- modeller_usage - salilab.org

too slow...
by noha lim 24 Jun '04

24 Jun '04

Dear all, I just started using modeller a few weeks ago. And now I'm doing an example(seq_search.top) in the website. But it takes so long time(about 3 hours). And I think that's right, because in the seq_search.log file from website it also took 2 hours. Then why is it so slow? Others(like BLAST or something) take only a few seconds to find sequences. What are the big differences?? Thank you!! Noha Lim _________________________________________________________________ FREE pop-up blocking with the new MSN Toolbar get it now! http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/

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some food for thought...
by Himanshu Grover 23 Jun '04

23 Jun '04

Hullo, am a novice user of modeller... need some help for a problem described below... my target protein contains 2 chains which need to be modelled. I am currently modelling them independently and then concatenating their pdbs to get the complete protein. Firstly, is is possible to model the 2 chains together, rather than independently, since that would mean taking one chain into context while modelling the other... Secondly, after generating the protein, i need to check its binding to another protein, with which it is always found complexed. For instance, in case of immunoglobulins, we have 2 chains to be modelled, and then these chains are always found complexed with a peptide-MHC... So I need that the optimization of the chains and loop refinement of the heavy and the light chains should take place taking into consideration the peptide-MHC as well. The reason i want to do this is that I tried to generate the structure of some xyz protein through modeller, whose crystallographic structure is also available. so i took xyz(crystallographic) as the template and tried to generate the same structure with modeller. the new struc. has an rmsd value of 0.19 as compared to the actual structure, which is quite good. however, at the binding site, there are some side chains that are not nicely fitting on top of the actual structure. and some interactions have gone down, resulting in poor binding. is there a way to rectify this problem?? i was thinking of doing the simulated annealing part taking into context the entire complex... that is, say, after we concatenate the light and heavy chain of immunoglobulin with p-MHC, and then applying molecular dynamics taking into consideration p-MHC also...but am not sure whether that is possible or not... any say?? sincerely, himan...

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Optimization/Refinement of Models
by Cvetan Stojkoski 22 Jun '04

22 Jun '04

Hey list, I'm doing automated modelling of 800+ targets based on 31 templates. 10 structures are produced for each target. Below are the scores (objective function, procheck) for 10 structures of one of the targets. struct obj func core allow gener disall 1 303.8717 88.20% 11.80% 0.00% 0.00% 2 328.9031 96.10% 3.90% 0.00% 0.00% 3 373.319 88.20% 9.80% 2.00% 0.00% 4 350.9386 94.10% 2.00% 3.90% 0.00% 5 337.4741 90.20% 7.80% 0.00% 2.00% 6 335.0486 90.20% 5.90% 3.90% 0.00% 7 329.6535 96.10% 2.00% 2.00% 0.00% 8 298.5056 96.10% 2.00% 0.00% 2.00% 9 319.118 92.20% 5.90% 2.00% 0.00% 10 333.3913 88.20% 11.80% 0.00% 0.00% I tried to optimize the refinement of the models and theoretically get better structures. To this end I changed the following parameters: SET LIBRARY_SCHEDULE = 1 SET MAX_VAR_ITERATIONS = 500 SET MD_LEVEL = 'refine_5' SET REFINE_HOT_ONLY = 0 SET RSTRS_REFINED = 2 SET REPEAT_OPTIMIZATION = 5 SET MAX_MOLPDF = 1E6 Although the calculations took a lot longer, I did not end up with better structures as indicated by the following scores: struct obj func core allow gener disall 1 773.4081 80.40% 9.80% 7.80% 2.00% 2 973.659 76.50% 7.80% 7.80% 7.80% 3 1356.805 76.50% 9.80% 9.80% 3.90% 4 1084.465 72.50% 15.70% 9.80% 2.00% 5 1073.4241 66.70% 13.70% 9.80% 9.80% 6 1287.894 74.50% 11.80% 7.80% 5.90% 7 823.8506 82.40% 5.90% 11.80% 0.00% 8 1074.581 74.50% 17.60% 7.80% 0.00% 9 909.5347 78.40% 13.70% 5.90% 2.00% 10 1129.2293 80.40% 11.80% 3.90% 3.90% Is it that refine_5 is not particularly good or is it a combination of the variables that is leading to poor final structures? I would be pleased if somebody could recommend more appropriate parameters for optimizing/refining models. I have also tried doing external refinement in CNS. However, without any restraints to pass to CNS, the calculations lead to the loss of secondary structure. I have been comparing the restraint file formats used by MODELLER and CNS. It is not entirely clear to a CNS novice such as myself how one would go about converting a MODELLER formatted restraint file to a CNS acceptable one. Has anybody else looked into this or can recommend another method for external refinement? Many thanks, Cvetan

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Energy profile
by mturano 22 Jun '04

22 Jun '04

Do exist a way to calculate with modeller the energy profile of a protein, having the only file pdb? Thank you M. Turano

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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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