April 2002 - modeller_usage

RE: RE: Segmentation Fault during modelling with modeller6v1
by Bozidar 22 Apr '02

22 Apr '02

Hi, I am running your examples. It will be 4 days before I can generate 1000 loops. In the mean time please not that you are selecting 2 residues on each side of every loop: SET GAP_EXTENSION = 2 2 That, along with the loop resides, selects almost 50% of your protein: SEGMENT RESNUM AA --- RESNUM AA LEN 1 11 : CYS --- 26 : ASP 16 2 43 : PRO --- 47 : VAL 5 3 50 : ALA --- 58 : PRO 9 4 63 : TRP --- 68 : GLY 6 which is computationaly rather extensive calculation (given the ab inition nature of loop modeling). After consulting the loop expert Andras Fiser, he suggested that you change your selection to zero residues: SET GAP_EXTENSION = 0 0 More later... Thanks, Bozidar -----Original Message----- From: Kees-Jan.Francoijs(a)P450.BC.WAU.NL [mailto:Kees-Jan.Francoijs@P450.BC.WAU.NL] Sent: Monday, April 22, 2002 3:52 AM To: bozidar(a)oboe.rockefeller.edu Subject: re: RE: Segmentation Fault during modelling with modeller6v1 Hi, Sorry for the delay. I send you the requested files. (ed) When running this top pir and pdb file the job crashes (crash.zip). When using another pir same top and pdb file everything goes oke(oke.zip). The log file a is included as zip file AVR4.zip in crash.zip. If there is anything else you want to know just ask. with regards Kees-Jan Francoijs - - - - - - - - - - - - - - Original Message - - - - - - - - - - - - - - On Thu Apr 18 19:06:31 2002, "Bozidar Jerkovic" <bozidar(a)oboe.rockefeller.edu> wrote: > >Hi, > >1. Please send me complete set of input files plus log files and I'll >run it on 6v2 (not public yet) to see if it happens there. > >2. Yes we went through this, as well. Prosa is not sensitive assessing >loops. Please read the comment on the use of statistical profile for >assessing loops, in Andras Fiser's Prot Sci 2000 loop modeling paper. >People should use modeller scores to rank them. > >Thanks, >Bozidar > > >-----Original Message----- >From: Kees-Jan.Francoijs(a)P450.BC.WAU.NL >[mailto:Kees-Jan.Francoijs@P450.BC.WAU.NL] >Sent: Tuesday, April 16, 2002 8:00 AM >To: bozidar(a)oboe.rockefeller.edu >Subject: Segmentation Fault during modelling with modeller6v1 > > >Hi Bozidar, > >I have been using modeller for 2 years now . I'm using modeller since >version 4. Recently I ran into a few problems maybe you can point me in >the right >direction. > >Two Questions: > >1.) When running modeller 6V1 on a pentium III redhat 7.2 with all >recommended patches applied. The following problem occurred. After I >started >a job doing loop modelling i generated 1000 models and every thing went >fine. >I changed the alignment a bit and try to run for an other 1000 models >the job >crashes after 198 models. So i decided to run on a other machine, >different >one 1.7 Ghz Dual Xeon, same problem. What can be the source of the >problem. >The job crashes with segmentation fault error. > >2.) I assessed the 1000 generated models with ProsaII to find the 20 >best models. I also used the value from the objective function from >modeller to >rank them. When doing this it was easy to see if there is any >correlation >between the rankings and guess what, there is none actual it seems >random. Is >there an explanation for this and which one is right or did i do >something >wrong ? This surprised me since Andrej uses the ProsaII score in many of >his >articles as an objective criterion for the quality of the models and one >would expect the objective function of Modeller to be related in >quality. > > >with regards > >C.J.J Francoijs > > - - - - - - - - - - - - End of Original Message - - - - - - - - - - - -

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randomize dihedrals
by Evers Andreas 18 Apr '02

