- modeller_usage - salilab.org

"Precision problem"
by Oliver Hucke 21 Dec '04

21 Dec '04

Hi all, I just started to use the newest version of modeller. I noticed unfamiliar warnings in the log file: conmin__610W> Precision problem; starting from scratch. conmin__611W> Precision problem; starting from scratch. Last such mesage in this OPTIMIZE What does this mean? Should I worry about this or can it be ignored? Thanks in advance, Oliver -- ________________________________________________________________ Oliver Hucke, Dr. Biomolecular Structure Center Health Sciences Building - K418C Dept. of Biochemistry 1959 NE Pacific St. University of Washington phone: (206) 685 7046 Box 357742 fax : (206) 685 7002 Seattle, WA 98195-7742 email: ohucke(a)u.washington.edu ________________________________________________________________

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Script for superimposing generated models
by Ivan Bosanac 17 Dec '04

17 Dec '04

Hello All, I have been having some problems superimposing generated models on top of my template coordinance. I have used SET FINAL_MALIGN3D = 1 command in my top file but not *_fit files were given. This is puzzling to me since using the same top script for a different modeling job worked well and *_fit files were generated. Let me say that I am very new to Modeller, and script driven software in general, and for that reason would greatly appreciate if somebody could explain to me why *_fit files were not created. Moreover, I would be very grateful if somebody could provide me with the script that could be used for the purpose of superimposing .B999000* onto the template file after top script has been executed. Thanks in advance, Ivan ps: This is my model.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 = 'align.ali' # alignment filename SET KNOWNS = 't1b1' # codes of the templates SET SEQUENCE = 't3b1' # code of the target SET ATOM_FILES_DIRECTORY = '' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 30 # index of the last model # (determines how many models to calculate) SET MD_LEVEL = 'refine_3' # defalt is 1; 5 is very slow with MD anne. SET FINAL_MALIGN3D = 1 # superimposis template and resulting pdb SET LIBRARY_SCHEDULE = 1 SET REPEAT_OPTIMIZATION = 10 SET RSTRS_REFINED = 2 SET MD_RETURN = 'FINAL' CALL ROUTINE = 'model' # do homology modelling

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array problem
by vivek sharma 17 Dec '04

17 Dec '04

Dear sir, I have included few residues in top_heav.lib and I am using MODELLER 6v2. After running it gave errors regarding array, it says array small for MAPRES, so I deleted some atoms from my defined residue and it worked a step better but now it gives another error, similar to that. Please explain what can be the reason. Error is: read_to_223E> Array too small. Increase MCNSRES current maximum, current need: 100 104 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Thanks in advance. Regards, Vivek Sharma -- VIVEK SHARMA HBG BI "You must be the change you wish to see in the world." MKG

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Bad Model
by A R 16 Dec '04

16 Dec '04

Hi, Im trying to model a 58% identity protein with the template, but after alignment, the model.top generates a very different model from the template. Can anybody suggests me what can I change in my model.top to make this better? Thanks. The alignment is using MALIGN with gap penalties of -600 and -400: >P1;1xxx structureX:1xxx: 5 :A: 689 :B:undefined:undefined:-1.00:-1.00 MAVKVEYDLKRLRNIGIAAHIDAGKTTTTERILYYTGRIHKIGEVHEGAATMDFMEQERERGITITAAVTTCFWK DHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVI RTMQERLGARPVVMQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDQAREYHEKLVEVAADFDE NIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVE IHPDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLG AVVGLKETITGDTLVGEDAPRVILESIEVPEPVIDVAIEPKTKADQEKLSQALARLAEEDPTFRVSTHPETGQTI ISGMGELHLEIIVDRLKREFKVDANVGKPQVAYRETITKPVDVEGKFIRQTGGRGQYGHVKIKVEPLPRGSGFEF VNAIVGGVIPKEYIPAVQKGIEEAMQSGPLIGFPVVDIKVTLYDGSYHEVDSSEMAFKIAGSMAIKEAVQKGDPV ILEPIMRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFFDH YQEVPKQVQEKLIKGQ* >P1;03883 sequence:03883: : : 696 : :::-1.00:-1.00 -MMARKFELKDYRNIGIMAHIDAGKTTTTERILFHTGKIHKIGETHDGVSQMDWMEQEKERGITITSAATTAFWK GKRINIIDTPGHVDFTVEVERSLRVLDGAVAVLDAQSGVEPQTETVWRQATNYSVPRIVYVNKMDKAGANFEASI ESVRTKLNGNAVAIQLNIGAEADFSGLIDLVEMKAYNYDGQKEEIEYEIPIPEDLFEKASQMRLALAEAVADYDE EIFNNLLEEKEILPEQLKAAIRAATITGNFFPVVCGSSFKNKGVKKMIDAVIDYLPSPVDVPPIKAFRDEEEIT- IEASDDQEFSALAFKIMNDPFVGSLTFFRVYSGVLKKGTYIINSTKGKKERVGRILAMHANSREEIDEVRTGDIG AFVGLKDTTTGDSLISEKAKTFVLERMNFPEPVISQSLEPFSKAEIEKLATALQKLANEDPTFKTWTDIETGQTI IAGMGELHLDIIVDRLKREFNVQARVGKPQVSYRETITKSAEVEGKYIKQSGGRGQYGHVWIKFEPNPE-EGFDF IDKIVGGKIPKEYIKSIQKGLEEKMQAGILAGYPLINLRATLFDGSFHEVDSSEMAFKIAASKALSRARDAVGTV LLEPIMDVSVFAPSEYAGDVMGDLSRRRGLVREQETRSDGANVIRGHVPLAEMFGYSTQLRSMTSGRGTYQMQFN HYEIVPKNISDVIVKQRAIKEDD* the model.top is: INCLUDE SET ALNFILE = 'malign.pir' SET KNOWNS = '1ktv' SET SEQUENCE = '03883' SET ATOM_FILES_DIRECTORY = './:../atom_files' SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 CALL ROUTINE = 'model' ___________________________________________________________ Moving house? Beach bar in Thailand? New Wardrobe? Win £10k with Yahoo! Mail to make your dream a reality. Get Yahoo! Mail www.yahoo.co.uk/10k

