October 2011 - modeller_usage

Request for papers.
by Sehrish Batool 18 Oct '11

18 Oct '11

Sir I request you to send me full length papers of the following, 1. N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, A. Sali. Comparative Protein Structure Modeling With MODELLER. Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006. 2. M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo, A. Sali. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000. 3. A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993. 4. A. Fiser, R.K. Do, & A. Sali. Modeling of loops in protein structures, Protein Science 9. 1753-1773, 2000 Thank you

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Re: [modeller_usage] Restraining Secondary Structure
by bharat lal 17 Oct '11

17 Oct '11

Hi, I am modelling a sequence in which I am restraining some portions of the sequence to be helix as I have copied that sequence from a known structure. But I want to ask whether the same restrained sequence would also be same in real or not. What is the basis of restraining the structure to be helix or sheets ?? --------- Bharat

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Changing the directory.
by Sehrish Batool 17 Oct '11

17 Oct '11

I am using Modeller9.10 and I am unable to define directry in Command Prompt using 'Dir' keyword. Please tell me how can I define it and where Did I made mistake. The command that I used is : Dir = C:\Program Files\Modeller9.10\examples\automodel

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Correct the small scripting error
by Ashish Runthala 17 Oct '11

17 Oct '11

Dear MODELLERS, I tried writing a script to automatically take 3 templates from the current folder and do iterative modeling for the same target sequence. i.e., I want to run Modeller with three templates (2 fixed (1SHWA, 1SHXA) + 1 variable, taken as different individual template files from the current folder iteratively). def align(fileName): #fileName iteratively contains name of all pdb files log.verbose() env = environ() env.io.atom_files_directory = ['.', '../atom_files'] pdbfile=fileName + 'A' aln = alignment(env) for (code,code,atomfile, chain) in (('1SHWA','1SHXA','1SHX','A'),(pdbfile,pdbfile,fileName,'A')): mdl = model(env, file=atomfile, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(mdl, atom_files=atomfile, align_codes=code) There is some mistake in last four lines as only two templates are coming in the alignment file and not the third one. So correct my mistake in this piece of code. Thanks, Ashish -- Ashish Runthala, Lecturer, Structural Biology Cell, Cabin: 3222-U Biological Sciences Group, Faculty Division III, Birla Institute of Technology & Science, Pilani Rajasthan, INDIA - 333 031 Website: https://sites.google.com/site/ashishrunthala/ Phone: +91-1596-245073-273 (O) +91-7597971146 (M) Fax: +91-1596-244183 E-mail: ashishr(a)bits-pilani.ac.in ashish.runthala(a)gmail.com

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energy
by Jin-Rui Xu 16 Oct '11

16 Oct '11

Hi there, What is the indication of modeller mod energy? The higher the better? Thanks!

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Regarding align2d & CS-BLAST alignments PLEASE ANSWER ME QUICKER ..I AM STUCK UP IN A FEW CASES
by Ashish Runthala 03 Oct '11