18 Apr '02

Hallo Modellers! I try to model protein binding sites including ligand information in terms of distance dependent atom pair potentials. For testing this approach I tried to predict the orientations of binding site residues. After generating 100 models of a protein I compare them with the actual crystal structures. The predictions are quite reasonable. However, there seem to be some problems in the side chain conformations of the aromatic amino acids (maybe because of steric hinderance). In some cases there is only one preffered conformation of, e.g. a tyrosine, i.e. only one preffered value of the CHI1 dihedral angle. I have read in the manual that there is the possibility to ROTATE_DIHEDRALS by randomizing. How do I have to set up my top file to tell MODELLER to select certain amino acids (e.g. by number) and to randomize the CHI1 and/or CHI2 angles and - if possible - to generate models with diverse CHI1 and/or CHI2 angles, even if some are not energetically favourable? The rest of the protein should be modelled as usual. Do you think this procedure an advisable way to do or do you have any better idea how I can constrain the modelling process to generate more diverse dihedral angles for selected amino acids? Thank you for your answer, nice regards, Andreas -- ###################################################################### # Andreas Evers # # # # Research group for Drug Design & X-ray Crystallography # # Institute of Pharmaceutical Chemistry # # Philipps-University of Marburg # # Marbacher Weg 6 phone2 +49-6421-28-25072 # # D-35032 Marburg FAX: +49-6421-28-28994 # # email: Andreas.Evers(a)mailer.uni-marburg.de # # AG-Klebe-Home: http://www.agklebe.de # ######################################################################

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theory info
by Luca Settimo 17 Apr '02

17 Apr '02

Dear Modeller friends, I would appreciate if you could suggest me some references (literature) about how an homology modeling program (like Modeller) is evaluated. I know that the rmsd between the model and the real structure (like the CASP approach, just to be clear) is the most common way to study this. But what about the rsmd of all atoms of the proteins versus the C alpha atoms? and what about the side chain position in the binding site? Are there some studies about that? I have start to read literature about that, but I must confess that I didn´t find answers... only C alpha and threading methods... Do you have more informations that can help me? What is the article that validate Modeller (from this point of view)? is it Proteins (1995) 23(3) 318-26? Thanks in advance Luca Settimo

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Loop modeling: old vs. new
by Mensur Dlakic 17 Apr '02

17 Apr '02

Hi, Has anyone done a real comparison between standalone loop refinment procedures in v4.x versus v6.x? Or, for that matter, is any objective benchmarking available that compares the two versions? I am one of those people who don't like to update the software that already works well, and one thing that would definitely motivate me to do so is the improvement in loop procedures. On a related note, is there any word about the DOS/Windows version of MODELLER? What is the lowest target/template identity that has still produced a good model of a 80+ residues protein? I am hoping to hear real examples and not only a generic answer ("depends on template resolution, alignment quality..."). I have made good models in a 10-20% range of indentities, but is it realistic to expect a good model with < 10% identity even after the iterative realignment? I am often tempted to model proteins falling into below 10% category but haven't done it more than 2-3 times, always with disappointing results. Thanks for your time. May your objectives be high and your objective function low, Mensur =========================================================================== | Mensur Dlakic, PhD | Tel: (734) 764-3554 | | Department of Biological Chemistry | Fax: (734) 615-3397 | | University of Michigan Medical School | http://www.umich.edu/~mensur/ | | 5416 Medical Science I | http://myprofile.cos.com/mensur | | Ann Arbor, MI 48109-0606 | E-mail: mensur(a)umich.edu | ===========================================================================

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modified residues (pyruvoyl)
by Gordon 17 Apr '02

17 Apr '02

I've found the following works for pyruvoyl residues top_heav.lib entry: RESI PVL 0.00000 ATOM O2 O -0.5500 ATOM C3 CD 0.5500 ATOM C2 CD 0.6000 ATOM O3 O -0.5500 ATOM C1 CT3 -0.1500 DELE ATOM N BOND O2 C2 C2 C1 C2 C3 C3 O3 C3 +N IMPR C1 C2 C3 +N IMPR O3 C3 C2 O2 IC O3 C3 C2 O2 1.2355 116.9032 15.0961 120.8798 1.2270 IC C1 C3 C2 O2 1.5090 128.5815 -171.5204 120.8798 1.2270 IC +N O2 C2 C3 1.3535 122.1373 175.9258 120.8798 1.4157 PATC FIRS NONE LAST NONE restyp.lib entry: 142 | PVL | O | PVL | pyruvoyl

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how to setup a nice modelling environment?
by Ari M. Siqueira 16 Apr '02

16 Apr '02

Hi, Just out of curiosity, and to help me configuring my own environment, what do people use besides Modeller in their modelling projects? I have an Intel/Linux box, 2 IBM workstations (AIX) and an Intel/MS-Win machine. My interest is in modelling peptides in the range of 40-120 amino acids, with high cysteine contents, homology with known structures usually below 50%. I would also like to do energy minimizations and molecular dynamics, and to analyse the MD trajectories. Software that I am somewhat familiar with are: MSI-Accelrys InsightII Modeller VMD SPDBViewer (Deep View) Rasmol/Rastop Cn3D WebLabViewer Procheck Antheprot Some additional software which I have access to but not much experience: gOpenMol ICMLite MolMol Whatif What would you Modellers suggest as an ideal lab setup for homology modelling + MD + visualizations of structures and trajectories, considering the hardware above? Please advise. Yours thankfully, Ari M. Siqueira, PhD (a hopeful modeller...)

