May 2003 - modeller_usage

FW: Modeller6v2 trouble
by Modeller Care 12 Jun '03

12 Jun '03

------ Forwarded Message From: Mario Garcia <sbioi000(a)cib.csic.es> Date: Fri, 21 Mar 2003 16:53:17 +0100 (CET) To: modeller-care(a)salilab.org Subject: Modeller6v2 trouble Dear Dr. Bozidar, I have some error after a modeling jot execution (mod script.top) in Modeller6v2 under an IRIX 6.2 box. Bellow, I include the corresponding .top and .ali input files and the resulting .log file. Could you give some hints to help me? Thank you very much in advance for your help. Regards, Mario Garcia. ------------------------------------------------------------------------- Mario Garcia de Lacoba, PhD. Phone : +341 915611800 (ext.4334) Fax : +341 915627518 Centro de Investigaciones Biologicas E-mail : mario(a)cib.csic.es C.S.I.C. c/ Velazquez, 144 28006-Madrid. SPAIN. ------------------------------------------------------------------------- ======================MOB3.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 = 'MOB4.ali' # alignment filename SET KNOWNS = '1cii' # codes of the templates SET SEQUENCE = '1mob' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # 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) CHECK_ALIGNMENT CALL ROUTINE = 'model' # do homology modelling ================MOB4.ali================================ C; mob_1cii.phy align >P1;1cii structureX:1cii EIMAVDIYVNPPRVDVFHGTPPAWSSFGNKTIWGGNEWVDDSPTRSDIEK RDKEITAYKNTLSAQQKENENKRTEAGKRLSAAIAAREKDENTLKTLRAG NADAADITRQEFRLLQAELREYGFRTEIAGYDALRLHTESRMLFADADSL RISPREARSLIEQAEKRQKDAQNADKKAADMLAEYERRKGILDTRLSELE KNGGAALAVLDAQQARLLGQQTRNDRAISEARNKLSSVTESLNTARNALT RAEQQLTQQKNTPDGKTIVSPEKFPGRSSTNDSIVVSGDPRFAGTIKITT SAVIDNRANLNYLLSHSGLDYKRNILNDRNPVVTEDVEGDKKIYNAEVAE WDKLRQRLLDARNKITSAESAVNSARNNLSARTNEQKHANDALNALLKEK ENIRNQLSGINQKIAEEKRKQDELKATKDAINFTTEFLKSVSEKYGAKAE QLAREMAGQAKGKKIRNVE-EALKTYEKYRADINKKINAKDRAAIAAALE SVKLSDISSNLNRFSRGLGYAGKFTSLADWITEFGKAVRTENWRPLFVKT ETIIAGNAATALVALVFSILTGSALGIIGYGLLMAVTGALIDESLVEKAN KFW* >P1;1mob sequence:1mob ------MSYMVARMQKMKAGNLGGAFKHNERVFETHSNKDINPSRSHLN- --YELTDRDRSVSYEKQIKDYVNENKVSNRAIRKDAVLCDEWIITSDKD- -----------FFEKLDEEQTRTFFETAKNYFAENYG-ESNIAYASVHLD ESTPHMHMGVVPFENGKLSSKAMFDREELKHIQEDLPR--YMSDHGFELE -------------------------------RGKLNSEAKHKTVAEFKRA MADMELKEELLEKYHAPLFVDERTG--ELNNDTEAFWHEKEFADMFEVQS PIRETTNQEKMDWLRKQYQEELKKLESSKKP-LEDDLSHLEELLDKKTKE YIKIDSEASERASELSKAEGYINTLEN--HSKSLEAKIECLESDNLQLEK Q----KATKLEAKALNES----ELRELKPKKNFLGKEHYELSPEQ---FE GLKAEVYRSRTLLHHKDIELEQAKRQVSLRASKNYFTASLERAKEKAKGE SIDR--LKSEIKRLKN------------E----N-SILRQQNDK-MLGKL RELMPDKAFKNLLSELKAIKP-----------IVNIIKKAIEKSLF---- ---* =====================MOB4.log================================= MODELLER 6v2, 17 Feb 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, IRIX64 akilonia 6.5 IP30 Date and time of compilation : 07/05/2002 17:12:26 Job starting time (YY/MM/DD HH:MM:SS): 2003/03/21 23:47:53.033 TOP_________> 105 705 SET ALNFILE = 'MOB4.ali' TOP_________> 106 706 SET KNOWNS = '1cii' TOP_________> 107 707 SET SEQUENCE = '1mob' TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './:../atom_files' TOP_________> 109 709 SET STARTING_MODEL = 1 TOP_________> 110 710 SET ENDING_MODEL = 1 TOP_________> 111 711 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND check_a_335E> No alignment. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2200483 2148.909 2.099 Starting time : 2003/03/21 23:47:53.033 Closing time : 2003/03/21 23:48:02.202 Total CPU time [seconds] : 0.00 ------ End of Forwarded Message

