '91:', SEG6 = '185:' '197:', SEG7 = '323:' '335:', SEG8 = '429:' '441:' SET DYNAMIC_SPHERE = off ENERGY WRITE_MODEL FILE = 'define_symmetry-1.atm' OPTIMIZE MAX_ITERATIONS = 300 WRITE_MODEL FILE = 'define_symmetry-2.atm' ENERGY SET DYNAMIC_SPHERE = on MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo' RANDOMIZE_XYZ DEVIATION = 3.0 SET MAX_ITERATIONS = 300, MD_RETURN = 'FINAL' OPTIMIZE OPTIMIZATION_METHOD = 1 # Conjugate gradients OPTIMIZE OPTIMIZATION_METHOD = 3 # Molecular dynamics OPTIMIZE OPTIMIZATION_METHOD = 1 # Conjugate gradients WRITE_MODEL FILE = 'define_symmetry-3.atm' ENERGY SUBROUTINE ROUTINE = 'defsym' SET ATOM_TYPES = 'MNCH' SET RES_TYPES = 'ALL' SET SELECTION_STATUS = 'INITIALIZE' SET SELECTION_SEARCH = 'SEGMENT' SET SYMMETRY_WEIGHT = 1.0 PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG1 PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG2 DEFINE_SYMMETRY ADD_SYMMETRY = on off SET SYMMETRY_WEIGHT = 1.0 PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG1 PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG3 DEFINE_SYMMETRY ADD_SYMMETRY = on off SET SYMMETRY_WEIGHT = 1.0 PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG1 PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG4 DEFINE_SYMMETRY ADD_SYMMETRY = on off SET SYMMETRY_WEIGHT = 1.0 PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG2 PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG3 DEFINE_SYMMETRY ADD_SYMMETRY = on off SET SYMMETRY_WEIGHT = 1.0 PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG2 PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG4 DEFINE_SYMMETRY ADD_SYMMETRY = on off SET SYMMETRY_WEIGHT = 1.0 PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG3 PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG4 DEFINE_SYMMETRY ADD_SYMMETRY = on off SET SYMMETRY_WEIGHT = 1.0 PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG5 PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG6 DEFINE_SYMMETRY ADD_SYMMETRY = on off SET SYMMETRY_WEIGHT = 1.0 PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG5 PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG7 DEFINE_SYMMETRY ADD_SYMMETRY = on off SET SYMMETRY_WEIGHT = 1.0 PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG5 PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG8 DEFINE_SYMMETRY ADD_SYMMETRY = on off SET SYMMETRY_WEIGHT = 1.0 PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG6 PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG7 DEFINE_SYMMETRY ADD_SYMMETRY = on off SET SYMMETRY_WEIGHT = 1.0 PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG6 PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG8 DEFINE_SYMMETRY ADD_SYMMETRY = on off SET SYMMETRY_WEIGHT = 1.0 PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG7 PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG8 DEFINE_SYMMETRY ADD_SYMMETRY = on off RETURN END_SUBROUTINE Many thanks for any help you can give. Gail Bartlett

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by tyss＠att.net 09 Sep '99

09 Sep '99

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Model Refinement
by Derek Smith 12 Aug '99

12 Aug '99

Dear Modellers I have a manually constructed model protein, which I would like to refine using the MODELLER default schedule. I have attempted this using the protocol based on question 12 in the MODELLER FAQ. However, I find that MODELLER reads the model.ini file, and then extracts restraints from the templates, which are then used in the optimization of the model. I would like to refine my model based only upon my initial conformation. Is this possible do do, and if so, how should I go about it? Thanks in advance, Derek Smith. ************************************************************************* Derek Smith phone: (01904) 432550 Structural Biology Laboratory email: derek(a)yorvic.york.ac.uk Department of Chemistry fax: (01904) 410519 University of York, Heslington, York. YO10 5DD United Kingdom. *************************************************************************

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refinement of initial structure
by Derek Smith 09 Aug '99

