modeller_usage

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modeller_usage@salilab.org

October 1999

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2 discussions

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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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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