February 2008 - modeller_usage

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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Antibody Modelling
by selva＠pnu.edu 13 Feb '08

13 Feb '08

I want to model an antibody structure with multiple templates for specific segments from each template based on the below alignment for two chains seperately. Since I know the domain interface residues, I could able to superimpose their relative orientation after modelling seperately. L-CHAIN TARGET__: AAAAAAAAAA11111AAAAAAAAAA22222AAAAAAAAAA33333AAAAAAAAAA L-CHAIN TEMPLATE: AAAAAAAAAAxxxxxAAAAAAAAAAxxxxxAAAAAAAAAAxxxxxAAAAAAAAAA LOOP-L1 TEMPLATE: xxxxxxxxxx11111xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx LOOP-L2 TEMPLATE: xxxxxxxxxxxxxxxxxxxxxxxxx22222xxxxxxxxxxxxxxxxxxxxxxxxx LOOP-L3 TEMPLATE: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx33333xxxxxxxxxx H-CHAIN TARGET__: BBBBBBBBBB44444BBBBBBBBBB55555BBBBBBBBBB66666BBBBBBBBBB H-CHAIN TEMPLATE: BBBBBBBBBBxxxxxBBBBBBBBBBxxxxxBBBBBBBBBBxxxxxBBBBBBBBBB LOOP-H1 TEMPLATE: xxxxxxxxxx44444xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx LOOP-H2 TEMPLATE: xxxxxxxxxxxxxxxxxxxxxxxxx55555xxxxxxxxxxxxxxxxxxxxxxxxx LOOP-H3 TEMPLATE: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx66666xxxxxxxxxx I wish to know how to specify the segment positions to be modeled from each template or Is there anyother easy way of modelling the same?. Selva --------------------------------- Never miss a thing. Make Yahoo your homepage.

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Taking into account additional residues
by valeria losasso 13 Feb '08

13 Feb '08

Hi all, my problem is the following: I want to model a structure based on another one. Both are trimers. My sequence (corresponding to the "unknown" proteins) has additional residues at the beginning of each chain, and I have to force them to make an alpha-helix. The problem is that when I try to add the restraints using as template the original chains-including PDB file and separating chains in the .ali file, the residues numbering seems to start from the residue 1 of the template, and I can't impose anything on my sequence. I've tried too to edit the template PDB file in order to delete the information about chains and to obtain a "normal" numbering, but in this case, obviously, Modeller is not able to separate the subunits and generates strange distortions to keep in contact the boundary residues. Last possibility would be to model separately the chains and to reconstruct the trimer at the end, but the modeling changes the coordinates and I can not imagine how to reassemble the single results. Any suggestion? thanks in advance _________________________________________________________________ Ti piace giocare con le lettere? Prova ABCLive! http://messengergiochi.it.msn.com/

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Taking into account additional residues
by valeria losasso 12 Feb '08

