- modeller_usage - salilab.org

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. > > > > > > >

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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. >

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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

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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

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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

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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

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D aminoacids
by Angelo Favia 20 May '03

20 May '03

How can I prevent the formation of D aminoacids? I'm trying to build a protein with a low degree of homology (25%) respect to the template. Is this the reason why I find in the final models so many D aminoacids? Angelo Favia

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How model two o more alignment automatic
by JP 15 May '03

15 May '03

I have two alignment , how I can automate the process for two o more alignments only one file? for example have this two alignment in one file "alignment.ali" : C; Alignment1 >P1;1efwA structureX:1efw:162:A:300:A:::: GFVQVETPFLTKSTPEGARDFLVPYR---HEPG----------------LFYALPQSPQL FKQMLMVAG-LDRYFQIARCFRDEDLRADRQPDFTQLDLEMSFVE--VE----------- ------DVLELNERLMAHVFREALGVELPLPFPRLSYEEAMERYGSDKPDLRFGLELK* >P1;whi6464 sequence:whi6464:9::186::::: GFVEVETPVLLKSTPEGAREFLVPTRTSASAPSVKSSIGGGPRESSSQPLFYALPQSPQQ PKQLLIASGAVDRYYQIAKCFRDEDGRKDRQPEFTQVDLEMAWVSWGIEPSNCSQGDHNV WRIGGKEVREIIERLIRKIWSTVEGIELPSSFTVMTYEEAMGRFGSDKPDTRFGLEVR* C; Alignment2 >P1;1cqjD structureX:1cqj:132:D:284:D:::: CKI--GIQPGHIHKPGKVGIVSRSGTLTYEAVKQTTDYGFGQSTCVGIGGDPIPGSNFID ILEMFEKDPQTEAIVMIGEIGGSAEEEAAAYIKEH-VTKPVVGYIAGVTAPKGK---RMG HAGAIIAGGKGTADEKFAALEAAGVKTVRSLADIGEALK* >P1;whi6880 sequence:whi6880:12::170::::: CSMMDNIIASKLYRPGSVGYVSKSGGMSNELNNILSLVTNGTYEGIAIGGDRYPGSTFID HLLRYENDPECKMLVLLGEVGGIEEYRVIEAVKKGLIKKPIVAWAIGTCAKMFTTEVQFG HAGSMANSDMETADAKNAAMRKAGFIVPDTFEDLPQVLR* and which is the configuration for file "TOP"? thanks

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bad pdb file error
by Mike Kurtz 12 May '03

12 May '03

Sorry for the bother, but I can't figure this out for the life of me... I'm attempting to do a 2d alignment of the R2R3 region of AtTT2 with the MYB 1MSF. However, when I try to run the align2d command (script below), it says that I am using a malformed pdb file. I am certain that is not the case, as I just recently got the file directly from the pdb. If anyone could help me out with this, it would be much appreciated. ____ <every ATOM definition in the pdb file, same as below> iup2crm_279W> IUPAC atom not found in topology library; residue type index: C4 25 Possible reasons are a non-standard PDB file, or a new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. fndatmi_285W> Number of residues <> number of atoms; atom code: 127 105 CA fndatmi_285W> Number of residues <> number of atoms; atom code: 127 105 CA openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//as1.sim.mat rdrrwgh_268_> Number of residue types: 20 dispers_247E> Internal error: 126 127 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 5936909 5797.763 5.662 Starting time : 2003/05/08 17:50:17.028 Closing time : 2003/05/08 17:50:26.897 Total CPU time [seconds] : 0.00 _____ The .top: SET OUTPUT_CONTROL 1 1 1 1 1 READ_TOPOLOGY FILE = '/home/osu3233/bin/modeller6v2/modlib/top_allh.lib' READ_MODEL FILE = '1MSF' SEQUENCE_TO_ALI ALIGN_CODES = '1MSF' ALIGN_CODES = '1MSF' #GENERATE_TOPOLOGY SEQUENCE = '1MSF' #SEQUENCE_TO_ALI ALIGN_CODES = '1MSF' READ_ALIGNMENT FILE = 'test.ali', ALIGN_CODES = 'AtTT2', ADD_SEQUENCE = ON ALIGN2D WRITE_ALIGNMENT FILE='AtTT2-1msf.ali', ALIGNMENT_FORMAT='PIR' WRITE_ALIGNMENT FILE='AtTT2-1msf.pap', ALIGNMENT_FORMAT='PAP' Thanks, Mike Kurtz

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Re: modeling question
by Modeller Care 12 May '03

12 May '03

forwarded by the list owner -------------------------------------------------------- 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 -- , Andras Fiser, PhD, assistant professor Dept. of Biochemistry & Seaver Center for Bioinformatics Albert Einstein College of Medicine 1300 Morris Park Ave, Bronx, NY 10461, USA phone:(718)430-3233 fax:(718)430-8565 http://www.fiserlab.org, mailto:andras@fiserlab.org ------ End of Forwarded Message

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