03 Oct '11

Dear Modellers and Sir Ben Webb, I am finding a critical difference in the pairwise alignment computed by MODELLER and the corresponding alignment cognitive to the CS-BLAST undertaken alignment. These are the differences. Will someone help me understanding why there is the case of shifted alignments in the the alignment case mentioned below for the following alignments of templates 2Q7BA and 3PP9A for the CASP8 target T0400? I have written TARGE in the MODELLER Alignment file for target sequence for better one-to-one alignment residue correlation. On top of it the CS-BLAST residue order is not available in the template PDB files. So i am confused..Where CS-BLAST has got the altered sequences from, when i precisely called the PDB for it. 2Q7BA ALIGNMENT MODELLER ALIGNMENT 2Q7BA>FQGMEIKEYENNPYHLAQLVDLINYCQNIEAKLDIKMAEQDDIFQIENYYQNRKGQFWIALEN-EKVVGSIALLRIDDKTAVLKKFFTYPKYRGNPVRLGRKLFERFMLFARASKFTRIVLDTPEKEKRSHFFYENQGFKQITRDELDVDYIFPDRDSRIYVKLL--* TARGE>M-AINIIEY-NRSY-KEELIEFILSIQKNEFNIKIDRDDQPDLENIEHNYLNSGGQFWLAINNHQNIVGTIGLIRLDNNMSALKKMFVDKGYR-N-LKIGKKLLDKVIMTCKEQNIDGIYLGTIDKFISAQYFYSNNGFREIKRGDLPSSFPKLDVDNRFYYRNLKD* CS-BLAST ALIGNMENT Query: 1 MAINIIEYNRSYKEELIEFILSIQKNEFNIKIDRDDQPDLENIEHNYLNSGGQFWLAINN 60 M I E N + +L++ I Q E + I +Q D+ IE+ Y N GQFW Sbjct: 20 MEIKEYENNPYHLAQLVDLINYCQNIEAKLDIKMAEQDDIFQIENYYQNRKGQFW-IALE 78 Query: 61 HQNIVGTIGLIRLDNNMSALKKMFVDKGYRN--LKIGKKLLDKVIMTCKEQNIDGIYLGT 118 ++ +VG+I L+R+D+ + LKK F YR +++G+KL ++ ++ + I L T Sbjct: 79 NEKVVGSIALLRIDDKTAVLKKFFTYPKYRGNPVRLGRKLFERFMLFARASKFTRIVLDT 138 Query: 119 IDKFISAQYFYSNNGFREIKRGDLPSSFPKLDVDNRFYYRNLK 161 +K + +FY N GF++I R +L + D D+R Y + L Sbjct: 139 PEKEKRSHFFYENQGFKQITRDELDVDYIFPDRDSRIYVKLLD 181 3PP9A ALIGNMENT MODELLER ALIGNMENT 3PP9A>SLLIRELETNDLDNFPEIDDSFIVNARLMLSLSKVNRRIEYTVEDVPSYEKSYLELVYNEYINKPNQIIYIALLHNQIIGFIVLKKNWNNYAYIEDITVDKKYRTLGVGKRLIAQAKQWAKEGNMPGIMLETQNNNVAACKFYEKCGFVIGGFDFLVYKGLNMTSDEVAIYWYLHF* TARGE>------M---AI-NIIEYNRSY-KEELIEFILS-I-QKNEFNIK-IDRDDQPDLENIEHNYLNSGGQFWLAINNHQNIVGTIGLIRLDNNMSALKKMFVDKGYRNLKIGKKLLDKVIMTCKEQNIDGIYLGTIDKFISAQYFYSNNGFREIKRGDLPSSFPKLDVDNRFYYRNLKD* CS-BLAST ALIGNMENT Query: 1 MAINIIEYNRSYKEELIE----------FILSIQKNEFNIKIDRDDQPDLEN-------- 42 M++ I E + + E +LS+ K I+ +D P E Sbjct: 4 MSLLIRELETNDLDNFPEIDDSFIVNARLMLSLSKVNRRIEYTVEDVPSYEKSYLQNDNE 63 Query: 43 --IEHNYLNSGGQFWLAINNHQNIVGTIGLIRLDNNMSALKKMFVDKGYRNLKIGKKLLD 100 + + Y+N Q H I+G I L + NN + ++ + VDK YR L +GK+L+ Sbjct: 64 ELVYNEYINKPNQIIYIALLHNQIIGFIVLKKNWNNYAYIEDITVDKKYRTLGVGKRLIA 123 Query: 101 KVIMTCKEQNIDGIYLGTIDKFISAQYFYSNNGFRE 136 + KE N+ GI L T + ++A FY GF Sbjct: 124 QAKQWAKEGNMPGIMLETQNNNVAACKFYEKCGFVI 159 Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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