- modeller_usage - salilab.org

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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multi domain protein help
by Ranjit Kumar 30 Nov '04

30 Nov '04

hi i have to model a protein that has 3 domains all crystallized in different organism.i am new in modelling, can anybody help me in this regard?

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combining two proteins
by Han Choe 29 Nov '04

29 Nov '04

Dear all, Let's say that I have two pdb files of protein A and protein B and that approximate interactions of the two proteins are known. Then can I get a complex structure using MODELLER by restraining the distances of two or three interactions between A and B in the top file with the following type of alignment file? >P1;A structureX:A --AAAAA--/------------* >P1;B structureX:B -------------/--BBBBB--* >P1;AB sequence:AB --AAAAA--/--BBBBB--* Cheers, Han

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problem
by vivek sharma 29 Nov '04

29 Nov '04

Dear sir, To generate a model containing Hydrogen atoms, is it necessary that templates should have Hydrogen atoms too or these will be modeled by MODELER itself? Thanking you, sincerely, Vivek Sharma -- VIVEK SHARMA HBG BI

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Modelling multiple chains
by gerald.quon＠utoronto.ca 29 Nov '04

29 Nov '04

Hi, I'm interested in modelling a dimer composed of two chains. I would definitely like to avoid modelling each chain separately, then combining the PDB files - is it possible to model them together in MODELLER? I would try just concatenating the two chains into one, but i'm guessing the discontinuity of the backbone will mess around with the minimization... Gerald

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upper and lower distance restraints
by Youbin Tu 29 Nov '04

29 Nov '04

Hi all: I want to define some restraints in the top file. Assume we know the maximum and minimum distances between two atoms (non-bond), Which form and group type should we use? since there are so many types of groups to define distance restraints, which one should I use for my case? I looked through the manual, but did not find enough talking about it. Here is an example, The maximum distance between Fe:513 and C7:514 is 6.0(1.0) The miminum distance between Fe:513 and C7:514 is 2.0(1.0) I included the following line in the top file: SUBROUTINE ROUTINE = 'special_restraints' ADD_RESTRAINT ATOM_IDS = 'FE:513' 'C7:514', ; RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 6.0 1.0 ADD_RESTRAINT ATOM_IDS = 'FE:513' 'C7:514', ; RESTRAINT_PARAMETERS = 1 1 1 21 2 2 0 2.0 1.0 RETURN END_SUBROUTINE Is it correct? Again, If I did so, does that mean that the program have to force the distance between those 2 atoms within that range even though it may take the risk to corrupt the whole structure? Or if some restraints will destroy the whole structure, the program will discard the user's restraints in order to " save" the final model? thanks. youbin ---------------------- Youbin Tu CCMM Lab,BPS Schoof of Pharmacy,WVU

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How to preserve internal coordinates for identical residues
by James T Metz 29 Nov '04

29 Nov '04

Modeller Users, Sorry if this is a FAQ, but ... Is there a simple command or set of TOP keywords that will preserve internal coordinates (especially dihedral angles) when an amino acid in my structure file and the amino acid in my alignment file are identical? In other words, I would like to constrain (fix) internal coordinates when there is no change of amino acids when building homology models. Please also comment if for some reason this is not a good idea. 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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