6 5

Command for distance restraint
by Modeller Care 28 May '03

28 May '03

non member submission forwarded by list owner --------------------------------------------------------------- Hi, Iam new to modeller. Can anyone tell me what is the command for restraining the distance between two specified atoms. thank you, sujatha ------ End of Forwarded Message

1 0

Problem with _ and - characters present in filenames
by Owen 27 May '03

27 May '03

I have recently started using modeller 6v4 (previously using modeller 4). When I ran identical files on 6v4 I got the error seen in the log file below. An example of the type of filename for .top and .ali files is this: P42460_3-TPR-317-350.ali When I removed all the _ and - characters from the filenames, and from the relevant lines in the top and alignments, the model was built no problems. Is there a reason why these characters are no longer allowed in modeller 6v4 and if so, is there a way to make it recognise them to save alot of time having to rename all my files? Thanks! MODELLER 6v2, 17 Feb 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, IRIX64 wolf 6.5 IP27 Date and time of compilation : 07/05/2002 17:12:26 Job starting time (YY/MM/DD HH:MM:SS): 2003/05/27 14:13:21.725 rdactio_534E> Command not recognized: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2190959 2139.608 2.089 Starting time : 2003/05/27 14:13:21.725 Closing time : 2003/05/27 14:13:26.674 Total CPU time [seconds] : 0.00

1 1

FW: MALIGN-3D: How to run it.
by Modeller Care 22 May '03

22 May '03

Message forwarded by list-owner ------ Forwarded Message From: "Mr.Sridhar" <sridhar(a)www.cdfd.org.in> Date: Thu, 22 May 2003 10:45:33 -0700 To: Modeller Care <modeller-care(a)salilab.org> Subject: MALIGN-3D: How to run it. Sir, I'll be very much grateful to you if you can help me in one of my modeller job submission. I am trying to superimpose some structures simultaneously using malign3D. My top script file and alignment file are as follows. I had attached the log file also. There structures were of ~410 residues and with heme and a bound ligand. I always failed to get the structural alignment, the reason I could not figure out. Please help me in running this program, also tell me what are the general steps to follow for doing structural alignments and where are the chances for potential errors. ###########################TOP SCRIPT################## SET OUTPUT_CONTROL = 1 1 1 1 2 SET STOP_ON_ERROR = 1 SET MAXRES = 2000 READ_ALIGNMENT FILE = 'str.ali' SEQUENCE_TO_ALI SET ALIGN_CODES = '1dz8' '2cpp' SET ATOM_FILES = ALIGN_CODES SET ATOM_FILES_DIRECTORY = './' MALIGN3D SET ADD_SEQUENCE = on SET CURRENT_DIRECTORY = on SET OUTPUT = 'LONG' SET GAP_PENALTIES_3D = 0.0 1.75 SET FIT_ATOMS = 'CA' SET WRITE_FIT = on SET WRITE_WHOLE_PDB = on WRITE_ALIGNMENT FILE = 'str_STR.pir' SET ALIGNMENT_FORMAT = 'PIR' #######################ALIGNMENT FILE###################### >P1;1dz8 structureX:1dz8: 11 :A: 414 :A:undefined:undefined: 9.99: 9.99 -----LAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNVPDLVWTRCNGGHWIA TRGQLIREAYEDYRHFSSECPFIPREAGEAYDFIPTSM---DPPEQRQFRALANQVVGMP VVDKLENRIQELACSLIESLRPQGQCNFTEDYAEPFPIRIFMLLAG--LPEEDIPHL-KY LTDQMT-----------RPDGS-MTFAEAKEALYDYLIPIIEQRRQKPGTD-----AISI VANGQVNGR--PITSDEAKRMCGLLLVGGLDTVVNFLSFSMEFLAKSPEHRQELIQRPER IP------------------AACEELLRRFS-LVADGRILTSDYEFHGVQLKKGDQILLP QMLSGLDERENACPMHVDFSRQKVS----------HTTFGHGSHLCLGQHLARREIIVTL KEWLTRIPDFSIAPGAQ--IQHKSGIVSGVQALPLVWDPATTKAV* >P1;2cpp structureX:2cpp: 10 : : 414 : :undefined:undefined: 1.63: 9.99 ----NLAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNVPDLVWTRCNGGHWIA TRGQLIREAYEDYRHFSSECPFIPREAGEAYDFIPTSM---DPPEQRQFRALANQVVGMP VVDKLENRIQELACSLIESLRPQGQCNFTEDYAEPFPIRIFMLLAG--LPEEDIPHL-KY LTDQMT-----------RPDGS-MTFAEAKEALYDYLIPIIEQRRQKPGTD-----AISI VANGQVNGR--PITSDEAKRMCGLLLVGGLDTVVNFLSFSMEFLAKSPEHRQELIERPER IP------------------AACEELLRRFS-LVADGRILTSDYEFHGVQLKKGDQILLP QMLSGLDERENACPMHVDFSRQKVS----------HTTFGHGSHLCLGQHLARREIIVTL KEWLTRIPDFSIAPGAQ--IQHKSGIVSGVQALPLVWDPATTKAV* ########################################################## Thanking you sridhar ------ End of Forwarded Message

