November 2000 - 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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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:pXXXX:.::.::::: CKPMSNFRF-GENHAIMGVAFTWVMALACAAPPLVGWS--RYIPEGMQC-SCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTH--------QGSDFGPIFMTIPAFFAKTSAVYNPVIYIMM* >P1;pAveM structure:pAveM:2::211::::: -----------VRWAKLYSLVIWGCTLLLSSPMLV-----------------------------EVFTNMLLNVVGFLLPLSVITFCTMQ---------------------ERRATVLVLVVLLLFIICWLPFQISTFLDTL----------------VITQIASFMAYSNSCLNPLVYVIV* >P1;Ali2 sequence:Ali2:::::::: VKTMSMGRMRGVRWAKLYSLVIWGCTLLLSSPMLVFRTMKEYSDEGHNVTACVISYPSL---IWEVFTNMLLNVVGFLLPLSVITFCTMQIMQVLRNNEMQKFKEIQT---ERRATVLVLVVLLLFIICWLPFQISTFLDTLHRLGILSSCQDERIIDVITQIASFMAYSNSCLNPLVYVIV* ####################################################################################################################################### Perhaps, something is wrong with file names or PDB codes.(I stored the pdb files as pXXXX.pdb) Can somebody help me? Thank you very much, Paola -- dott. Paola D'Alessio (PhD student) Universita' degli Studi di Salerno Dipartimento Scienze Farmaceutiche via Ponte Don Melillo, 84084 Fisciano (Sa), Italy tel.+39 089 962822; e-mail: pdalessio(a)unisa.it

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dihedral restraints
by Isabelle Ortmans 12 Jan '01

12 Jan '01

Hi, we are trying to generate 3D-models for a short peptide, on the basis of two template structures. We would like to restrain the mainchain dihedral angles in the central region of our peptide during the modelling procedure. To do this, we tried to modify the following input file which allowed us to use the 'model' routine and some special restraints at the same time. ======================================================================= #Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 2 2 2 2 2 SET ALNFILE = 'ali1.pir' # alignment filename SET KNOWNS = 'sero_c' 'sero_o' # codes of the templates SET SEQUENCE = 'agen7' #code of the target SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model CALL ROUTINE = 'model' # do homology modelling STOP SUBROUTINE ROUTINE = 'special_restraints' SET ADD_RESTRAINTS = on MAKE_RESTRAINTS RESTRAINT_TYPE = 'strand', RESIDUE_IDS = '3' '6' RETURN END_SUBROUTINE ========================================================================== We thought it would be possible to modify the 'special_restraints' routine on the basis of the example file enforcing a cis conformation for a proline residue: =========================================================================# Example for: ADD_RESTRAINT, DELETE_RESTRAINT # This will enforce cis conformation for Pro-56. # Make a model and stereochemical restraints: DEFINE_STRING VARIABLES = ATOM_IDS1 ATOM_IDS2 READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' READ_PARAMETERS FILE = '$(LIB)/par.lib' READ_MODEL FILE = '1fas' SEQUENCE_TO_ALI ATOM_FILES = '1fas', ALIGN_CODES = '1fas' SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES '1fas.ini', ; ALIGN_CODES = ALIGN_CODES '1fas-ini' GENERATE_TOPOLOGY SEQUENCE = '1fas-ini' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ = off MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo' # Change the Pro-56 restraint from trans to cis: CALL ROUTINE = 'cispeptide', ATOM_IDS1 = 'O:56' 'C:56' 'N:57' 'CA:57', ; ATOM_IDS2 = 'CA:56' 'C:56' 'N:57' 'CA:57' WRITE_RESTRAINTS FILE = '1fas.rsr' ENERGY SUBROUTINE ROUTINE = 'cispeptide' # Delete the old restraint on the same atoms: DELETE_RESTRAINT ATOM_IDS = ATOM_IDS1 # Add the new restraint: ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 3 3 4 2 0 3.141593 0.087 DELETE_RESTRAINT ATOM_IDS = ATOM_IDS2 ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 3 3 4 2 0 0.0 0.087 RETURN END_SUBROUTINE ========================================================================= Doing this, we succeeded in writing the correct restraints file, but the 'model' routine stopped and no new model was generated. We thought maybe it might be necessary to proceed in two steps: 1. writing the restraints file 2. reading this restraint file prior to run the 'model' routine. Any help or suggestion would be appreciated. Thank you Isabelle

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phi/psi distribution in alpha region
by richard charles garratt 02 Nov '00

02 Nov '00

Dear modeller users, I have a question concerning the phi/psi distribution in the alpha region. The homology models which I generate seem to have a curious phi/psi distribution within the allowed alpha region. Almost all the residues within procheck's red region are sharply clustered into two peaks (one at the classical alpha helical angles of around -60, -40) and the other at the gamma region ( -90, 0). I often get a couple of minor lateral peaks as well. This is very different from crystal structures (including my template), where there is a more homogenous spread within the allowed region, although obviously showing a greater density of points towards -60, -40. I wonder why this happens and if I am doing something obviously stupid. It would seem that the sigmas on binormal restrainsts for phi/psis are very small. Can I easily adjust these values and what is the easiest way? This question is related to a similar one concerning proline phis angles which I note have a tendancy to drift away from -65. I have in the past used special restraints on all prolines in order to reduce sigma(phi) for which the default value seems to be rather generous. I would be most grateful for any comments/suggestions/help. Thanks, Richard Garratt University of Sao Paulo

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