April 2005 - modeller_usage

joining of the same domain
by rathankar rao 18 Apr '05

18 Apr '05

Dear sir i have a query protein of 300 residues which has 14 zinc finger binding motifs and each motif is not identically the same. i have a template which has 3 chains with each chain having only 87 residues, all the chains being identical. if i need to build a model to my query, i thought of chopping my query sequence in to three parts nearly such that each part resemble my template of 87 residues. it is seen that the sequence identity is nearly 50% for each part with the template. if i build models for these independent regions, 1. how do i join them. 2. how do i know their relative orientation and 3. how do i account for the dna which binds to it, plz explain. --------------------------------- Do you Yahoo!? Plan great trips with Yahoo! Travel: Now over 17,000 guides!

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Modelling Hydrogen bond in helix
by Panapat Uawithya 17 Apr '05

17 Apr '05

Hi, I have generate a model. However the hydrogen bond distances in the helices are shorter than normal value eg. 2.5-2.9 Angstrom. The hydrogen bond of the template are in normal range 2.9-3.5 Angstrom. How can I correct this proble? I have tried energy minimaztion but distance come a little bit shorter. Panapat __________________________________ Yahoo! Mail Mobile Take Yahoo! Mail with you! Check email on your mobile phone. http://mobile.yahoo.com/learn/mail

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(no subject)
by Michael Grabe 13 Apr '05

13 Apr '05

dear modellers, what should i do if i want the homology derived restraints to have a larger weight in the creation of a model. that is i want my model to look more like the template structure at the expense of stereochemical considerations. thanks, michael ------------------------------------------------------------------------ -------------------------- Michael Grabe, Ph.D. HHMI/UCSF Genetics Development & Behavioral Science Building 1550 4th Street, GD 481 San Francisco, CA 94143-0725 tel: ++ 415.476.0421 http://itsa.ucsf.edu/~mgrabe

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tutorial on mod7v7
by Paula R.=?ISO-8859-1?Q?_Kuser_Falc=E3o?= 11 Apr '05

11 Apr '05

Hi, I am trying to do the modeller tutorial on a linux machine, with version mod7v7. After running seq_search for the TvDLH model the seqsearch.dat is empty, and I get the .log file as shown below. Would you know why I can't get any answer from my search? Thanks, Paula. Kind, OS, HostName, Kernel, Processor: 4, Linux japiim.cbi.cnptia.embrapa.br 2.4.20-42.9.legacysmp i 686 Date and time of compilation : 09/14/2004 11:06:39 Job starting time (YY/MM/DD HH:MM:SS): 2005/04/11 16:50:46.106 Dynamically allocated memory at amaxseq [B,kB,MB]: 69639 68.007 0.066 TOP_________> 2 2 SET SEARCH_RANDOMIZATIONS = 100 TOP_________> 3 3 SET MAXRES = 300 TOP_________> 4 4 SET FILE = 'TvLDH.seq' TOP_________> 5 5 SEQUENCE_SEARCH ALIGN_CODES = 'TvLDH', DATA_FILE = ON Dynamically allocated memory at amaxseq [B,kB,MB]: 614337 599.938 0.586 Dynamically allocated memory at amaxbnd [B,kB,MB]: 32806393 32037.492 31.287 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib//as1.sim.mat rdrrwgh_268_> Number of residue types: 20 openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.seq Searching a list of chains for similarity with a given sequence: Target sequence : TvLDH.seq List of test chains : ${MODINSTALL7v7}/modlib//CHAINS_3.0_40_XN.cod Number of test chains : 0 Residue-residue metric: ${MODINSTALL7v7}/modlib//as1.sim.mat Gap penalties U, V : -900.00 -50.00 Randomizations : 100 +/- range for sig2&3 : 10 SIGNIF_CUTOFF : 4.00 5.00 Top chains are listed : 20 (see the corresponding $MODINSTALL/modlib/seqfilt_*.grp file for more related PDB codes) RELATED_SEQUENCES # CODE_1 CODE_2 LEN1 LEN2 NID %ID %ID SCORE SIGNI SIGNI2 SIGNI3 ----------------------------------------------------------------------------- --- openf5__224_> Open 14 UNKNOWN SEQUENTIAL seqsearch.dat Dynamically allocated memory at finish [B,kB,MB]: 32806393 32037.492 31.287 Starting time : 2005/04/11 16:50:46.106 Closing time : 2005/04/11 16:50:46.882 Total CPU time [seconds] : 0.58 Paula Kuser Falcão Laboratório de Bioinformática Estrutural Embrapa Informática Agropecuária -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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problem!
by vivek sharma 09 Apr '05

