- modeller_usage - salilab.org

queries
by Dr Ahsan Salim 29 Nov '99

29 Nov '99

I have been doing structural studies on various eye lens crystallins by homology modelling using modeller 4. I have some queries in this regard. 1.The final models have no residues in the disallowed region of the Ramachandaran plot as well as there are no bad contacts. Is this evaluation enough for structure verification? 2. I want to mutate one residue in these models and I have gone thru the top files for mutation. For reasons unknown to me, I could not use it correctly. Besides the file needs the name of the residue to be mutated and the one to be inserted instead but not the position. If the specific name is given, all residues of the same name gets mutated. 3. The other important studies that I want to carry out is the effect of sugar binding to the structure as well as binding of the small molucules like phosphate, cyanate etc. I used Web lab Viewer Pro version to paste and connect the small mol. to my protein.When I cleaned the entire structure using "clean structure" command in Web lab, it leaves so many bad contacts and many residues in the disallowed region of the Ramachandaran plot. So I decided to use the molecular dynamics and energy minimization by MODELLER. The topology files do not have these small molecules in the list. So it leaves the structure to be more disturbed. Can you make the topology files if specified or can you help me sort out how to make one? Well these are so many questions! Can you please suggest something. Thanks asmat salim HEJ Res Inst of Chem Univ of Karachi Pakistan PS:How can I join your mailing list?

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loop refinement
by M. Germana Paterlini 10 Nov '99

10 Nov '99

I generated several loop conformations using the 'loop' routine. The top file is similar to example 3 of the manual, with the addition of gemetrical constraints on the end of loops. I am refining 20 a.a. out of a 27-loop segment. The refined loop conformations still have residues located in unfavorable regions of the phi/psi plot, i.e. phi> 0 (non Gly, or Asn). Typically, there are 1-4 residues in these regions. Only 2% of my conformations have all residues with phi<0. Are such occurrencies typical of the refinement procedure? If not, how can I prevent this for happening? Thanks Germana Germana Paterlini Dept. of Medicinal Chemistry Minneapolis, MN 55455 germana1(a)vwl.medc.umn.edu

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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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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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