- modeller_usage - salilab.org

side chain packing issues
by teca calcagno galvao 27 Mar '06

27 Mar '06

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error saying max_pdf exceeded reg
by Bala Murugan 27 Mar '06

27 Mar '06

Hi modellers, I am new to this list and to modeller too. I was wondering that anybody faces the problem connected with max_pdf error. I have submitted modeller a job to model a protein of around 1200 residues. In the log it says that, >>summary of failed models 1fdx.B999900001.PDB obj.func. (109595.656) exceeded max_molpdf (100000.000). I don't know what is meant by max_molpdf. How should i proceed from this point? Thanks in advance. With best regards, P.Balamurugan Yours truly, P.BalaMurugan. -------------------------------------------------- "Science is built up of facts, as a house is built up of stones,but an accumulation of facts is no more a science than a heap of stones is a house"-Henri Poincare

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calculate RMSD
by Xia Jiang 22 Mar '06

22 Mar '06

Dear MODELLER developers/users, I have a question regarding caculating RMSD between residues. Using MODELLER command SUPERPOSE, we can get number of residues that within some cutoff (e.g. 3A).But how can we get which exact pairs of residues are within this cutoff? We also tried COMPARE command, but it does not give us detail of RMSD between residues given an alignment. Do you know what is the top command to do so? Thanks Xia Jiang ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Prof. Sjolander's Group BioEngineering Dept. UC Berkeley xiajiang(a)berkeley.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Please help me with tutorial error
by Claire Wei 21 Mar '06

21 Mar '06

Hi Modellers, I am pretty new using MODELLER. I met some problem with the tutorials. http://www.salilab.org/modeller/7v7/tutorial/basic.html I am using MODELLER 8v2. Thanks a lot if someone could tell me what might be wrong. Here is the seq_search.top file: SET SEARCH_RANDOMIZATIONS = 100 SET FILE = 'TvLDH.ali' READ_SEQUENCE_DB SEQUENCE_SEARCH ALIGN_CODES = 'TvLDH', DATA_FILE = ON Here is the seq_search.log file: --------- Kind, OS, HostName, Kernel, Processor: 4, Linux localhost.localdomain 2.6.9-22.ELsmp i686 Date and time of compilation : 02/28/2006 18:28:36 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2006/03/21 11:52:24.775 SEQ_DATABASE_FILE : ${MODINSTALL8v2}/modlib//CHAINS_all.seq SEQ_DATABASE_FORMAT : PIR CHAINS_LIST : ${MODINSTALL8v2}/modlib//CHAINS_3.0_40_XN.cod CLEAN_SEQUENCES : T MINMAX_DB_SEQ_LEN : 0 999999 Number of sequences : 6869 Number of residues : 1543994 Length of longest sequence: 1491 sequenc_587E> Run alignment.append() or make alignment first. top_error__E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 5317486 5192.857 5.071 Starting time : 2006/03/21 11:52:24.775 Closing time : 2006/03/21 12:35:30.209 Total CPU time [seconds] : 2585.59 ------------ --------------------------------- Yahoo! Mail Use Photomail to share photos without annoying attachments.

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Re: [modeller_usage] Protein + Metal Ion
by Anshul Awasthi 21 Mar '06

21 Mar '06

Modeller Caretaker wrote: <mailto:modeller_usage@salilab.org> > Anshul Awasthi wrote: > >> I am trying to model the structure of a protein that contains Zn ion >> in the active site, using modeller 7v7. For the modeling purpose I am >> using 5 templates and one of them contains 2 His residues coordinated >> with Zn ion, and these residues are conserved among all the templates >> and the target sequence. > > > > I suggest that you use the latest version, Modeller 8v2, instead. Not > only does it incorporate a number of bug fixes, but it gives more > informative diagnostics for problems like this one. It will read old > TOP scripts just fine, provided they have the .top file extension. > >> I have put /z* at the end of the alignment file as follows: >> >> P1;1WVR >> structureX:1WVR: 9 :A: 181 ::::: >> PRKPEIQNEIIDLHNSLRRSVN------------PTASNMLKMEWYPEAAANAERWAYRCIESHSSRDSRVIGG- >> >> ---IKCGENIYMAT-----YPAKWTDIIHAWHGEYKDFKYGVGAVPSD----AVIGHYTQIVWYKSYRAGCAAAY >> >> CPSSKYS------YFYVCQYCPAGNIIGKTATPYKSGPPCGDCP-SD-C-DN--GLCTN/z/* > > > > The final / is unnecessary here, since nothing follows the ion. > >> ================================================================== >> But when I run the modeller i get an error message stating "SEQUENCE >> DIFFERENCE BETWEEN ALIGNMENT AND PDB " >> >> rdabrk__291E> Sequence difference between alignment and pdb : >> >> STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- >> 2 174 30 ZN2 24 UNK GLCTNz > > > > Your PDB file appears to have an UNK residue rather than a Zn atom > here. It's hard to say what your problem might be, as I'm guessing > your PDB is modified from code 1wvr (since the A chain continues to > residue 221, and the ion is cadmium, not zinc). > > If your problem continues, send me your full input files, and I'll > take a look. > > Ben Webb, Modeller Caretaker Dear Ben, I was able to run the programme and got a model with Zn ion. But I was only able to do it without adding the restraints to the His residues and the Zn ion. But when I put the following subroutine at the end of my .top file, I get an error. SUBROUTINE ROUTINE = 'special_restraints' SET ATOM_IDS 'NE2:420' 'ZN2:1436' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 SET ATOM_IDS 'NE2:892' 'ZN2:1436' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 RETURN END_SUBROUTINE Following is the last portion of the log file with the error; TOP_________> 231 199 MAKE_RESTRAINTS make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 19104 19104 make_re_423_> Number of previous, current selected restraints: 18913 18913 TOP_________> 232 200 DELETE_ALIGNMENT TOP_________> 233 201 RETURN TOP_________> 234 165 CALL ROUTINE = 'special_restraints' TOP_________> 235 810 SET ATOM_IDS 'NE2:420' 'ZN2:1436' TOP_________> 236 811 ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0; .1 add_res_442E> One or more atoms absent from MODEL: NE2:420 ZN2:1436 top_error__E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 The number of the residues I have used correspond to the modeller numbering system (*.ini file). I am not sure about the RESTRAINT_PARAMETERS I have put in the subroutines as I have duplicated it from one of the earlier posts. I tried to know more about them from the manual but could not understand. I shall be glad if you could also explain the meaning of various fields being used in the parameters. With regards, Anshul

