- modeller_usage - salilab.org

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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problem
by vivek sharma 29 Sep '04

29 Sep '04

Dear Sir, Thank you very much for all previous replies. I am having some problems, please provide a solution to them. 1. Is the value of objective function obtained after complete process of MODELER , system size specific? I mean when I model a system of > 500 residues (target), it generates >50000 restraints (3 templates used) and final value of objective function is >20000, but when I model a part of the target , taking respectively aligned template portions, approx 150 residues (target), the restraints generated are around 9000 and final value of objective function comes to 2000 units. So, this shows that smaller the system , lower the final value of objective function, same restraints selected in both cases and assume no violations. Please comment 2. Also, how can one decide that such high values of objective function are acceptable or not, assume there are no violations? (Please specify if you have such experience/idea of Modelling bigger proteins.) 3. Thirdly, from documentation I came to understand that, that when one wants to generate non bonded pair restraints as static ones, he has to include them in MAKE_RESTRAINTS command and keep all DYNAMIC_SPHERE, LENNARD, COULOMB, etc off. Can you tell me which is better , non bonded restraints used as static or non bonded restraints as dynamic (generated automatically by MODELER on fly)? Please explain. Thank you very much in advance. sincerely, Vivek Sharma Graduate Student (Biochemistry/Biophysics) University of Helsinki.

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use NMR as template
by remo 27 Sep '04

27 Sep '04

hi i'm Remo and i'm new with modeller... i'd like to know if : - is possible to use an NMR file with 24 structures as template - how to make in any way an averaged structure and then use this one as template - there are some useful tricks to handle NMR structures i hope in your help -- ----------------------------------------------------------- Dr Remo Calabrese, PhD Student Dipartimento di Biologia Evoluzionistica Sperimentale University of Bologna Via Irnerio,42 40126 Bologna Italy email: remo(a)biocomp.unibo.it tel. + 39 051 2094005 fax. + 39 051 242576 -----------------------------------------------------------

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problem
by vivek sharma 23 Sep '04

23 Sep '04

Dear Sir, I went through the model.top script and and tried to understand that how it works. But there are few problems in understanding that script, please guide me for these mentioned problems. 1. In OPTIMIZE process (VTFM optimization), the addition of restraints is governed by PICK_RESTRAINTS which in turn depend on SCHEDULE file (3rd column, NRNG), meaning thereby that only those restraints will be taken into consideration which applies on atoms, which comes in category as specified by Schedule file (3rd column). Although in .log file I found restraints are added step by step (N_SCHEDULE step) during optimization , are the atoms also added continously, or just explain a bit how this profile goes? 2. Out of curiosity I ask this question, if all restraints and all atoms are taken into consideration at a time, and then optimization is done, will that be better/efficient than the method it takes in model.top? 3. Also, I observed that this addition of restraints (for every N_SCHEDULE step) during optimization increases the value of objective function , and it finally stops at a higher value, will that value be considered final one or various such consequent optimization cycles should be carried out to finally lower down the value? Please reply , I will be very thankful to you. Hope to receive explainatory reply. Thanking you in advance, sincerely, -- VIVEK SHARMA Graduate Student, (Biochemistry/Biophysics) University of Helsinki

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Defining the centre of a helix and restraints
by John Simms 22 Sep '04

22 Sep '04

Hi All, I have a small problem. I work on GPCRs and would like to use some electron crystallography data. However, the data given are distances between the centres of transmembrane alpha helices rather than a specific atom eg CA. Does anyone know how I would specify the centre of a helix when using distance restraints?. Many Thanks in advance John

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Crash under 7v7
by John Penniston 21 Sep '04

21 Sep '04

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Problem with alignment file
by 柳田　亮 17 Sep '04

