January 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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FW: [Fwd: Modeller mysteries]AF: handling HETATM entries in the middle of PDB file
by Kevin Truong 27 Jan '00

27 Jan '00

-----Original Message----- From: andras(a)rockvax.rockefeller.edu [mailto:andras@rockvax.rockefeller.edu]On Behalf Of Andras Fiser Sent: January 27, 2000 10:39 AM To: Andrej Sali; kevin.truong(a)utoronto.ca Subject: Re: [Fwd: Modeller mysteries]AF: handling HETATM entries in the middle of PDB file Hi Kevin, In this strange pdb file the hetatm entries inserted at several intermediate positions in the coordinate file. You tried to include them by including X-es in your alignment but it does not work like this. At first, if you do not read in HETATM entries, which is the default situation, (look at command HETATM_IO) than Modeller skips these entries so you do not need to include them in your alignment file either. Second, even if you include them you should not stick on the PDB file residue numbering (it is often chaotic): for some reason in your case the numbering skips by three at the HETATM enty although there is only one HETATM entry. You included 3 X-es accordingly, you need only one. Modeller renumbers the file by simply reading in order all the coordinate entries from the file irrespectively what numbering is associated with the entries in the PDB file. Third, if you do include HETATM entries you should indicate it by "." and not by "X". If you just replace your X-es to "." and instead of XXX you use a single "." your setup already works for me. I suggest you send your questions to the Modeller mailing list in the future, you might have answers from others and others also can learn. Please look at: http://salilab.org/cgi-bin/lwgate/lwgate/MODELLER_USAGE/ if you do not consider this mail as confidential please forward it to the list: modeller_usage(a)salilab.org best wishes, Andras > > Subject: Modeller mysteries > Date: Wed, 26 Jan 2000 19:51:03 -0500 > From: "Kevin Truong" <kevin.truong(a)utoronto.ca> > To: <sali(a)rockvax.rockefeller.edu> > > Hi Prof. Sali: > > My name is Kevin. I'm from Ikura's lab at the Ontario Cancer Institute. > I'm having some problems using modeller that I hope you can help me with. > I'm trying to model the RFP sequence with the GFP structure. > > I download the pdb file of 1ema from the PDB protein bank. > I ran the Modeller and it was not able to produce the predicted pdb file. > I have attached the following files: > > pdb1ema.ent pdb file used for Modeller > cFP484.ali ali generated by Threader > cFP484.top top script for Modeller > cFP484.log result of the Modeller run. > > I have no clue why this does not work. Can you help me? > > Thanks! > Kevin -- , 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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a question
by Helene Valadie 25 Jan '00

25 Jan '00

Hello, I am student in France and I would like to know if it is possible to build a model with adding water molecules on a part of my molecule (for example, add water molecules only on the Nterm atoms of my molecule). Thank you, Helene VALADIE valadie(a)urbb.jussieu.fr

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ACCESSIBILITY_TYPE
by M. Germana Paterlini 18 Jan '00

18 Jan '00

How do I (or is it possible to ) to specify the solvent accessibility of residues with ACCESSIBILITY_TYPE in MAKE_CONSTRAINTS ? Is there a specific RESTRAINT_TYPE associated with it ? Here is my input # Test for restraints on accessibility (?) READ_TOPOLOGY FILE '$(LIB)/top_heav.lib' READ_PARAMETERS FILE ='$(LIB)/par.lib' SET ATOM_FILES_DIRECTORY = './' READ_MODEL FILE = 'test.ent', MODEL_SEGMENT = '1:' '7:' SEQUENCE_TO_ALI ATOM_FILES = 'test.ent', ALIGN_CODES = 'test.ali' SEQUENCE_TO_ALI ADD_SEQUENCE = on , ATOM_FILES = ATOM_FILES 'test.ini', ; ALIGN_CODES = ALIGN_CODES 'test-ini' GENERATE_TOPOLOGY SEQUENCE = 'test-ini' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ = off WRITE_MODEL FILE 'test.ini' SET ACCESSIBILITY_TYPE = 8 MAKE_RESTRAINTS RESTRAINT_TYPE = 'sphere' WRITE_RESTRAINTS FILE = 'test-1.rsr' ENERGY DYNAMIC_SPHERE = off ENERGY WRITE_DATA FILE = 'test' , OUTPUT='psa' Thanks Germana Paterlini Department of Medicinal Chemistry University of Minnesota Minneapolis, MN 55455

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Modeller stops with error
by Daniel John Rigden 07 Jan '00

07 Jan '00

Hi Modellers I wonder if anyone can help me solve a problem I'm having with modeller. I'm using two templates to construct a model of a protein. Modeller stops with the following messages iup2crm_E> IUPAC atom not found in topology library: OG iup2crm_E> residue type undefined recover__> MODELLER_STATUS >= STOP_ON_ERROR: 1 1 This happens when it's calculating Ca-Ca restraints. I can't find any strange residues in my input file and asking for maximum output from modeller doesn't give me any new information. I think the problem lies with the second message since I have had the first making earlier models with just a single template and modeller did not stop. I'll attach a larger chunk of the log file at the end of this message. Thanks very much in advance for any help. Daniel Rigden +-------------------------------------------------------------------------+ | Dr Daniel John Rigden | | CENARGEN/EMBRAPA | e-mail: daniel(a)cenargen.embrapa.br | | S.A.I.N. Parque Rural, Final W5 | http://www.cenargen.embrapa.br | | Asa Norte | Phone: +55 (61)348-4741 | | 70770-900, Brasilia-D.F.-BRAZIL | Fax: +55 (61)340-3624 | +-------------------------------------------------------------------------+ TOP______> 159 125 SET RES_TYPES = 'STD' TOP______> 160 126 SET DISTANCE_RSR_MODEL = 5, MAXIMAL_DISTANCE = MAX_CA-CA_; DISTANCE TOP______> 161 127 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = ON TOP______> 162 128 SET RESTRAINT_GROUP = 9 TOP______> 163 129 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA' Number of atoms to choose from, total : 4025 4025 Atom types to be searched for (ATOM_TYPES) : CA Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 510 1: 510: Selection residue step (SELECTION_STEP) : 1 selatm___> Number of selected atoms : 510 List of segments of contiguous residues with at least one selected atom: SEGMENT RNUM AA --- RNUM AA LEN 1 1 SER --- 510 LEU 510 TOP______> 164 130 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'CA' Number of atoms to choose from, total : 4025 4025 Atom types to be searched for (ATOM_TYPES) : CA Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 510 1: 510: Selection residue step (SELECTION_STEP) : 1 selatm___> Number of selected atoms : 510 List of segments of contiguous residues with at least one selected atom: SEGMENT RNUM AA --- RNUM AA LEN 1 1 SER --- 510 LEU 510 TOP______> 165 131 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Restraint type to be calculated: distance iup2crm_E> IUPAC atom not found in topology library: OG iup2crm_E> residue type undefined recover__> MODELLER_STATUS >= STOP_ON_ERROR: 1 1

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