June 2004 - modeller_usage

unsuscribe
by En Yun 22 Jun '04

22 Jun '04

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Chimeric model
by Benoit Charloteaux 17 Jun '04

17 Jun '04

Dear Modeller users, I want to build a model of a chimeric protein based on two distinct structures. I have tried as explained in the FAQ section of the manual (question 4), but I only get completely unfolded structures. Is it possible to build a chimeric model with this procedure? Where does this problem come from? Any possible explanation or suggestion would be greatly appreciated! To check my procedure, I have tried the following : I used an older prediction that worked and which is based on a single template structure. Target xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx proteinA aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa I made a copy of the template structure file and renamed it to do as if there was two distinct template structures. I tried to build a kind of chimeric model based on these template structures as follow : Target xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx proteinA aaaaaaaaaaaaaaaaaaaaaaaaaaaa---------------------------------- proteinA -------------------------aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa Since the two template structures used for the prediction correspond to the same file, the relative orientation of both structures is correct (the atom coordinates are the same). The predicted 3-D model is completely unfolded too. Sincerely, CHARLOTEAUX Benoit Centre de Biophysique Moleculaire Numerique Faculte Universitaire des Sciences Agronomiques de Gembloux Passage des deportes, 2 B-5030 Gembloux Belgium Tel1:+32(0)81/62.25.32 Tel2:+32(0)81/62.25.21 Fax:+32(0)81/62.25.22 e-mail: charloteaux.b(a)fsagx.ac.be http://www.fsagx.ac.be/bp/

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using modeller under Xp
by Edoardo Saccenti 17 Jun '04

17 Jun '04

Dear friends, I'm trying to use modeller for win Xp. I have put my files (script.top, pdb files and alignment files in the directory c:\mod6v2 from the directory C:\mod6v2\bin> I run the command: mod.bat C:\mod6v2\script.top The program start but it stops. The following is reported: fullfn___230E> File not found : tacealn tacealn is my alignment file (PIR frmat) that i have put in C:\mod6v2 My question is: I must change something in script.top or i have to change the path for the alignment file? If yes, where?? greetings Dr. Edoardo Saccenti CERM - Centro Risonanze Magnetiche via Luigi Sacconi 6, 50019 Sesto Fiorentino (FI) ITALY Tel: +39 055 4574193 Mob: +39 333 2289912 saccenti(a)cerm.unifi.it www.cerm.unifi.it

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hello sir
by V Nadeem Ahmad 13 Jun '04

13 Jun '04

Dear sir, I am Nadeem from India.I want to know is it possible to do heterodimer modelling for proteins which has no obvious target protein . what points one has to take care when he dies dimer modeling . looking forward to hearing from you with regards, Nadeem Ahmad V

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CHECK_ALIGNMENT accepts it, but ROUTINE = 'model' does not.
by Javier Satulovsky 08 Jun '04

08 Jun '04

Hi, I'm learning how to use modeller (release 6 with linux red hat 9). While CHECK_ALIGNMENT seems accept my alignment, calling the routine 'model' gives me an error when trying to read that same alignment. I 'm trying to model 41 residues into the first chain of the PDB file 1GL2.pdb (after this 'practice run' I will try to model the four chains of the structure at the same time). Following are relevant parts of scripts+logs. Any ideas will be greatly appreciated!!! Javier. modeller.alignment.ali ---------------------- > >P1;1GL2 > structureX:1GL2:20:A:60:A:Endobrevin:rattus norvegicus:1.9:0.1370 > EGVKNIMTQNVERILARGENLDHLRNKTEDLEATSEHFKTT > * > > >P1;1GGX > sequence:1GGX:1: :41: :ykt6:rattus norvegicus:: > DETKIILHNTMESLLERGEKLDDLVSKSEVLGTQSKAFYKT > * chech_alignment.top ------------------- > SET OUTPUT_CONTROL = 1 1 1 1 1 > SET ATOM_FILES_DIRECTORY = './../atom_files' > > READ_ALIGNMENT FILE = 'modeller.alignment.ali', ALIGN_CODES = 'all' > WRITE_ALIGNMENT FILE = 'alignment.ali' > CHECK_ALIGNMENT chech_alignment.log (last part of the file) ------------------- > openf5__224_> Open 11 OLD SEQUENTIAL modeller.alignment.ali > > Read the alignment from file : modeller.alignment.ali > Total number of alignment positions: 41 > > # Code #_Res #_Segm PDB_code Name > ------------------------------------------------------------------------------- > 1 1GL2 A 41 1 1GL2 Endobrevin > 2 1GGX 41 1 1GGX ykt6 > TOP_________> 4 4 WRITE_ALIGNMENT FILE = 'alignment.ali' > > openf5__224_> Open 14 UNKNOWN SEQUENTIAL alignment.ali > TOP_________> 5 5 CHECK_ALIGNMENT > > check_a_343_> >> BEGINNING OF COMMAND > openf5__224_> Open 11 OLD SEQUENTIAL ./../atom_files/1GL2.atm > > check_ali___> Checking the sequence-structure alignment. > > Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: > > ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST > ---------------------------------------------- > END OF TABLE > check_a_344_> << END OF COMMAND > > Dynamically allocated memory at finish [B,kB,MB]: 3061621 2989.864 2.920 > Starting time : 2004/06/08 16:10:06.379 > Closing time : 2004/06/08 16:10:13.541 > Total CPU time [seconds] : 3.47 modelling.top ------------- > INCLUDE > > SET OUTPUT_CONTROL = 1 1 1 1 1 > SET ALNFILE = './alignment.ali' > SET KNOWNS = '1GL2' > SET SEQUENCE = '1GGX' > SET ATOM_FILES_DIRECTORY = '../atom_files' > SET STARTING_MODEL= 1 > SET ENDING_MODEL = 1 > > > CALL ROUTINE = 'model' modelling.log (last part of the file) ------------- TOP_________> 111 711 CALL ROUTINE = 'model' TOP_________> 112 399 CALL ROUTINE = 'getnames' TOP_________> 113 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 114 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 115 511 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 116 512 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 117 513 SET ROOT_NAME = SEQUENCE TOP_________> 118 514 RETURN TOP_________> 119 400 CALL ROUTINE = 'homcsr' TOP_________> 120 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL ./alignment.ali Dynamically allocated memory at amaxbnd [B,kB,MB]: 3061621 2989.864 2.920 openf5__224_> Open 11 OLD SEQUENTIAL ./alignment.ali read_al_375E> Unknown residue type,position,sequence: 1 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 3061621 2989.864 2.920 Starting time : 2004/06/08 16:07:55.650 Closing time : 2004/06/08 16:08:04.684 Total CPU time [seconds] : 4.30 ---------------------------------------------- Mailblocks - A Better Way to Do Email http://about.mailblocks.com/info