1 0

Re: RMSDs including experimental error
by Modeller Care 21 May '03

21 May '03

Non-member submission forwarded by the list owner ---------------------------------------------------------------------- Hi, This is a reply to "modeling question" by Douglas Kojetin, but may be useful for others interested in the difference between models and crystal structures: One way you can check for similarity to the experimental structure whilst including experimental error in a rigorous way is to calculate the RMSD weighted by the B-factors. I have a description of a method to do this in a paper in Proteins that is due to be online/published in a couple of days. Ref: Forrest LR, Woolf TB, "Discrimination of native loop conformations in membrane proteins: Decoy library design and evaluation of effective energy scoring functions", 2003. Essentially the method is this: define the 'experimental uncertainty' as a sphere around the atom coordinate, whose radius is dependent on the B-factor of that atom. This depends on the relationship between root mean square fluctuation and B-factor (B = 8 * pi^2 * RMSF^2 / 3). If the distance between the model atom and the xray atom (centers) is more than the radius of the sphere, then you define the effective distance as zero (the atom is within the 'experimental uncertainty'). If the model atom falls outside the sphere, then you subtract the radius of the sphere from the distance between the atom centers. Then you calculate the Root-mean-squared deviations of these effective distances, rather than the distances between the centers. I bet you find that the model of the 100% identical structure has a B-factor-weighted RMSD of less than 0.1A. Good luck, Lucy Forrest -------------------------------------------------------- Hi, for question 1, i think it is normal and expected that a model, even if built on a sequentially 100% identical template, will be somewhat different compared to an experimental solution. Although it should not go beyond let us say 0.5, or certainly not beyond 1.0 Ang RMSD. It is below the "experimental error" i.e. if the same protein is solved experimentally in different crystal forms, or at different resolution levels, or solved at high resolution but once by X-ray and once by NMR, you will still see an approx <1 Ang RMSD difference among the structures. So there is nothing special to see that your model is not exactly identical to the experimental one. for a reference you can look up figure 6 (and text) in chapter 7 (pp.167-206), book: Protein Structure (determination, analysis and applications for drug discovery) editor: DI Chasman, 2003 Marcel Dekker. question 2: it is a very interesting and useful survey that you did. Unfortunately it is difficult to generalize, because in each modeling case the set of available templates (their sequence identity to the target and structural variability with each other) is different. However your experiment about a proper "essay" is near exhaustive within your specific experiment, so you are certainly in a position to make a point. Of course the best would be to use instead of Procheck or other programs the actual experimental structures to verify the best "essay", e.g. re-model your protein A without the 100 % identical template and explore the same question you did for protein B. In this case you can compare your resulting models with the actual X-ray structure. Andras On Mon, 2003-05-12 at 15:52, Douglas Kojetin wrote: > please see the message, originally directed towards dr. sali, below. > > if anyone has any comments, please send them! > > many thanks, > doug kojetin > > Begin forwarded message: > > > Dr. Sali: > > > > I am a graduate student in the Department of Molecular and Structural > > Biochemistry at North Carolina State University. I have a question > > more about modeling process itself rather than the program MODELLER. > > > > I have used your program, MODELLER, to create models of a subfamily of > > proteins our lab and collaborators are interested in (total ~ 30). > > There are approximately 10 solved structures to the domain of > > interest. One of these solved structures (structure A) is in the same > > subfamily within the same species of proteins we are modeling (model > > A), whereas the other 29 proteins are of unknown solved structure. My > > question concerning the use of templates in the modeling process. > > > > ############## > > my main question > > ############## > > > > (if this is confusing, please let me know and i will rephrase) ... > > > > Would using a solved structure (structure A) to model a protein of > > exact sequence (model A) which will be used in a comparison of 29 > > other structures with no known structures (and lower 'homology' > > compared to that of structure A to model A -- which is 100%) bias > > model A? Overall, we are interested in comparing all 30 structures. > > This comes mostly from outside comments that our modeled protein does > > not look 'exactly' like the solved structure. As one would like it to > > look as close as possible to the solved structure, it is a model after > > all, and perhaps we just need to be more descriptive in explaining our > > results, especially pertaining to this specific model. > > > > ##################### > > how i modeled the proteins > > ##################### > > > > I performed a 'modeling parameter assay' to find the number of > > templates to use to model a protein (model B), ranging from 1 to ~8 > > templates. In addition, I 'assayed' the amount of refinement to use. > > > > Overall, I had an assay 'shaped' like a matrix with, for example, > > refinement across the top and # of templates going down. I produced 50 > > models for each and ran a variety of analyses on the models (including > > Ca RMSD to the most homologous protein, ERRAT, PROCHECK, etc) and > > computed the average 'value' output from the respective analyses. > > > > All in all, using four (4) templates and a refinement value of 1 > > produced the 'stereochemically best' models. > > > > I applied the same rationale to another protein of interest (model C), > > and the same trends were extrapolated. > > > > question > > --> is this rationale 'acceptable'? or how would you do something > > similar? > > > > Many thanks for your input, and I'm sorry for the long-winded email. > > > > Douglas Kojetin ------ End of Forwarded Message

