- modeller_usage - salilab.org

keeping original residue numbers in final model
by Mauricio Carrillo Tripp 11 Nov '08

11 Nov '08

Hi, I'm new in Modeller (9v4) and I haven't been able to find an answer to the following question anywhere I've looked: Is there a way to keep the original target's residue numbering in the final model instead of having them sequentially numbered starting at 1? As an example, this is my target's sequence (NOTE: "-" are not gaps, are missing/unknown residues): >P1;1s58 SEQUENCE:1s58.ali : 19 :A: 554 :A:::0.00:0.00 ------------------NPVKSMWSEGATFSANSVTCTFSRQFLIPYDP EHHYKVFSPAASSCHNASGKEAKVCTITPIMGYSTPWRYLDFNALNLFFS PLEFQHLIENYGSIAPDALTVTISEIAVKDVTDKTGGGVQVTDSATGRLC MLVDHEYKYPYVLGQGQDTLAPELPIWVYFPPQYAYLTVGDVNTQGISGD SKKLASEESAFYVLEHSSFQLLGTGGTATMSYKFPPVPPENLEGCSQHFY EMYNPLYGSRLGVPDTLGGDPKFRSLTHEDHAIQPQNFMPGPLVNSVSTK -------------TGLSTGTSQNTRISLRPGPVSQPYHHWDTDKYVTGIN AISHGQTTYGNAEDKEYQQGVGRFPNEKEQLKQLQGLNMHTYFPNKGTQQ YTDQIERPLMVGSVWNRRALHYESQLWSKIPNLDDSFKTQFAALGGWGLH QPPPQIFLKILPQSGPIGGIKSMGITTLVQYAVGIMTVTMTFKLGPRKAT GRWNPQPGVYPPHAAGHLPYVLYDPTATDAKQHHRHGYEKPEELWTAKSR VHPL * The final model's PDB starts with residue number 1 and ends with residue number 523 (number of residues in the sequence). What I would like to get is a model's PDB starting at residue 19, jumping from residue 300 to residue 314 and so, ending at residue 554. Thanks in advance for any pointers! -- 0 | Mauricio Carrillo Tripp, PhD / | Department of Molecular Biology, TPC6 0 | The Scripps Research Institute \ | 10550 North Torrey Pines Road 0 | La Jolla, California 92037 / | trippm(a)scripps.edu 0 | http://www.scripps.edu/~trippm ** Aut tace aut loquere meliora silentio **

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to build ions
by vidhya ganesh 11 Nov '08

11 Nov '08

Hi, I am new to modeller. I am using mod9v4. I have quite few doubts. I performed homology modeling of particular protein , done all steps and got a model. But i have to know, how to build ions in my model?? Thanks Best Regards vidhya

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template alignment challenge
by Chinwe Ekenna 11 Nov '08

11 Nov '08

Good day... pls sir i wasn't able to download pdb locally so i did a blast and got my target structure and sequence ...right now i'm at a loss of how to get an alignment file as build _profile would not suffice for this... how do i create an alignment file for my input or how do i create a pir file from my template... thanks

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mutate script from modeller site
by DimitryASuplatov 11 Nov '08

11 Nov '08

Hello, I am trying to use mutate.py script from modeller site http://salilab.org/modeller/wiki/Mutate%20model I have python2.5 core and devel packages installed. When I run > mod9v5 - 1klc.nodummies.chains.pdb 500 ARG B < mutate.py > out (according to the instructions in the header of the script) I get the following error ========================================== 'import site' failed; use -v for traceback Traceback (most recent call last): File "(stdin)", line 2, in ? ImportError: No module named os ========================================== Setting $PYHTONHOME to /usr/lib64/python2.5 (where os.py is located) does not help. Copying os.py to local folder results in the following error ======================================================================= 'import site' failed; use -v for traceback Traceback (most recent call last): File "<string>", line 1, in ? File "/usr/local/modeller/modlib/modeller/__init__.py", line 45, in ? import os.path, re, sys File "os.py", line 134 from os.path import (curdir, pardir, sep, pathsep, defpath, extsep, altsep, ^ SyntaxError: invalid syntax ======================================================================= I seriously doubt that there is an error in os.py file of my python distribution. Any suggestions? Thanks!