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Question about Make_restraints
by Alejandra Leo 08 Jun '04

08 Jun '04

Hi all, I have a problem using Modeller and maybe someone could give a hand. I have my alignment (ecoli-FINAL.pir), my query sequence (Nei1Ecoli_exp), and as structural template I have a trace of C-alpha atoms (E_Coli_Test85) that is very important that do not move from their initial positions. The only thing I want to do is to add the other atoms needed to complete the backbone to my C-alpha trace. I created this script for running modeller: ---------------------------------------------------- READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' READ_PARAMETERS FILE = '$(LIB)/par.lib' READ_ALIGNMENT FILE = 'ecoli-FINAL.pir', ALIGN_CODES = 'E_Coli_Test85' MALIGN3D FIT = off SET ADD_SEQUENCE = on READ_ALIGNMENT FILE = 'ecoli-FINAL.pir', ALIGN_CODES = ALIGN_CODES 'Nei1Ecoli_exp' CHECK_ALIGNMENT GENERATE_TOPOLOGY SEQUENCE = 'Nei1Ecoli_exp' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ = off WRITE_MODEL FILE = 'Nei1Ecoli-test.ini' MAKE_RESTRAINTS RESTRAINT_TYPE = 'DISTANCE', DYNAMIC_SPHERE = on MAKE_RESTRAINTS DISTANCE_RSR_MODEL = 5 WRITE_RESTRAINTS FILE = 'Nei1Ecoli.rsr' READ_MODEL FILE = 'Nei1Ecoli-test.ini' PICK_RESTRAINTS #OPTIMIZE ENERGY WRITE_MODEL FILE = 'Nei1Ecoli-test_1.final' -------------------------------------------------------------------------- And everything was fine until the make_restraints point. Nei1Ecoli.rsr created file only contains a header line and the rest is empty. I supposse that I am not using this command in the right way, but what I want to do is to tell the program that keep fix the C-alpha coordinates and add the rest, and make the optimization (now in comments), without moving it. Or if it woult be strictly necesary, to get a final structure with a RMS value as low as possible, with respect to my starting C-alpha trace. Any ideas about creating the restraints file and invoke it from the top script? Thanks in advance, any help will be very appreciated! Best, Sandra

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Restricting to Strand
by John Penniston 07 Jun '04

07 Jun '04

I've been trying to restrict portions of my molecule to be alpha helix and other portions beta strand. I did it using the following addition to my special_restraints subroutine: #This one is to put helices & sheets in the PMCA insert SET ADD_RESTRAINTS = on MAKE_RESTRAINTS RESTRAINT_TYPE = 'alpha', RESIDUE_IDS = '254' '274' MAKE_RESTRAINTS RESTRAINT_TYPE = 'alpha', RESIDUE_IDS = '293' '302' MAKE_RESTRAINTS RESTRAINT_TYPE = 'strand', RESIDUE_IDS = '275' '285' The alpha restraints work fine, but the strand restraint seems to have no effect at all. When I look at a Ramachandran plot of the region which was supposed to be beta strand, the angles are all over the plot. I noticed on looking over the history of this forum that a French group had this same problem in 2002, but I can't find any solution to it. This difficulty has happened in a number of different circumstances. John T. Penniston, Ph.D. Lab of Membrane Biology Massachusetts General Hospital Boston, MA, USA

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