1 0

RE: error STDEV < 0:
by Andrej Sali 21 May '03

21 May '03

The interpretation below makes all the sense. The aligned parts of the template structures need to be similar to each other. Regards, Andrej -- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4258 Email sali(a)salilab.org; Web http://salilab.org > -----Original Message----- > From: Guittet, Muriel [mailto:Guittet@vegmail.ucdavis.edu] > Sent: Wednesday, May 21, 2003 9:15 AM > To: Ben.Tehan(a)vcp.monash.edu.au > Cc: sali(a)salilab.org > Subject: RE: error STDEV < 0: > > > Hi, > This is not a huge help, but I encountered that problem too > when using different templates which do not belong to the > same family. Their structures were too far from each other in > some parts of the sequence. Actually, they were kinases and > the alignment of the kinase domain was not so bad but the > beginning of the sequence was very different in each > template. I could run modeller with these different templates > by using all the templates I wanted for the kinase domain but > just that with the best alignment for the beginning of the > sequence. Anyway, even if it ran, the log file pointed out > many problems (in the check alignment command, in the > restraints violations..) as well as the Procheck report... I > decided , but maybe I am wrong, to use only one template (or > all those of the same family) for the major part of the model > and if necessary, some parts of other templates if I had > important gaps with the major template. Best regards Muriel > > -----Original Message----- > From: Andrej Sali [mailto:sali@salilab.org] > Sent: Tue 5/20/2003 1:40 PM > To: 'Benjamin Tehan' > Cc: modeller_usage(a)salilab.org > Subject: RE: error STDEV < 0: > > > > Hi, > > I hope you do not mind I cc-ed modeller_usage here. > > I am guessing you are using more than one template > structure. If so, the > problem probably arises because the input alignment > aligns a distance in the > target sequence with two or more distances in the > template structures that > are very different from each other. I suggest that you > use the output of > CHECK_ALIGNMENT to follow up on this suggestion and, if > appropriate, edit > the alignment of the structures with each other so that > pairs of aligned > residues in known structures do not span very different > distances. > > Best regards, Andrej > > -- > Andrej Sali, Professor > Departments of Biopharmaceutical Sciences and > Pharmaceutical Chemistry, and > California Institute for Quantitative Biomedical Research > Mission Bay Genentech Hall > 600 16th Street, Suite N472D > University of California, San Francisco > San Francisco, CA 94143-2240 (CA 94107 for direct > delivery by courier) > Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 > Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, > 4233, 4258 > Email sali(a)salilab.org; Web http://salilab.org > > > > -----Original Message----- > > From: Benjamin Tehan [mailto:Ben.Tehan@vcp.monash.edu.au] > > Sent: Tuesday, May 20, 2003 1:19 AM > > To: sali(a)salilab.org > > Subject: error STDEV < 0: > > > > > > Dear Professor Sali, > > > > I am having a problem in regards to > > > > Two basis restraints have means too far apart: > > error STDEV < 0: > > > > I noted on the mailing list that someone else had encountered > > this problem and you advised them to modify file > > $MODINSTALL6v2/modlib/messages.lib > > by adding @S1 to the end of > > M 644 3 1 > > etc... > > > > I have not been able to find a response to this this problem > > and thus have attached the log file that I recieved as output. > > > > I would appreciate any advice that you are able to give me in > > regards to this matter. > > > > yours sincerely, > > Ben Tehan. > > > > PhD student > > Monash University > > Australia. > > > > > > >