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How to constrain internal coordinates for identical residues
by James T Metz 10 Dec '04

10 Dec '04

Modeller Users, Does anyone know how to constrain internal coordinates, especially dihedral angles, only for residues which are identical between my X-ray template and my unknown sequence. In other words, if I am building a lysine on top of a lysine, how can I get the internal coordinates to be exactly the same? Is there a way to automate the generation of the constraints rather than having to do this for each and every template/unknown sequence pair? Thanks in advance. Regards, Jim Metz James T. Metz, Ph.D. Research Investigator Chemist GPRD R46Y AP10-2 Abbott Laboratories 100 Abbott Park Road Abbott Park, IL 60064-6100 U.S.A. Office (847) 936 - 0441 FAX (847) 935 - 0548 james.metz(a)abbott.com This communication may contain information that is legally privileged, confidential, or exempt from disclosure. If you are not the intended recipient, please note that any dissemination, distribution, use, or copying of this communication is strictly prohibited. Anyone who receives this message in error should notify the sender immediately by telephone or return email and delete it from his or her computer.

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Re: [modeller_usage] alignment question
by aline 07 Dec '04

07 Dec '04

Thank you all for the answers. I've corrected the problem that Windows gave me. Windows made some terrible things with my sequence, but apparently nothing was going wrong. now everything is going just fine. Darren Thompson escreveu: > You must have an unnecessary space or carriage return in your .top > file. The command not recognized happens when modeller interprets a > carriage return and the next line does not have a modeller command. > > good luck! > Darren > On Tuesday, December 7, 2004, at 06:47 AM, Aline Rossi wrote: > > Hi, > Im trying to make an alignment, but i receive an error: > Kind, OS, HostName, Kernel, Processor: 4, SunOS caprichosa 5.8 sun4u > Date and time of compilation : 09/12/2004 21:16:03 > Job starting time (YY/MM/DD HH:MM:SS): 2004/12/07 11:29:11.627 > > rdactio_534E> Command not recognized: > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > Dynamically allocated memory at finish [B,kB,MB]: > 56755 55.4 > 25 0.054 > Starting time : > 2004/12/07 11:29:11.6 > 27 > Closing time : > 2004/12/07 11:29:13.0 > 97 > Total CPU time [seconds] : 0.00 > The .seq is: > >P1;03883 > > sequence:03883: : : 696 : :::-1.00:-1.00 > > -MMARKFELKDYRNIGIMAHIDAGKTTTTERILFHTGKIHKIGETHDGVSQMDWMEQEKERGITITSAATTAFWK > > > GKRINIIDTPGHVDFTVEVERSLRVLDGAVAVLDAQSGVEPQTETVWRQATNYSVPRIVYVNKMDKAGANFEASI > > > ESVRTKLNGNAVAIQLNIGAEADFSGLIDLVEMKAYNYDGQKEEIEYEIPIPEDLFEKASQMRLALAEAVADYDE > > > and so go....... > > >P1;1KTV > > structureX:1KTV: 1 :B : 691 :B : Elongation Factor G: The > > MAVKVEYDLKRLRNIGIAAHIDAGKTTTTERILYYTGRIHKIGEVHEGAATMDFMEQERERGITITAAVTTCFWK > > > DHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVI > > > and so go..... > > > > And the align2d.top is: > > INCLUDE > > READ_MODEL FILE = '1KTV' > > SEQUENCE_TO_ALI ALIGN_CODES = '1KTV' > > READ_ALIGNMENT FILE = '03883.seq', ALIGN_CODES = ALIGN_CODES > '03883', ADD_SEQUENCE = on > > ALIGN2D > > WRITE_ALIGNMENT FILE='03883-KTV.ali', ALIGNMENT_FORMAT = 'PIR' > > WRITE_ALIGNMENT FILE='03883-KTV.pap', ALIGNMENT_FORMAT = 'PAP' > > > > Whats wrong???? > > > > Thank you very much > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > http://salilab.org/mailman/listinfo/modeller_usage > >