09 Aug '99

Dear Modellers, I have a manually constructed model and I would like to use the MODELLER optimisation protocol. I have attempted to follow the FAQ question 12, but I find that although MODELLER reads in the 'model.ini' file I give it, it then extracts restraints from the templates to refine the model. Is there a way of presenting MODELLER with a model (minus any other details) and using the program purely as a structure refinement tool? Any help would be appreciated, Derek Smith -- ************************************************************************* Derek Smith phone: (01904) 432550 Structural Biology Laboratory email: derek(a)yorvic.york.ac.uk Department of Chemistry fax: (01904) 410519 University of York, Heslington, York. YO10 5DD United Kingdom. *************************************************************************

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heteroatoms
by Timothy A. Springer Ph.D. 28 Jun '99

28 Jun '99

I do not get a Mn heteroatom to appear in my .ini or model file. I am copying some fields that worked before for ca, so i do not understand my problem. Please help. thanks, Tim Springer ******************************************************************************* * Timothy A. Springer, Ph.D. * * Latham Family Professor of Pathology * * Harvard Medical School e-mail: springer(a)sprsgi.med.harvard.edu * * Center for Blood Research phone: 617-278-3200 * * 200 Longwood Ave. Room 251 fax: 617-278-3232 * * Boston MA 02115 * *******************************************************************************

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About ADs in MODELLER_USAGE list
by Marc A MARTI-RENOM 07 Jun '99

07 Jun '99

Dear MODELLER_USAGE users, Lately we have had some ADs going into MODELLER_USAGE list. We are trying to stop them, if this continues we will include some filters to avoid this problem. Hopefully this has not disturb you so much. Thank you, Marc A. Marti-Renom, phD (List Manager)

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06 Jun '99

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Re: Modeller Manual FAQ #4
by Azat Badretdinov 04 Jun '99

04 Jun '99

Please be aware that FAQ #4 is misleading in the > ? the alignment part (2 template should have at least three residues > ? overlap). > ? > ? Few of MODELER users acquired wrong perception of chimeric modelling > ? because in FAQ #4 two templates do not overlap at all (though there is a > ? warning about mutual orientation of two parts). Azat Badretdinov.

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Re: [Fwd: limit in READ_RESTRAINTS]
by Andras Fiser 25 May '99

25 May '99

Hi Dong, you can deal with your problems (too many pseudoatoms) in two ways: either explicitly defining all the pairs of atoms (or at least a few of them - you defined 291 independent pseudoatom) that you restraining, or using a modeller version suited for this particular problem. Since this morning you can find a modeller executable with 2000 possible pseudo atoms, on our ftp site: ftp salilab.org /pub/outgoing/mod_r10000 Andras -- , Andras Fiser, PhD # phone: (212) 327 7206 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras

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Re: [Fwd: limit in READ_RESTRAINTS]
by Andras Fiser 24 May '99

24 May '99

Mensur, The description of the form of restraints is given in the manual setion 2.5 page 73. Dong, we got your modeller files that failed to deal with the nmr restarints. You gave 2 files of restraints with 500 and 1000 input lines and the larger one failed to work with modeller, modeller crashed with memory fault. The same effect was reproduced here, but it happened not because of the larger restraints file. Multiplying the size of the smaller file (beyond 1000 entry lines) worked fine. The real problem is that in total you use more than 200 pseudatom in your larger file (undefined number of restrained Hydrogens is counted as pseudoatom). The number of pseduoatom in your smaller file (in total) is 159, that is while it worked. Modeller 4 uses static arrays, so the array sizes are predefined, as you can see in the header of the log file (and below), the array size of pseudoatoms is 200. mod 5, which will come out soon, uses dynamic memory allocation and you will not have this problem. Best wishes Andras ----------- mod4 default ---------------- Array dimensions (!8/9/96!): Maximum number of residues : 2000 Maximum number of atoms : 32000 Maximum length of alignment : 2000 Maximum number of sequences in alignment : 20 Maximum number of restrained features : 320000 Maximum number of restraint parameters : 3200000 Maximum number of restraint atoms : 960000 Maximum number of non-bonded atom pairs : 180000 Maximum number of non-bonded restraint types : 1 Maximum number of non-bonded restraint type parms: 1 Maximum number of explicitly excluded pairs : 100 Maximum number of pseudo atoms : 200 Maximum optimization schedule length : 50 ----------------------------------------------- -- , Andras Fiser, PhD # phone: (212) 327 7206 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras

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