12 Feb '08

Hi all, my problem is the following: I want to model a structure based on another one. Both are trimers. My sequence (corresponding to the "unknown" proteins) has additional residues at the beginning of each chain, and I have to force them to make an alpha-helix. The problem is that when I try to add the restraints using as template the original chains-including PDB file and separating chains in the .ali file, the residues numbering seems to start from the residue 1 of the template, and I can't impose anything on my sequence. I've tried too to edit the template PDB file in order to delete the information about chains and to obtain a "normal" numbering, but in this case, obviously, Modeller is not able to separate the subunits and generates strange distortions to keep in contact the boundary residues. Last possibility would be to model separately the chains and to reconstruct the trimer at the end, but the modeling changes the coordinates and I can not imagine how to reassemble the single results. Any suggestion? thanks in advance > From: modeller_usage-request(a)salilab.org > To: valelos(a)hotmail.it > Subject: confirm 392af0e853ea4879fdb3eb3ac0b3f1a1fbc59de1 > Date: Tue, 12 Feb 2008 01:55:35 -0800 > > Mailing list subscription confirmation notice for mailing list > modeller_usage > > We have received a request from giorgione.sbp.op.sissa.it for > subscription of your email address, "valelos(a)hotmail.it", to the > modeller_usage(a)salilab.org mailing list. To confirm that you want to > be added to this mailing list, simply reply to this message, keeping > the Subject: header intact. Or visit this web page: > > https://salilab.org/mailman/confirm/modeller_usage/392af0e853ea4879fdb3eb3a… > > > Or include the following line -- and only the following line -- in a > message to modeller_usage-request(a)salilab.org: > > confirm 392af0e853ea4879fdb3eb3ac0b3f1a1fbc59de1 > > Note that simply sending a `reply' to this message should work from > most mail readers, since that usually leaves the Subject: line in the > right form (additional "Re:" text in the Subject: is okay). > > If you do not wish to be subscribed to this list, please simply > disregard this message. If you think you are being maliciously > subscribed to the list, or have any other questions, send them to > modeller_usage-owner(a)salilab.org. _________________________________________________________________ Organizza le tue feste e condividine le foto con Windows Live Eventi! http://home.services.spaces.live.com/events/

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I'm a beginner
by Lella Sana 11 Feb '08

11 Feb '08

Greetings Forum users I have recently installed modellerv9.2 on my system and am having real difficulty in getting started.I've tried to use the basic example tutorial, but I've a lot of questions: 1. How can i get PIR format for the input? I've only the sequence of my protein in fasta format. 2. From BLAST, i've a file.aln. Must I convert it in PIR format or in a file.ALI? How? 3, Then, how can i get a model of my protein's structure having one template (a pdb file)? 4. In the test.cod, for running my experiment, i've to insert all the template? Many thanks in advance for your help, have a good day. --------------------------------- --------------------------------- L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail

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Question about alignment.align()
by Vadim Patsalo 11 Feb '08

11 Feb '08

Hello Modeller Users, I am trying to take a pseudo-symmetric heterodimeric (AB) structure, and build homodimer (AA) and (BB) structures. The chains have ~30-50% identity, nearly the same in length. The way I am doing this is aligning the AA sequence with the AB sequence derived from the PDB with alignment.align(); However, Modeller keeps doing something weird at the ends of the second chain, placing breaks after the first and before the last residue. Chain A is 3 residues shorter than chain B. Example, with underscores inserted instead of the actual sequence: template ___DLH/SVIEN___VNLED/../.. model ___DLH/H-IAN___VDL-H/../.. I would expect to have the model be "-HIA" in the beginning and "DLH-" at the end. This is the alignment that I get from Clustal, and the alignment that makes sense to me. I've tried setting 'overhang=1', using a number of different matrices from '$LIB', to no avail. With other matrices (Gonnet), I get a _horrible_ alignment, like so: VNLED/../.. VDLH/-../.. How could it insert a gap into a HETATM chain? Is there a better way to do this, perhaps aligning only the chains that are changed in the sequence (align A to B), instead of AA with AB? Thanks for your help! Vadim -- five.sentenc.es is a personal policy that all email responses regardless of recipient or subject will be five sentences or less. It's that simple.

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Modeller 9v3 release
by Modeller Caretaker 05 Feb '08

05 Feb '08

The new version of Modeller, 9v3, is now available for download! Please see the download page at http://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9v3 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9v3 is primarily a bugfix release relative to the last public release (9v2). Major user-visible changes include: # Mac OS X 10.5 (Leopard) is now supported (with Python 2.5). # PIR alignment file headers are now checked more closely, to avoid potential problems with these headers going unnoticed. # alignment.align() and alignment.consensus() no longer take a max_gap_length parameter, as it is not used in any case. See the Modeller manual for a full change log: http://salilab.org/modeller/9v3/manual/node38.html If you encounter bugs in Modeller 9v3, please see http://salilab.org/modeller/9v3/manual/node10.html for information on how to report them. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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