- modeller_usage - salilab.org

error on 'special_patches' routine for PATCH S-S bonds
by Dr. Daniel James White PhD 25 Oct '04

25 Oct '04

Hi Modellers, I get a "command not recognized" error, see log below when trying to use the 'special_patches' routine, to tell modeller to make 2 S-S bonds in a loop I am modelling, I can't see any error in my top file or alignment, I used the code directly from the manual FAQ number 6, define additional disulphides not in template, with appropriate changes, see top file below. any ideas what I am doing wrong? cheers Dan top file: # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'loop1.ali' # alignment filename SET KNOWNS = '4DPV' # codes of the templates SET SEQUENCE = 'lop1' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' STOP # Redefine the special_patches routine to include the additional disulfides # (this routine is empty by default): SUBROUTINE ROUTINE = 'special_patches' # A disulfide between residues 226 and 234 in chain A: PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '226:A' '234:A' # A disulfide between residues 228 and 232 in chain A: PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '228:A' '232:A' RETURN END_SUBROUTINE log file: Kind, OS, HostName, Kernel, Processor: 4, Linux modeling.bio.jyu.fi 2.6.8-1.521 i686 Date and time of compilation : 09/14/2004 11:06:39 Job starting time (YY/MM/DD HH:MM:SS): 2004/10/12 15:04:54.106 rdactio_534E> Command not recognized: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 56755 55.425 0.054 Starting time : 2004/10/12 15:04:54.106 Closing time : 2004/10/12 15:04:55.092 Total CPU time [seconds] : 0.94 ali file: >P1;4DPV-CPVVP-withDNAZ structure:4DPV:22 :Z:593 :Z:::: GSGNGSGGGGGGGSGGVGISTGTFNNQTEFKFLENGWVEITANSSRLVHLNMPESENYRR VVVNNMDKTAVNGNMALDDIHAQIVTPWSLVDANAWGVWFNPGDWQLIVNTMSELHLVSF EQEIFNVVLKTVSE----PPTKVYNNDLTASLMVALDSNNTMPFTPAAMRSETLGFYPWK PTIPTPWRYYFQWDRTLIPSHTGT---------SGTPTNIYHGTDPDDVQFYTIENSVPVHLLRTGDEF ATGTFFFDCKPCRLTHTWQTNRALGLPPFLNSLPQSEGATNFGDIGVQQDKRRGVTQMGN TNYITEATIMRPAEVGYSAPYYSFEASTQGPFKTPIAAGRGGAQTDENQAADGNPRYAFG RQHGQKTTTTGETPERFTYIAHQDTGRYPEGDWIQNINFNLPVTNDNVLLPTDPIGGKTG INYTNIFNTYGPLTALNNVPPVYPNGQIWDKEFDTDLKPRLHVNAPFVCQNNCPGQLFVK VAPNLTNEYDPDASANMSRIVTYSDFWWKGKLVFKAKLRASHTWNPIQQMSINVDNQFNY VPSNIGGMKIVYEKSQLAPRKLY* >P1;COAT_PAVC2_VP2 sequence:lop1:22 :A:593 : :A::: GSGNGSGGGGGGGSGGVGISTGTFNNQTEFKFLENGWVYITANSSRLVHLNMPESENYRR VVVNNMDKTAVNGNMALDDIHAEIVTPWSLVDANAWGVWFNPGDWQLIVNTMSELHLVSF EQEIFNVVLKTVSESATQPPTKVYNNDLTASLMVALDSNNTMPFTPAAMRSETLGFYPWK PTIPTPWRYYFQWDRTLIPSHTGTCDCRGDCFCSGTPTNIYHGTDPDDVQFYTIENSVPVHLLRTGDEF ATGTFFFDCKPCRLTHTWQTNRALGLPPFLNSLPQSEGATNFGDIGVQQDKRRGVTQMGN TNYITEATIMRPAEVGYSAPYYSFEASTQGPFKTPIAAGRGGAQTDENQAADGNPRYAFG RQHGKKTTTTGETPERFTYIAHQDTGRYPEGDWIQNINFNLPVTNDNVLLPTDPIGGKTG INYTNIFNTYGPLTALNNVPPVYPNGQIWDKEFDTDLKPRLHVNAPFVCQNNCPGQLFVK VAPNLTNQYDPDASANMSRIVTYSDFWWKGKLVFKAKLRASHTWNPIQQMSINVDNQFNY VPSNIGGMKIVYEKSQLAPRKLY* Dr. Daniel James White BSc. (Hons.) PhD Cell Biology, Ambiotica C242 Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 14 260 4183 (work) +358 468102840 (mobile) http://www.chalkie.org.uk dan(a)chalkie.org.uk white(a)cc.jyu.fi

