- modeller_usage - salilab.org

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.

2 3

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/

2 1

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/

1 0

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

2 1

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.

2 1

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

1 0

Theory regarding filling of gaps
by Samuel Genheden (a03samge) 01 Feb '08

01 Feb '08

Hello, Modeller users! My question regards the theory behind and how Modeller creates the models. The case is that I have been using the Missing residue-script from the Modeller wiki-page to fill in a gap of 14 missing residues. But how does Modeller build the gap when it does not have any template structure as in my case? Best regards, Samuel

2 1

Re: [modeller_usage] December 74% OFF
by Doctor Harriett Lacey 29 Dec '07

29 Dec '07

1 0

multiple target sequences
by Han Choe 20 Dec '07

20 Dec '07

Dear Modellers, If you have accession numbers of multiple, say hundreds, target sequences, what could be an easy way to model the target protein structures from a template structure? Cheers, Han

1 0

model-loop
by Urszula Uciechowska 19 Dec '07

19 Dec '07

Hi, Thanks Marcin,this part works now after putting the brackets but now after starting the script model-loop.py I am getting: 'import site' failed; use -v for traceback Traceback (most recent call last): File "model-loop.py", line 15, in ? a.starting_model= 1 # index of the first model TypeError: 'tuple' object has only read-only attributes (assign to .starting_model) in my input file I have: a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.md_level = None # No refinement of model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 4 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level How should I define the starting model? What is exactly the "index of the first model"? Thank you in advance for any help Best Regards, Urszula MSc.PhD Student Medicinal Chemistry Group University of Halle-Wittenberg

1 0