- modeller_usage - salilab.org

Respected Sir.
by sameer hassan 10 Nov '03

10 Nov '03

Respected Sir, I am interested in knowing more about modeller. So, I request you to help me for the same. The following are the questions: 1) what is the protocol for starting with the top scripts, i.e, starting with alignment that what..? 2)is transfer_xyz.top to be carried out first before model-default or the other way? 3) will not modeller(model-default.top) itself build the loop. Then why is the loop top script for? if i want to bulit the loop separately using loop top script, is it that i have to carry out loop topscript first before model-default top script or the other way? 4)During model-default. top, if for certain residues co-ordinates are not assigned then what is the solution for that? 5)In one of the article, i have read, after building the model it is to compare the Z score for both the template and the target. where will be the Z score given, will it be given in the log file of model-default. 6)will modeller show any error if the target and the template sequences differ in lenght? 7)After building a model for the target, how will i be able to improve the structure? if i iterate the same procedure will it improve the structure? I would be grateful to you if you could help me in finding answers for the above questions. Thanking you and waiting for your reply. Sincerely, Sameer. H

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Installation on MacOSXvx
by bose 06 Nov '03

06 Nov '03

Hi, I have tried to install Modeller6v2 on the MacOSXv2 and it seems like the installation works but then the mod6v2 command is not recognized. My .cshrc file has been modified and contains all the settings that is suggested in the ReadMe file. Could I have some advice on how to get the program kicking. Thank you. Regards, Bose.

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How many swap space does MODELLER need??
by B.Liu 06 Nov '03

06 Nov '03

A silly problem, but it is a problem. Thanks for any advice. Binbin

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modelling problem
by Francesco Musiani 04 Nov '03

04 Nov '03

hello everyone, I want to model a big protein (a trimer of about 840 aa) using three template structures. When I try to model with only one template there is no problem, when I add the second template structure the program bombs in the way I report below, can someone help me, please? Francesco P.S. I'm running Modeller 6v2 on a RehHat 7.2 linux workstation ------------------- TOP_________> 162 131 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'CA' Number of atoms to choose from, total : 19104 19104 Atom types to be searched for (ATOM_TYPES) : CA Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 2520 1: 2520: selatm__462_> Number of selected atoms : 2520 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 2520 : PHE 2520 TOP_________> 163 132 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 121143079 118303.800 115.531 make_re_417_> Restraint type to be calculated: distance r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: --------- a lot of these lines --------- r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 stdevs__397E> STDEV < 0: -0.0995 Set to 1E-5. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 121143079 118303.800 115.531 Starting time : 2003/11/04 15:14:45.269 Closing time : 2003/11/04 15:16:33.274 Total CPU time [seconds] : 91.05 -- ------------------------------------------------------- Francesco Musiani Department of Agro-Environmental Science and Technology University of Bologna Phone: 051-2096233 - 051-2096236 --- Fax. 051-2096203 mail: fmusiani(a)agrsci.unibo.it -------------------------------------------------------

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hello
by Chaitanya Reddy.A 29 Oct '03

29 Oct '03

hello everyone.. Can anyone give the description of formats of .RSR,.V9999????,.B9999????,.schedule files?? Thanks in advance A.Chaitanya Reddy

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Bug in user distance restraints ?
by Thorsten Schweikardt 28 Oct '03

28 Oct '03

Hello to all, I am having problems to use the user distance restraints, they are ignored completely by Modeller 6v1/6v2latest, Windows and Linux- versions: at first I thought they were not met entirely, but then I ran some tests, with and without the restraints: The 50 models I get when using the restraints are identical to those that are modeled using no restraints at all... Modeller really reads the commands (because using a "0.0" as standard deviation crashes it), but it does not seem to incorporate the distances into the model. Changing the form of the restraints (gaussian, LJ, cosine etc) or using different atoms (CA instead of OG) did not help. My goal is to model the n-terminus of a protein that's available as pdb with the help of measured distances from Electron Spin Resonance. Could you please tell me whether I am doing something wrong (syntax?) or if there is a bug of some kind? I would be very grateful for an answer. Thanks again for listening, Thorsten Schweikardt University of Mainz My Top-File: ----------------------------- INCLUDE SET ALNFILE = 'alignment.ali' SET KNOWNS = 'protein1' SET SEQUENCE = 'protein1plusnterm' SET ATOM_FILES_DIRECTORY = './' SET STARTING_MODEL= 1 SET ENDING_MODEL = 20 SET LIBRARY_SCHEDULE = 4 SET FINAL_MALIGN3D = 1 CALL ROUTINE = 'model' SUBROUTINE ROUTINE = 'special_restraints' #eg. Distance Serine-OH AA3 to Serine-OH AA169: 30Angstrom SET ATOM_IDS = 'OG:3' 'OG:169' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 30.0 1.0 SET ATOM_IDS = 'OG:116' 'OG:169' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 40.0 0.0 SET ATOM_IDS = 'CA:42' 'CA:169' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 40.0 1.0 SET ATOM_IDS = 'CA:3' 'CA:42' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 21.0 4.0 SET ATOM_IDS = 'CA:3' 'CA:116' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 50.0 1.0 RETURN END_SUBROUTINE

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hello
by Chaitanya Reddy.A 28 Oct '03