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where can I get file.crv file.cav by write_date
by Shu-Qun Liu 21 Oct '04

21 Oct '04

Dear Modeller Users and Developers, The WRITE_DATA command can write the selected types of data (such as PSA DIH NGH SSM CRV CAV CROSS-SECTIONS) about the MODEL to a corresponding file. The example script write_data.top in the path 'modeller7v7/example/commands' is: # Example for: WRITE_DATA # This will calculate solvent accessibility, dihedral angles, and # residue-residue neighbors for a structure in the PDB file. SET OUTPUT_CONTROL = 1 1 1 1 1 # Get topology library for radii and the model without waters and # HETATMs: READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' SET HETATM_IO = off, WATER_IO = off READ_MODEL FILE = '1fas' # Calculate residue solvent accessibilities, dihedral angles, and # residue-residue neighbors: SET RADII_FACTOR = 1.0 # The default is 0.82 (for soft-sphere restraints) WRITE_DATA FILE = '1fas', OUTPUT = 'PSA DIH NGH SSM CRV' After I run this script, I can get corresponding files: 1fas.dih 1fas.ngh 1fas.psa 1fas.sol 1fas.ssm. However, when I changed the last line "WRITE_DATA FILE = '1fas', OUTPUT = 'PSA DIH NGH SSM CRV'" into "WRITE_DATA FILE = '1fas', OUTPUT = 'ALL'" or "WRITE_DATA FILE = '1fas', OUTPUT = 'CRV CAV CROSS-SECTIONS'", I can not find 1fas.crv, 1fas.cav in the ouput directory. And there is no information on writing 1fas.crv and 1fas.cav in write_data.log file. Where can I get these two files or information about mainchain curvatures and protein internal cavity volums? is it a bug? Best regards Shuqun Liu

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hetatms placed far away from the backbone
by Michael Knoll 20 Oct '04

20 Oct '04

Dear Modellers, I'm trying to model a ZN-containing (two zn ions) protein with modeller6v2. I used : 'SET HETATM_IO = on' in the .top file and the following syntax in the .ali file : ------------------------------------------ >P1;template structure:template:2:A: :A: : : : ANHD...VGN---LYPE-/zz* >P1;target sequence:target: : : : : : : : ANHD...VGNPL-LYR-G/zz* --------------------------------------------- I renamed the ZN in the template pdb file to ZN2 and the residue numbers are continuous. The model building results in a model where the overall structure of the model looks almost good, but the zn atoms are PLACED FAR AWAY from the model backbone. I tried to solve this problem many times without success so far. So, I would be very happy if anybody could help me. Thanks to all in advance, Michael ******************************************** Michael Knoll email : michael.knoll(a)itb.uni-stuttgart.de ********************************************

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Modeller stopped with no specific error message
by 서주현 20 Oct '04

20 Oct '04

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calling subroutine defsym
by amc 20 Oct '04

20 Oct '04

Dear modellers, I am modelling a homotetramer protein and curious when or by what the subroutine 'defsym' is called. Cheers, Han

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Alignment file.
by bcur001＠ec.auckland.ac.nz 13 Oct '04

