December 2004 - modeller_usage

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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