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phospo-serine residues
by Voula Kanelis 15 Apr '02

15 Apr '02

Hello, I am currently using Modeller 4 and need a phosphoserine residue. Unfortunately, this residue is not defined in the modlib files and I do not have access to CHARM or QUANTA to be able to create it (a problem to be fixed shortly - hopefully). Does anyone have such a residue defined and would be willing to share? Thanks in advance, Voula Kanelis --

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RE: Reading_PDB_File
by Bozidar 15 Apr '02

15 Apr '02

Hi, Please make sure that you define SET ATOM_FILES_DIRECTORY = .... One more thing: make sure that your PDB file doesn't have a chain identifier (A, B, C, etc), or make sure that your .ali file has one (currently it's empty), but I guess you already know this. NB. Would you please post any questions you might have in the future on the list first, because other people might have the same problem and may benefit from or already have the answer as well. Good luck, Bozidar -----Original Message----- From: Krzysztof Lazarski [mailto:lazarski@anl.gov] Sent: Monday, April 15, 2002 12:45 PM To: Bozidar Jerkovic Cc: Andrzej Joachimiak; Andrej Sali Subject: Reading_PDB_File Hello, I need a help. My task was to see if we can model sequence with unknown structure which has >90% similarities (Protein Blast) to our X-Ray determined structure recently deposited to PDB from our Structural Genomics Project (MCSG; http://www.mcsg.anl.gov ). The known structure name is: 1g2r. I named sequence my_ 15900466 (Where I can find rules for assigning a name to unknown structure?). I tried DESCRIBE with following .top file: -- SET OUTPUT_CONTROL = 1 1 1 1 2 SET ATOM_FILES = '1g2r', ALIGN_CODES = '1g2r' READ_MODEL FILE = '1g2r', MODEL_SEGMENT = '@:@' 'X:X' DESCRIBE -- There were no problems. I've got nice report in .log file. When I tried to run modelling .top: -- INCLUDE SET ATOM_FILES_DIRECTORY = './:../atom_files' SET ATOM_FILES = '1g2r', ALIGN_CODES = '1g2r' READ_MODEL FILE = '1g2r', MODEL_SEGMENT = '@:@' 'X:X' SET SEGFILE = 'align-jerzy.seg' SET KNOWNS = '1g2r' SET SEQUENCE = 'my_15900466' SET OUTPUT_CONTROL = 1 1 1 1 2 CALL ROUTINE = 'full_homol' -- where align-jerzy.seg is: -- >P1;1g2r structureX:1g2r:1::100:::: GSHMKTRKIPLRK SVVSNEVIDKRDL LRIVKNKEGQVFI DPTGKANGRGAYI KLDNAEALEAKKK KVFNRSFSMEVEE SFYDELIAYVDHK VKRRELGLE* >P1;my_15900466 sequence:my_15900466:1 : :97 : : : : : MKTRKIPLRKSVVSNEVIDKRDLLRIVKNKEGQVFIDPTGKANGRGAYIKLDNAEALEAK KKKVFNRSFSMEVEESFYDELIAYVDHKVKRRELGLE* -- It created align-jerzy.seg.ali, but it stopped on full_homology when reading .pdb file, which it read properly for describing protein. Here it is 25 last lines from .log file (tail -25 ..): -- # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------ ------- 1 1g2r 100 1 1g2r 2 my_159004 97 1 my_15900466 TOP_________> 140 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./1g2r.pdb rdpdb___303E> No atoms were read from the specified input PDB file: 1) Possibly because an incorrect/non-existent PDB file is specified. 2) Possibly because the segment is specified incorrectly in the alignment file or by the TOP variable MODEL_SEGMENT. That is, the beginning residue number and/or chain id in MODEL_SEGMENT may not be found in the input PDB file; MODEL_SEGMENT: 1: To find out more, switch on maximal output by 'SET OUTPUT_CONTROL = 1 1 1 1 2' rdabrk__288W> Protein not accepted: 1 rdabrk__290E> Number of residues in the alignment and pdb files are different: 100 0 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 4890025 4775.415 4.663 Starting time : 2002/04/15 11:20:01.978 Closing time : 2002/04/15 11:20:05.387 Total CPU time [seconds] : 3.14 -- Thank you for any suggestions, Christopher. -- Dr. Krzysztof Lazarski, Argonne National Laboratory 9700 S. Cass Ave, Building 202, RQ106, Argonne, IL 60439 ph: 630-252-3855, e-mail: lazarski(a)anl.gov, fax: 630-252-6126