28 Oct '03

hello everyone... I am novice in using modeller.Thanks for your reply for my previous mail. the file /mod6v2/modlib/CHAINS_3.0_40_XN.GRP; has pdb codes in the following format 1xnb : 1c5hA 1refA 1bvv 2bvvA 1xnd 1redA 1reeA 1xnb 1ukrA 1xnc 1xypA 1yna 1bk1 1xyn 1xyoA 1bcx 1enxA 1pvxA 1c5iA 1qh6A 1qh7A 1hv0A 1hv1A 1hixA 1hixB 1bpyA : 8icfA 8icvA 9icfA 9icvA 7icfA 7icvA 1zqfA 2bpfA 8icgA 8icwA 9icgA 9icwA 7icgA 1zqgA 2bpgA 8ictA 9ictA 7ictA 1zqdA 1zqtA 1bpd 8iceA 8icuA 9iceA 9icuA 7iceA 7icuA 1zqeA 1bpe 8icbA 8icrA 9icbA 9icrA 7icrA 1zqbA 1zqrA 8iccA 8icsA 9iccA 9icsA 7icsA 1zqcA 1zqsA 8icpA 9icpA 7icpA 1zqpA 8icaA 8icqA 9icaA 9icqA 7icqA 1zqaA 1zqqA 8icnA 9icnA 7icnA 1zqnA 8icoA 9icoA 7icoA 1zqoA 8iclA 9iclA 7iclA 1zqlA 8icmA 9icmA 7icmA 1zqmA 8icjA 8iczA 9icjA 7icjA 1zqjA 1bpzA 8ickA 9ickA 7ickA 1zqkA 8ichA 8icxA 9ichA 9icxA 7ichA 1zqhA 1bpxA 8iciA 8icyA 9iciA 9icyA 7iciA 1zqiA 1bpyA 1cf6A 1huoA 1huzA .......................... ..................... ........................ .................................... Doubts: a)Why the PDB code 1xnb is seperated from the other PDB codes with a colon.(:) b)Why the pdb codes aren't listed continuously.Why are they listed on seperate lines? Thanks in advance A.Chaitanya Reddy

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Hello
by Chaitanya Reddy.A 28 Oct '03

28 Oct '03

Hello everyone.. Could anyone explain me the "SET OUPUT_CONTROL " command? Thanks in advance With regards A.Chaitanya Reddy.

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rdactio_534E> Command not recognized: INPUT :
by Joseph Toth 27 Oct '03

27 Oct '03

Hi, I have been trying to run the model script and it keeps crashing with the message: rdactio_534E> Command not recognized: INPUT : recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Someone else used a similar model script successfully on the same machine but I can't figure out what is wrong with my input files. I would appreciate any suggestions. Is this a TOP or a fortran formatting error? How do I narrow down the problem? MODEL.top # 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 = 'Pab1.seg.ali' # alignment filename SET KNOWNS = '1CVJ 1G2E 1FXL 1FNX 1HL6 1P1T' # codes of the templates SET SEQUENCE = 'Pab1' # 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 = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling Pab1.seg.ali >P1;Pab1 sequence:Pab1:FIRST:@:LAST:@:polyadenylate-binding protein 1:Saccharomyces cerevisiae:-1.00:-1.00 MADITDKTAEQLENLNIQDDQKQAATGSESQSVENSSASLYVGDLEPSVSEAHLYDIFSPIGSVSSIRVCRDAIT KTSLGYAYVNFNDHEAGRKAIEQLNYTPIKGRLCRIMWSQRDPSLRKKGSGNIFIKNLHPDIDNKALYDTFSVFG DILSSKIATDENGKSKGFGFVHFEEEGAAKEAIDALNGMLLNGQEIYVAPHLSRKERDSQLEETKAHYTNLYVKN INSETTDEQFQELFAKFGPIVSASLEKDADGKLKGFGFVNYEKHEDAVKAVEALNDSELNGEKLYVGRAQKKNER MHVLKKQYEAYRLEKMAKYQGVNLFVKNLDDSVDDEKLEEEFAPYGTITSAKVMRTENGKSKGFGFVCFSTPEEA TKAITEKNQQIVAGKPLYVAIAQRKDVRRSQLAQQIQARNQMRYQQATAAAAAAAAGMPGQFMPPMFYGVMPPRG VPFNGPNPQQMNPMGGMPKNGMPPQFRNGPVYGVPPQGGFPRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEE AAGKITGMILDLPPQEVFPLLESDELFEQHYKEASAAYESFKKEQEQQTEQA* >P1;1CVJ StructureX:1CVJ:FIRST:A:LAST:A:POLYDENYLATE BINDING PROTEIN 1:HOMO SAPIENS: 2.60: 0.23 -----------------------------------ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRR SLGYAYVNFQQPADAERALDTMNFDVIKGKPV--RIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG NILSCKV-------------------------------------------------------------------- --------------------------------------------------------------------------- ----------------------------------------------------VCDENGSKGYGFVHFETQEAAER AIEKMNGMLL----------------------------------------------------------------- --------------------------------------------------------------------------- -------------------------------NDRKVFVGRFKSRKER-----* ...this file continues with more entries like the second ICVJ.atm HEADER GENE REGULATION/RNA 23-AUG-99 1CVJ TITLE X-RAY CRYSTAL STRUCTURE OF THE POLY(A)-BINDING PROTEIN IN TITLE 2 COMPLEX WITH POLYADENYLATE RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYDENYLATE BINDING PROTEIN 1; COMPND 3 CHAIN: A, B, C, D, E, F, G, H; COMPND 4 FRAGMENT: RESIDUES 1-190; ...this file continues with the standard pdb format --joe

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None
by Cevdet NACAR 27 Oct '03

27 Oct '03

Hello Friends, Are there any docs about TOP language? (except MODELLER manual) ----------------------------------- *-Bu mail Antivirus taramasından geçmiştir. *-This e-mail was scanned by Antivirus.

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