17 Sep '04

Please help me. I cannot figure out this error. -- MODELLER 7v7, Sep 12, 2004 09:15pm Kind, OS, HostName, Kernel, Processor: 4, Darwin 7.5.0 Power Macintosh Date and time of compilation : 09/14/2004 09:31:49 Job starting time (YY/MM/DD HH:MM:SS): 2004/09/17 20:55:55.058 TOP_________> 109 749 SET ALNFILE = 'align.txt' TOP_________> 110 750 SET KNOWNS = '1stc' TOP_________> 111 751 SET SEQUENCE = 'pkcAcat' TOP_________> 112 752 SET ATOM_FILES_DIRECTORY = './' TOP_________> 113 753 SET STARTING_MODEL = 1 TOP_________> 114 754 SET ENDING_MODEL = 1 TOP_________> 115 755 SET HETATM_IO = ON TOP_________> 116 756 CALL ROUTINE = 'model' TOP_________> 117 419 CALL ROUTINE = 'getnames' TOP_________> 118 534 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 119 535 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 120 536 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 121 537 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 122 538 SET ROOT_NAME = SEQUENCE TOP_________> 123 539 RETURN TOP_________> 124 420 CALL ROUTINE = 'homcsr' TOP_________> 125 112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 84067 82.097 0.080 openf5__224_> Open 20 OLD SEQUENTIAL align.txt rdpir___270E> Error reading/processing file: align.txt recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 84067 82.097 0.080 Starting time : 2004/09/17 20:55:55.058 Closing time : 2004/09/17 20:55:57.131 Total CPU time [seconds] : 1.88 -- >P1;1stc structureX:1stc:15::350::::: GNAAAAKKGSEQESVKEFLAKAKEDFLKKWESPAQNTAHLD-----QFERIKTLGTGSFG RVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVN-FPFLVKLEFSFKDNS NLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLI DQQGYIQVTDFGFAKRVKGR---TWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEM AAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDI KNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEE-------EIRVSINEKCG KEFSEF* >P1;pkcAcat sequence:pkcAcat:1::336::::: EGDEEGNMELRQKFEKAKLGPAGNKVISPSEDRKQPSNNLDRVKLTDFNFLMVLGKGSFG KVMLADRKGTEELYAIKILKKDVVIQDDDVECTMVEKRVLALLDKPPFLTQLHSCFQTVD RLYFVMEYVNGGDLMYHIQQVGKFKEPQAVFYAAEISIGLFFLHKRGIIYRDLKLDNVML DSEGHIKIADFGMCKEHMMDGVTTRTFCGTPDYIAPEIIAYQPYGKSVDWWAYGVLLYEM LAGQPPFDGEDEDELFQSIMEHNVSYPKSLSKEAVSICKGLMTKHPAKRLGCGPEGERDV REHAFFRRIDWEKLENREIQPPFKPKVCGKG-AENFDKFFTRGQPVLTPPDQLVIANIDQ SDFEGF*

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RE: [modeller_usage] Problem with alignment file
by Schweikardt, Thorsten 17 Sep '04