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Submission of alignments
by Dinesh Soares 14 Apr '02

14 Apr '02

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FW: FW: MODELLER
by Bozidar 12 Apr '02

12 Apr '02

Hi, Everything is fine, but the format has changed a little bit, instead of 'refine2' use 'refine_2' in your LOOP_MD_level call (refine_1, refine_2, refine_3) Andras Bozidar Jerkovic wrote: > > Thanks, > Bozidar > > -----Original Message----- > From: AA_Canutescu(a)fccc.edu [mailto:AA_Canutescu@fccc.edu] > Sent: Wednesday, April 10, 2002 1:18 PM > To: Bozidar Jerkovic > Subject: Re: MODELLER > > Hi, > > I attached a tar.gz that contains top, log and pdb input file. In > case 'loop' routine is not anymore supported in mod6v1, what would be > a get around for my problem? > > Thanks for your help. > > Adrian > > Quoting Bozidar Jerkovic <bozidar(a)salilab.org>: > > > > > Hi, > > > > Can you please send me your .top and .log and all input files and > > I'll > > > run it here. I can't actually see which part of .top fails. I > > presume it's "CALL > > ROUTINE = 'loop' # do loop modeling", but I don't wanna guess. > > > > Best, > > Bozidar > > > > > > > > On 8/4/02 3:24 PM, "AA_Canutescu(a)fccc.edu" <AA_Canutescu(a)fccc.edu> > > wrote: > > > > > Dear Bozidar, > > > > > > > > > I downloaded the last version of MODELLER and I am running into > > > some problems. For the time being, I use MODELLER mostly for loop > > > modeling. > > Using > > > the > > > previous version(mod6a), I used to create a top file like this, > > > and > > everything > > > worked ok: > > > > > > INCLUDE > > > SET OUTPUT_CONTROL = 1 0 0 1 0 # Set to 1 1 1 1 0 for > debugging. > > > SET SEQUENCE = '1dysA_47-50' > > > SET LOOP_MODEL = '1dysA_47-50.pdb' > > > SET LOOP_MD_LEVEL = 'refine2' # refine3 - fastest > > > # refine2 - medium > > > # refine1 - most thorough SET > > > LOOP_STARTING_MODEL = 1 SET LOOP_ENDING_MODEL = 3 # number of > > > loop models > > > SET RAND_SEED = -38901 # change for different starting models > > > CALL ROUTINE = 'loop' # do loop modeling > > > > > > # Pick model residues that need to be refined. > > > > > > SUBROUTINE ROUTINE = 'select_loop_atoms' # Uncomment if you also > > > want > > to > > > optimize the environment: > > > # SET SELECTION_SEARCH = 'SPHERE_SEGMENT', SPHERE_RADIUS = 6 > > > PICK_ATOMS SELECTION_SEGMENT = '47:A' '50:A', SELECTION_STATUS = > > 'initialize' > > > RETURN > > > END_SUBROUTINE > > > > > > > > > With the newest version of MODELLER that I downloaded last week, > > doesn't work > > > anymore. I receive an error message in the end of.log file like > > > this: > > > > > > act10___551E> No such routine: > > > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > > > > > Dynamically allocated memory at finish [B,kB,MB]: > > 28478873 > > > 27811.400 27.160 > > > Starting time : > 2002/04/08 > > > 14:20:40.274 > > > Closing time : > 2002/04/08 > > > 14:20:51.421 > > > Total CPU time [seconds] : > 11.00 > > > > > > > > > Could you help me please regarding this matter? Could you also > > > tell me > > if > > > there is any dependency needed(some libraries, fortran, etc)? I am > > using > > > RedHat > > > 7.2 with kernal 2.4.7-10 > > > > > > > > > > > > Thanks, > > > > > > Adrian Canutescu > > > > > > ------------------------------------------------------------------------ > Name: mod_files.tar.gz > mod_files.tar.gz Type: Unix Tape Archive (application/x-tar) > Encoding: base64 -- , Andras Fiser, PhD # phone: (212) 327 7216 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras

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