- modeller_usage - salilab.org

Using only partial information for the model
by Stéphane Téletchéa 28 Feb '08

28 Feb '08

Dear colleagues, I'm willing to use modeller in a specific modelling procedure where only specific parts of the model are wanted. In fact, i have two beta sheets and two helices in the pdb template, and there are linked via loops. I would like to know the procedure i need to follow in order to model only those subparts of the system (and use modloop for the linking part). For instance this will be for the alignment: >template; structureX:18:A 63:A ::: XYZXYZ-----AAAAALLL----BBBBBLLL---AAAAALLLLL--BBBBBLLL-------* >target; sequence:1::::: ------CCCCCAAAAA---CCCCBBBBB---CCCAAAAA-----CCBBBBB---CCCCCCC* The matching sections are 'A' (alpha) and 'B' (beta), other letters being for illustration. The template pdb contains all the coordinates for the important structures, but not for loop LLLLL (third one). Do i need to adjust the alignment or the python script (or both)? I've searched through the archives and tutorials without clue, i'm probably not getting all the process properly. Thanks a lot in advance, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901

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Modelling complexes
by Chido Mpamhanga 28 Feb '08

28 Feb '08

Dear all, I'm new with modeller, I have used it to do simple models.. However I'm now trying to model a tri-metric complex where the active site of the complex is includes all three subunits. How do i go about this? kind regards Chido -------------------------------------------------- Dr Chido M'pamhanga Biological Chemistry and Molecular Microbiology School of Life Sciences University of Dundee Dow St. Dundee, DD1 5EH U.K. +44 (0)1382 386229(phone) +44 (0)1382 386373 (fax) http://www.brenkgroup.dundee.ac.uk

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building loops in crystal structure
by Simpson, Lisa M 28 Feb '08

28 Feb '08

Hi everyone, I have a question about Modeller - I have a crystal structure with missing loops. Does anyone know if there is a way I can build in the loops using Modeller and still preserve the current coordinates of the crystal structure? Cheers, lmsimp

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Improper packing
by jit＠mcbl.iisc.ernet.in 26 Feb '08

26 Feb '08

Hello, I am a bit new to this modeller though managed to use it with success for homology modeling. However, in some cases the model looks horrible without proper packing & cross-checking in VERIFY 3D gives a "FAIL" message! What do I do? I have changed templates quite a few times but in vain. Please suggest! -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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Using Fortran 90 with modeller
by Lee, Jinwoo 25 Feb '08

25 Feb '08

Dear Modeller Users, I would like to use modeller library in my own Fortran 90 code, and implement extensions to Modeller in Fortran 90. What is the best way of doing this ? Thanks for your help! Jinwoo

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fuse 3-residue peptide into a protein
by Bingding Huang 25 Feb '08

25 Feb '08

Dear Modeller, I am new to Modeller. Now I want to fuse 3-residue peptide, for example 3 Histine, to the N term of a structure-known protein like 2g2u, chain B. Any idea about that? Thanks a lot! Regards Bingding -- Bingding Huang EML Research gGmbH Schloss-Wolfsbrunnenweg 33 69118 Heidelberg Germany Tel: +49-6221-533 262 Fax: +49-6221-533 298 Email: bingding.huang(a)eml-r.villa-bosch.de http://www.eml-r.org

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code to generate canonical alpha-helix from sequence
by Yun He 24 Feb '08

24 Feb '08

Hi, Can Modeller generate canonical alpha-helix coordinates from only a peptide sequence without any other template structure? Who can paste some sample code here? Thanks. Yun

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Some tutorial issues
by Michael Mayhew 19 Feb '08

19 Feb '08

Greetings, I am using python2.5.1 and modeller version 9v3 on a Mac desktop (OSX 10.4.8). I saw a similar post in the discussion board regarding the compare.py script of the tutorial where the function call generated an error message. However, the information therein didn't really help me. I also referred to the user manual and found that in my version of modeller, malign_3d has been deprecated and that I should use salign. However, salign (in the context of the tutorial exercise) does not return an object that can be used to continue the tutorial. I am running the compare.py script from a directory on my Desktop separate from the modeller installation directory (should I be running the script from within the modeller directory?) For posterity, I have included my 'version' of the compare.py script and the error message from the python interpreter. Thanks for your time and consideration in this matter. Michael Mayhew <<< compare.py >>> from modeller import * env = environ() aln = alignment(env, file='pdball.pir', align_codes=('1b8pA', '1bdmA', '1civA', '5mdhA', '7mdhA', '1smkA')) aln. malign() aln.malign3d() aln.compare_structures() aln.id_table(matrix_file='family.mat') env.dendogram(matrix_file='family.mat', cluster_cut=-1.0) <<< python traceback error message >>> Multiple dynamic programming alignment (MALIGN): Residue-residue metric : $(LIB)/as1.sim.mat ALIGN_BLOCK : 1 Gap introduction penalty: -900.0000 Gap extension penalty : -50.0000 Length of alignment : 384 pdbnam_____E> Filename for PDB code not found: 1b8p Directories: Extensions : :.atm:.pdb:.ent:.crd (Also tried prepending 'pdb', and looking for .Z, .gz, .bz2) Traceback (most recent call last): File "compare.py", line 8, in <module> aln.malign3d() File "/Library/modeller-9v3/modlib/modeller/alignment.py", line 295, in malign3d edit_file_ext) IOError: pdbnam_____E> Filename for PDB code not found: 1b8p Directories: Extensions : :.atm:.pdb:.ent:.crd (Also tried prepending 'pdb', and looking for .Z, .gz, .bz2)

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Alignment editors?
by Esben Jannik Bjerrum 19 Feb '08

19 Feb '08

Hi, This is not entirely modeller specific, but related. Do anyone know of an alignment editor which accepts, but doesn't delete the PIR comment lines? So far I have just hand edited the PIR file from a fasta file, but now I'm trying to model a multimeric and multidomain protein which makes it very complicated and cumbersome. Best Regards Esben ____________________________________________________________________________________ Get easy, one-click access to your favorites. Make Yahoo! your homepage. http://www.yahoo.com/r/hs

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Strange results from loop modelling
by Samuel Genheden (a03samge) 14 Feb '08

14 Feb '08

Hello, Modeller users I have a dimer in which I have used Modeller to fill in a missing loop region (one in each chain). I started to fill in the two gaps at the same time with the automodel class. Then I selected the best structure and I did loop refinement with the loopmodel class but only on one of the loops. From this step I took out the 10 best structures and did loop refinement on the other loop. Now the strange thing is that it seems that Modeller has refined the second loop in exactly the same way for all the 10 starting structures. The loop from the first loop is different but each refinement of the second loop is identical. I have not been able to find any error in the log-files or in my script and Modeller has not complained about anything. So my question is: are these results reliable? Is it possible that the loop modelling behaves like this? Best regards, Samuel

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