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alignment question
by Aline Rossi 07 Dec '04

07 Dec '04

Hi, Im trying to make an alignment, but i receive an error: Kind, OS, HostName, Kernel, Processor: 4, SunOS caprichosa 5.8 sun4u Date and time of compilation : 09/12/2004 21:16:03 Job starting time (YY/MM/DD HH:MM:SS): 2004/12/07 11:29:11.627 rdactio_534E> Command not recognized: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 56755 55.4 25 0.054 Starting time : 2004/12/07 11:29:11.6 27 Closing time : 2004/12/07 11:29:13.0 97 Total CPU time [seconds] : 0.00 The .seq is: >P1;03883 sequence:03883: : : 696 : :::-1.00:-1.00 -MMARKFELKDYRNIGIMAHIDAGKTTTTERILFHTGKIHKIGETHDGVSQMDWMEQEKERGITITSAATTAFWK GKRINIIDTPGHVDFTVEVERSLRVLDGAVAVLDAQSGVEPQTETVWRQATNYSVPRIVYVNKMDKAGANFEASI ESVRTKLNGNAVAIQLNIGAEADFSGLIDLVEMKAYNYDGQKEEIEYEIPIPEDLFEKASQMRLALAEAVADYDE and so go....... >P1;1KTV structureX:1KTV: 1 :B : 691 :B : Elongation Factor G: The MAVKVEYDLKRLRNIGIAAHIDAGKTTTTERILYYTGRIHKIGEVHEGAATMDFMEQERERGITITAAVTTCFWK DHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVI and so go..... And the align2d.top is: INCLUDE READ_MODEL FILE = '1KTV' SEQUENCE_TO_ALI ALIGN_CODES = '1KTV' READ_ALIGNMENT FILE = '03883.seq', ALIGN_CODES = ALIGN_CODES '03883', ADD_SEQUENCE = on ALIGN2D WRITE_ALIGNMENT FILE='03883-KTV.ali', ALIGNMENT_FORMAT = 'PIR' WRITE_ALIGNMENT FILE='03883-KTV.pap', ALIGNMENT_FORMAT = 'PAP' Whats wrong???? Thank you very much

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Extend the helix
by Narasimhamurthy. 02 Dec '04

02 Dec '04

dear all, i am modeling a hepta-helical membrane protein. I want to elongate couple of my helices one-two loop more. Say for example, I have already modelled a helix 1-35 and extend it up 45 residue. I am using SUBROUTINE ROUTINE = 'special_restraints' MAKE_RESTRAINTS RESTRAINT_TYPE = 'ALPHA', RESIDUE_IDS = '35:' '45:' RETURN END_SUBROUTINE It works but in that process, it always disturbs the helical conformation at the boundary, in this example, for 34-36 residues. There ia a trivial way to use special restriant, to model alpha helix for whole 1-45 residue, but I dont want to do that since, this way, all the conserved kinks and helical bent would be lost. Is there any way to extend the helix appropriately. Thanks, T. Narasimhamurthy Bioinformatics Center IISc Bangalore

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chain identifiers
by John Simms 02 Dec '04

02 Dec '04

Hi All, I am generating a number of models based on soluble protein. There is a large loop in the protein which i dont wish to include in my models, but i do want to add a chain break. Is there a way for the residues in the resulting models to have different chain identifiers before and after the break? Any help would be very gratefully received John

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Re: [modeller_usage] multi domain protein help
by Mr.Sridhar 01 Dec '04

01 Dec '04

Hi Ranjit, There should be atleast a small region of overlapping structure between the consecutive domains to get the domains in their proper orientation. Make a structural alignment of the three domains, and to this profile align your sequence. Use this for modeller. Regards.

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