1 0

RE: error STDEV < 0:
by Andrej Sali 21 May '03

21 May '03

Hi, I hope you do not mind I cc-ed modeller_usage here. I am guessing you are using more than one template structure. If so, the problem probably arises because the input alignment aligns a distance in the target sequence with two or more distances in the template structures that are very different from each other. I suggest that you use the output of CHECK_ALIGNMENT to follow up on this suggestion and, if appropriate, edit the alignment of the structures with each other so that pairs of aligned residues in known structures do not span very different distances. Best regards, Andrej -- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4258 Email sali(a)salilab.org; Web http://salilab.org > -----Original Message----- > From: Benjamin Tehan [mailto:Ben.Tehan@vcp.monash.edu.au] > Sent: Tuesday, May 20, 2003 1:19 AM > To: sali(a)salilab.org > Subject: error STDEV < 0: > > > Dear Professor Sali, > > I am having a problem in regards to > > Two basis restraints have means too far apart: > error STDEV < 0: > > I noted on the mailing list that someone else had encountered > this problem and you advised them to modify file > $MODINSTALL6v2/modlib/messages.lib > by adding @S1 to the end of > M 644 3 1 > etc... > > I have not been able to find a response to this this problem > and thus have attached the log file that I recieved as output. > > I would appreciate any advice that you are able to give me in > regards to this matter. > > yours sincerely, > Ben Tehan. > > PhD student > Monash University > Australia. >

2 1

Re: 0.25 backbone RMSD/2.9 heavy atoms
by Jianhui Wu 20 May '03

20 May '03

Hi, Shiyong, Sure. The RMSD are from the LS superimposed structures. Using the crystal structure of the same protein as the template (perfect alignment here), the backbone RMSD are great (under 0.3) but if all the heavy atoms are selected, the RMSD jumped to around 3.0 angstroms. Here, only 10 models (instead of 50) generated. So, it is an 'initial' result. But 3.0 angstrom is really surprising given the perfect template. Since the only parameter changed is the MD_level, all other default parameters were used. Perhaps the result is what we expect? Best wishes, Jian Hui

1 0

0.25 backbone RMSD/2.9 heavy atoms
by Jianhui Wu 20 May '03

20 May '03

Dear Modeller users, I am using Modeller6.2. To test the quality of the model, I tried to build a model for a protein (300 aa)using its crystal structure as the template. With MD_level = refine_1 or 3, the backone RMSD is 0.25-0.3, which is great. However, in both refinement conditions, the RMSD of the heavy atoms of the backbone plus chainchains is close to 3.0 angstroms. By visual inspection of the superimposed structures, the sidechains of the model indeed do not overlap with its crystal structure so well. My questions: Did you observe similar result? How do you refine the sidechains? MD simulation of the sidechains with backbone restrained (in explicit water solution) is in my mind. I would appreciate your suggestion and experience. Regards, Jain Hui Wu Lady Davis Institute McGill Universty

1 0

info log file
by Angelo Favia 20 May '03

20 May '03

I find in the log file this message: Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- 424 1 424 425 R Y 16.817 END OF TABLE Is it a big problem? Can I ignore it? Thanks in advance. Angelo Favia

1 0