13 Oct '04

I'm doing something wrong, I'm a novice though, so I know what what. I'm using a fairly simple TOP script to generate a model a nitroreductase. I've used blast on NCBI to find a simialr protein to the one I have the pdb model for. The blast results look like this : Query: 1 MDIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARV 60 MDIISVALKRHSTKAFDASKKLT E+AE+IKTLLQYSPSSTNSQPWHFIVASTEEGKARV Sbjct: 1 MDIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARV 60 Query: 61 AKSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKG 120 AKSAAG YVFNERKMLDASHVVVFCAKTAMDD WL+ VVDQE+ADGRF TPEAKAAN KG Sbjct: 61 AKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKG 120 Query: 121 RKFFADMHRKDLHDDAEWMAKQVYLNVGNFXXXXXXXXXXXXPIEGFDAAILDAEFGLKE 180 R +FADMHR DL DD +WMAKQVYLNVGNF PIEGFDAAILD EFGLKE Sbjct: 121 RTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKE 180 Query: 181 KGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTE 216 KG+TSLVVVPVGHHSVEDFNATLPKSRLP + +TE Sbjct: 181 KGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTE 216 How do I then transform this into a successful alignment file? My attempt looks something like this: >P1;1OO5 structureX:1OO5: 2 :A: 217 :D:undefined:undefined:-1.00:-1.00 mdiisvalkrhstkafdaskkltpeqaeqiktllqyspsstnsqpwhfivasteegkarvaksaagnyvfnerkml dashvvvfcaktamddvwlklvvdqedadgrfatpeakaandkgrkffadmhrkdlhddaewmakqvylnvgnfll gvaalgldavpiegfdaaildaefglkekgytslvvvpvghhsvedfnatlpksrlpq nitltev* >P1;1NEC sequence:1NEC: 2 :A: 216 :D:undefined:undefined:-1.00:-1.00 DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKML DASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFL LGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTE* I've basically taken the Query sequence (1OO5) which I have the pdb file for and placed it in the sequence section, then taken the result sequence which has been matched to it (1NEC) and placed it in the second position of the alignment file with the sequence label. However, when I run it, in my mod.log file, I'm getting the error: Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL 1OO5.ali Dynamically allocated memory at amaxbnd [B,kB,MB]: 5377489 5251.454 5.128 openf5__224_> Open 11 OLD SEQUENTIAL 1OO5.ali read_al_375E> Unknown residue type,position,sequence: m 1 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 As far as I can gatherThis means that it doesn't like the residue at position one. I don't however know what it doesn't like about the residue at that position. Am I creating the alignment file in the wrong manner? Is there something else wrong? In case it of any use, the top file looks like: INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = '1ICV.ali' # alignment filename SET KNOWNS = '1ICV' # codes of the templates SET SEQUENCE = '1NEC' # code of the target # SET HYDROGEN_IO = on SET HETATM_IO = on SET ATOM_FILES_DIRECTORY = '../pdb' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 10 # index of the last model # (determines how many models to calculate) SET PDB_EXT = '.modlr.pdb' SET MD_LEVEL = 'refine_5' SET LIBRARY_SCHEDULE = 1 CALL ROUTINE = 'model Thanks. Ben.

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bumps in model
by Marc Gasser 13 Oct '04

13 Oct '04

dear Modellers, I used MUTATE_MODEL to mutate ALA into ILE. now the ILE bumps into another residue. turning the dihedral of the ILE sidechain manually in a viewer will solve this. but I want to include an automatic minimization process in the mutate.top script, which will do it for me. In the FAQ section I saw the question 2. which describes a similar problem, it refers to examples/tutorial-model/model-segment.top . but it's not so clear to me how to merge the mutate.top and the model-segment.top in one both_steps.top, does it really need an alignment for doing this optimization of one residue? thank you for good tips. marc

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PDB updates for Modeller
by Bruno Afonso 07 Oct '04

07 Oct '04

Dear modeller hackers :), I'm trying to use modeller to find good PDB templates and there is at least one structure that is missing from modeller's database, which is good since it was deposited Jun 2003 in PDB, released in august. Could it be because it is 3.3 A? Since I know this PDB is probably a good model and it won't come up in seq_search I was wondering how I could manually update CHAINS_all.seq or create my own sequence database. best, BA ps: I found in the archives a person asking a similar question regarding a PDB database update but no script or url was given to get a newer version, or without resolution cut-off. :-) -- Bruno Afonso http://brunoafonso.net http://dequim.ist.utl.pt/~bruno/sciTocs/ - Bruno's SciTocs! http://freebsd-pt.org/forum/ - Portuguese FreeBSD forum

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Markus Jaritz is out of the office.
by markus.jaritz＠pharma.novartis.com 04 Oct '04

04 Oct '04

I will be out of the office starting 10/04/2004 and will not return until 10/18/2004. I will answer your mail when I am back.

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Modeller 7v7 AIX binary: now available
by Modeller Caretaker 01 Oct '04

01 Oct '04

For those of you who wish to use the new Modeller release, 7v7, on AIX systems: an AIX binary is now available. This is distributed as part of the 'Other Linux/Unix' download, at: http://salilab.org/modeller/download_installation.html Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mailing list: http://salilab.org/mailman/listinfo/modeller_usage

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