09 Apr '05

Dear sir, Please have a look to this error. I made a normal modeller run (7v7) to generate 50 structures for a target sequence of about 500 residues using 3 different templates. But after generating 6 intial structure, it died with this following details, this log file was pretty big in size and contained this detail. I regularly use MODELER , but this a new kind of error I faced, what can be the reason? ---------------------- 25 Phi/Psi pair of dihedral restraints : 1.0000 26 Distance restraints 4 (SDCH-SDCH) : 1.0000 27 Distance restraints 5 (X-Y) : 1.0000 28 NMR distance restraints 6 (X-Y) : 1.0000 29 NMR distance restraints 7 (X-Y) : 1.0000 30 Minimal distance restraints : 1.0000 31 Non-bonded restraints : 1.0000 32 Atomic accessibility restraints : 1.0000 33 Atomic density restraints : 1.0000 34 Absolute position restraints : 1.0000 35 Dihedral angle difference restraints : 1.0000 Initial value of energy before optimization : ---------------- Current energy : ???????????????? Symmetry term within energy : 0.0000 Number of iterations : 200 Number of calls to energy function : 0 Number of updates of dynamic contacts : 5 Number of non-updates of dynamic contacts : 196 Final maximal atomic shift : ???????? TEMPERATURE : 150.000 EQUILIBRATE : 20 EQUILIBRATE : T Seed for the random number generator (RAND_SEED) : 1 Molecular dynamics time step (MD_TIME_STEP) : 4.000 CAP_ATOM_SHIFT : 0.390 Maximal energy, step : ---------------- 0 Minimal energy, step : ???????????????? 200 Average energy, stand.dev. : ???????????????????????????????? Average atomic shift along one axis : ???????? MODEL returned : FINAL ------before this whole log file was filled up with this; -------------- ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? --------------- looks like some bond/bonds has gone too short and that might have affected the energy of system to go out of limits. But how can I found out which bond is that or some details like that? Hoping for a quick reply, Best regards, Vivek -- VIVEK SHARMA HBG BI "I never think of the future - it comes soon enough." A.Einstein

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(no subject)
by Michael Grabe 08 Apr '05

08 Apr '05

dear modellers, i use the BUILD_MODEL command to introduce a mutation into a template structure, but I want to generate different rotomer conformations and get some kind of score for the trial without going through the entire "model" routine. I just want to look at very local rearrangements and not worry about the rest of the protein that is exactly the same. does anyone have any suggestions or test scripts that can help me with this. thanks a lot, michael ------------------------------------------------------------------------ -------------------------- Michael Grabe, Ph.D. HHMI/UCSF Genetics Development & Behavioral Science Building 1550 4th Street, GD 481 San Francisco, CA 94143-0725 tel: ++ 415.476.0421 http://itsa.ucsf.edu/~mgrabe

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Same coordinates
by Joanne Hanna 08 Apr '05

08 Apr '05

Hi I am trying to use modeller to rebuild 5 missing resdiues from a protein that I wish to do some MD on. Whilst I have managed to do this, the x, y and z corrdinates of the modeller output models are all slightly different for each atom for the region of the protein of known structure (i am modelling the sequence against its structure minus the 5 residues). As I was hoping to add to this new complete structure the coordinates of the ligands in the original pdb file, I was wondering if there is any way to define that all the coordinates should be excactly the same as those from the original structure and the only alterations would be the addition of the positions of the 5 'new' residues. Thanks Jo

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question re. Modeller6v2 (re. fold)
by Vicente Reyes 04 Apr '05

04 Apr '05

Dear Dr. Sali & colleagues, I used Modeller6v2 to build 3-D models of some unsolved protein sequences, using as input sequence alignments obtained from the threading program, 123D. Since Modeller performs a partial rfefinement of the structure it builds, do you think it is possible that the fold of the final 3-D structure would be different from the fold of the alignment template found by 123D? Have you seen a case where the fold was altered by the refinement performed by Modeller? How often does this happen and in what particular cases? Thank you very much for your time and your help. Very sincerely yours, V. Reyes ====================================================== >>>>>>>>>>>> VICENTE M. REYES, Ph.D. <<<<<<<<<<<< Dept. of Pharmacol., Sch. of Pharm. & Pharm. Sci., & Integrative Biosci. Dept., S.D. Supercomputer Center Univ. of California-San Diego, La Jolla, CA 92093-0505

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request
by selvaraj manikandan mani 04 Apr '05

04 Apr '05

Respected sir, I have downloaded MODELLER and when I want to use it I could not get the concept like how to get the alignment file and the script file when I went through the manual.I would like to do a modelling of the following sequence: >dmpr MPIKYKPEIQHSDFKDLTNLIHFQSMEGKIWLGEQRMLLLQFSAMASFRREMVNTLG IERAKGLFLRHGYQSGLKDAELARKLRPNASEVGMFLAGPQMHSLKGLVKVRPTELD IDKEYGRFYAEMEWIDSFEVEICQTDLGQMQDPVCWTLLGYACAYSSAFMGREIIFKE VSCRGCGGDKCRVIGKPAEEWDDVASFKQYFKNDPIIEELYELQSQLLSLRTNLDKQE GQYYGIGQTPAYQTVRNMMDKAAQGKVSVLLLGETGVGKEVIARSVHLRSKRAAEPFV AVNCAAIPPDLIESELFGVEKGAFTGATQSRMGRFERADKGTIFLDEVIELSPRAQASL LRVLQEGELERVGDNRTRKIDVRVIAATHEDLAEAVKAGRFRADLYYRLNVFPVAIPAL RERREDIPLLVEHFLQRFHQEYGKRTLGLSDKALEACLHYSWPGNIRELENVIERGIIL TDPNESISVQALFLRAPEEPQTASERVSLDGVLIQPGNGQGSWISQLLSSG LSLDEIEESLMREAMQQANQNVSGAARLLGLSRPALAYRLKKIGIEG and the PDB ID for the templete is 1NY5. Sir,please do help me how can I proceed further.

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