17 Sep '04

Hi Charles (?), check your input pdb file, find out if all aminoacids in your alignment are present in your pdb file. You should also specify the chain ID in your alignment, your chain of interest is called "E": structureX:1stc:15:E:350:E:::: do you really have a space in front of "P1;1stc"? Maybe that's also a problem, but I do not know how your system handles this (you are using a Mac, right?) Best wishes, Thorsten Schweikardt Molecular Biophysics University of Mainz, Germany > -----Original Message----- > From: modeller_usage-bounces(a)salilab.org > [mailto:modeller_usage-bounces@salilab.org] On Behalf Of ?? ? > Sent: Friday, September 17, 2004 2:06 PM > To: modeller_usage(a)salilab.org > Subject: [modeller_usage] Problem with alignment file > > > Please help me. I cannot figure out this error. > > -- > > MODELLER 7v7, Sep 12, 2004 09:15pm > > Kind, OS, HostName, Kernel, Processor: 4, Darwin 7.5.0 Power > Macintosh > Date and time of compilation : 09/14/2004 09:31:49 > Job starting time (YY/MM/DD HH:MM:SS): 2004/09/17 20:55:55.058 > > TOP_________> 109 749 SET ALNFILE = 'align.txt' > > TOP_________> 110 750 SET KNOWNS = '1stc' > > TOP_________> 111 751 SET SEQUENCE = 'pkcAcat' > > TOP_________> 112 752 SET ATOM_FILES_DIRECTORY = './' > > TOP_________> 113 753 SET STARTING_MODEL = 1 > > TOP_________> 114 754 SET ENDING_MODEL = 1 > > TOP_________> 115 755 SET HETATM_IO = ON > > TOP_________> 116 756 CALL ROUTINE = 'model' > > TOP_________> 117 419 CALL ROUTINE = 'getnames' > > TOP_________> 118 534 STRING_IF STRING_ARGUMENTS = MODEL > 'undefined', OPERATION; > = 'EQ', THEN = 'STRING_OPERATE > OPERATION = > CONCATENA; > TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = > MODEL' > > TOP_________> 119 535 STRING_IF STRING_ARGUMENTS = CSRFILE > 'undefined', OPERATI; > ON = 'EQ', THEN = 'STRING_OPERATE > OPERATION = > CONCATE; > NATE, STRING_ARGUMENTS = SEQUENCE > .rsr, RESULT = > CSRFILE; > ' > > TOP_________> 120 536 STRING_OPERATE OPERATION = > 'CONCATENATE', > ; > STRING_ARGUMENTS = SEQUENCE '.sch', > RESULT = > SCHFILE > > TOP_________> 121 537 STRING_OPERATE OPERATION = > 'CONCATENATE', > ; > STRING_ARGUMENTS = SEQUENCE '.mat', > RESULT = > MATRIX_FI; > LE > > TOP_________> 122 538 SET ROOT_NAME = SEQUENCE > > TOP_________> 123 539 RETURN > > TOP_________> 124 420 CALL ROUTINE = 'homcsr' > > TOP_________> 125 112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = > KNOWNS SEQUE; > NCE > > > Dynamically allocated memory at amaxseq [B,kB,MB]: > 84067 > 82.097 0.080 > openf5__224_> Open 20 OLD SEQUENTIAL align.txt > rdpir___270E> Error reading/processing file: align.txt > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > Dynamically allocated memory at finish [B,kB,MB]: > 84067 > 82.097 0.080 > Starting time : > 2004/09/17 > 20:55:55.058 > Closing time : > 2004/09/17 > 20:55:57.131 > Total CPU time [seconds] : 1.88 > > -- > >P1;1stc > structureX:1stc:15::350::::: > GNAAAAKKGSEQESVKEFLAKAKEDFLKKWESPAQNTAHLD-----QFERIKTLGTGSFG > RVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVN-FPFLVKLEFSFKDNS > NLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLI > DQQGYIQVTDFGFAKRVKGR---TWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEM > AAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDI > KNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEE-------EIRVSINEKCG > KEFSEF* > > > >P1;pkcAcat > sequence:pkcAcat:1::336::::: > EGDEEGNMELRQKFEKAKLGPAGNKVISPSEDRKQPSNNLDRVKLTDFNFLMVLGKGSFG > KVMLADRKGTEELYAIKILKKDVVIQDDDVECTMVEKRVLALLDKPPFLTQLHSCFQTVD > RLYFVMEYVNGGDLMYHIQQVGKFKEPQAVFYAAEISIGLFFLHKRGIIYRDLKLDNVML > DSEGHIKIADFGMCKEHMMDGVTTRTFCGTPDYIAPEIIAYQPYGKSVDWWAYGVLLYEM > LAGQPPFDGEDEDELFQSIMEHNVSYPKSLSKEAVSICKGLMTKHPAKRLGCGPEGERDV > REHAFFRRIDWEKLENREIQPPFKPKVCGKG-AENFDKFFTRGQPVLTPPDQLVIANIDQ > SDFEGF* > > >

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Announcing MODELLER 7v7
by Modeller Caretaker 16 Sep '04

16 Sep '04

Dear MODELLER user, MODELLER 7v7 is now available for download, for Linux (both i686 PC, and Itanium 2), Windows, Mac OS X, Sun, SGI and Alpha (AIX binaries to follow shortly). This release fixes a number of minor bugs in 6v2, introduces some new commands for handling profiles, improves structure handling by using PDB rather than CHARMM naming for toplogy libraries, and offers many other new features. Please refer to the Modeller website at http://salilab.org/modeller/, in particular the 7v7 release notes at http://salilab.org/modeller/release.shtml, for futher information on downloading, registering, and installing Modeller. 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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