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Protein + Metal Ion
by Anshul Awasthi 19 Mar '06

19 Mar '06

Dear Modeller users, I am trying to model the structure of a protein that contains Zn ion in the active site, using modeller 7v7. For the modeling purpose I am using 5 templates and one of them contains 2 His residues coordinated with Zn ion, and these residues are conserved among all the templates and the target sequence. I have included these lines in my top file SET HETATM_IO = on SUBROUTINE ROUTINE = 'special_restraints' SET ATOM_IDS 'NE2:493' 'ZN:1422' SET ATOM_IDS 'NE2:921' 'ZN:1422' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 RETURN END_SUBROUTINE ================================================================== I have put /z* at the end of the alignment file as follows: P1;1WVR structureX:1WVR: 9 :A: 181 ::::: PRKPEIQNEIIDLHNSLRRSVN------------PTASNMLKMEWYPEAAANAERWAYRCIESHSSRDSRVIGG- ---IKCGENIYMAT-----YPAKWTDIIHAWHGEYKDFKYGVGAVPSD----AVIGHYTQIVWYKSYRAGCAAAY CPSSKYS------YFYVCQYCPAGNIIGKTATPYKSGPPCGDCP-SD-C-DN--GLCTN/z/* ================================================================== But when I run the modeller i get an error message stating "SEQUENCE DIFFERENCE BETWEEN ALIGNMENT AND PDB " Following is the portion of the generated log file: read_al_374_> Non-standard residue type,position,sequence: z 210 2 Read the alignment from file : templates.ali Total number of alignment positions: 210 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1RC9 173 1 1RC9 2 1WVR 174 2 1WVR 3 1XX5 173 1 1XX5 4 1U53 186 1 1U53 5 1QNX 170 1 1QNX 6 GLiPR 181 1 GLiPR TOP_________> 137 113 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER; ATION = 'ne', THEN = 'GO_TO __ACCELRYS1' TOP_________> 138 117 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./1RC9.pdb openf5__224_> Open 11 OLD SEQUENTIAL ./1WVR.pdb rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 2 174 30 ZN2 24 UNK GLCTNz rdabrk__288W> Protein not accepted: 2 openf5__224_> Open 11 OLD SEQUENTIAL ./1XX5.pdb openf5__224_> Open 11 OLD SEQUENTIAL ./1U53.pdb openf5__224_> Open 11 OLD SEQUENTIAL ./1QNX.pdb check_a_337E> Structure not read in: 2 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 =================================================================================== Can anyone suggest where things might be going wrong? With regards, Anshul

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build a homopentamer
by Giovanni Grazioso 17 Mar '06

17 Mar '06

Dear Modellers, I'd like to know if mod8v2 is able to build a homopentamer copying only the first chain from the heteropentameric template and then building the remaining 4 chains by axial symmetry. This is important because only one chain is highly conserved while the others are different. Any help will be much appreciated. Thank you Giovanni

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DOPE
by helenaa＠webmail.ibilce.unesp.br 16 Mar '06

16 Mar '06

Does anyone out there know if it is possible to find a description of the DOPE score? I have been searching the manual, the MODELLER web-site and the www... Helen ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/

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ordering of atoms in the PDB
by Robin Stamler 16 Mar '06

16 Mar '06

Hello I'm sure this is answered somewhere but I couldn't find it. The ordering of atoms in a residue in Modeller output as in (a) is different from that usually seen in PDB files (b) This is a problem when using the output in some other servers. Can the Modeller output be changed? Thanks Robin Stamler Dept Molecular Genetics University of Cincinnati (a) ATOM 1 N ALA B 1 10.145 12.378 3.667 1.00 25.81 1SG N+2 ATOM 2 CA ALA B 1 11.592 12.105 3.515 1.00 25.81 1SG C+3 ATOM 3 CB ALA B 1 12.225 11.817 4.886 1.00 25.81 1SG C+4 ATOM 4 C ALA B 1 11.834 10.932 2.631 1.00 25.81 1SG C+5 ATOM 5 O ALA B 1 11.538 10.968 1.437 1.00 25.81 1SG O+6 (b) ATOM 586 N ALA A 86 -33.616 77.292 18.556 1.00 27.93 N ATOM 587 CA ALA A 86 -34.153 76.748 17.311 1.00 27.40 C ATOM 588 C ALA A 86 -33.329 77.134 16.085 1.00 27.32 C ATOM 589 O ALA A 86 -32.386 77.921 16.172 1.00 25.96 O ATOM 590 CB ALA A 86 -35.591 77.205 17.124 1.00 24.83 C

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Perl Script to plot DOPE
by Vimalkumar Velayudhan 16 Mar '06

16 Mar '06

Hello Modeller users, I have written a perl script to plot the energy profiles obtained at the model evaluation step. This script is available at http://salilab.org/modeller/wiki/Plotdope The input for the program is the Alignment of the target and the template and the profile files. The script uses gnuplot to produce the output. Regards, -- Vimalkumar Velayudhan

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