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How to change directory path for atom files
by khuram sb 11 Nov '08

11 Nov '08

Hi, I want to ask that when modeller directory (Work Station) is changed from C directory (default) than how path of atom files is changed? I want to know the whole procedure of changing directories and giving the right path for atom files. Thanks, Khramsb

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Building a tetramer
by Nicky Thrupp 11 Nov '08

11 Nov '08

Hi, I am building a protein with four chains (based on a tetrameric template). I was wondering about the algorithms that Modeller uses - does it build all four chains simultaneously, or does it build them one at a time? I am worried about steric clashes if the chains are built indiviudally and then put together afterwards. Thanks in advance for any help. Nicky

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Help
by nagaraju ngaraju 11 Nov '08

11 Nov '08

Dear sir/madam I want to do project in homology modelling using modeller but I am unable to crete .pir file Can you suggest me in this regard Thanks In adavance I.Nagaraju Sugen Life Sciences Tirupati 9949860196 Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/

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Re: [modeller_usage] Heme
by Bo Yang 04 Nov '08

04 Nov '08

Hi, Rubben: I use dot (.) . Heme is shown as BLK in the model. Using Chimera and VMD, the whole molecule of heme is there, but not Fe. If I select "Fe" from "element", no selection returns. The "Fe" is in the pdb file as shown below: HETATM 3620 FE BLK 455 -54.160 -1.094 -33.073 1.00999.99 1SG3621 HETATM 3621 CHA BLK 455 -55.567 -1.736 -30.032 1.00999.99 1SG3622 HETATM 3622 CHB BLK 455 -53.632 -4.396 -33.562 1.00999.99 1SG3623 HETATM 3623 CHC BLK 455 -53.011 -0.451 -36.189 1.00999.99 1SG3624 HETATM 3624 CHD BLK 455 -54.469 2.229 -32.529 1.00999.99 1SG3625 HETATM 3625 NA BLK 455 -54.569 -2.714 -32.020 1.00999.99 1SG3626 HETATM 3626 C1A BLK 455 -55.107 -2.789 -30.763 1.00999.99 1SG3627 HETATM 3627 C2A BLK 455 -55.133 -4.176 -30.354 1.00999.99 1SG3628 HETATM 3628 C3A BLK 455 -54.608 -4.886 -31.328 1.00999.99 1SG3629 HETATM 3629 C4A BLK 455 -54.246 -3.991 -32.395 1.00999.99 1SG3630 HETATM 3630 CMA BLK 455 -54.416 -6.422 -31.313 1.00999.99 1SG3631 HETATM 3631 CAA BLK 455 -55.621 -4.804 -29.030 1.00999.99 1SG3632 HETATM 3632 CBA BLK 455 -56.992 -4.376 -28.593 1.00999.99 1SG3633 HETATM 3633 CGA BLK 455 -57.255 -5.010 -27.253 1.00999.99 1SG3634 HETATM 3634 O1A BLK 455 -56.915 -4.439 -26.202 1.00999.99 1SG3635 HETATM 3635 O2A BLK 455 -57.828 -6.104 -27.233 1.00999.99 1SG3636 HETATM 3636 NB BLK 455 -53.437 -2.204 -34.573 1.00999.99 1SG3637 HETATM 3637 C1B BLK 455 -53.311 -3.583 -34.605 1.00999.99 1SG3638 HETATM 3638 C2B BLK 455 -52.782 -3.991 -35.882 1.00999.99 1SG3639 HETATM 3639 C3B BLK 455 -52.616 -2.872 -36.580 1.00999.99 1SG3640 HETATM 3640 C4B BLK 455 -53.040 -1.749 -35.784 1.00999.99 1SG3641 HETATM 3641 CMB BLK 455 -52.468 -5.428 -36.363 1.00999.99 1SG3642 HETATM 3642 CAB BLK 455 -52.091 -2.736 -38.019 1.00999.99 1SG3643 HETATM 3643 CBB BLK 455 -51.725 -3.825 -38.678 1.00999.99 1SG3644 HETATM 3644 NC BLK 455 -53.752 0.535 -34.116 1.00999.99 1SG3645 HETATM 3645 C1C BLK 455 -53.394 0.607 -35.442 1.00999.99 1SG3646 HETATM 3646 C2C BLK 455 -53.466 1.977 -35.904 1.00999.99 1SG3647 HETATM 3647 C3C BLK 455 -53.869 2.676 -34.858 1.00999.99 1SG3648 HETATM 3648 C4C BLK 455 -54.062 1.807 -33.747 1.00999.99 1SG3649 HETATM 3649 CMC BLK 455 -53.156 2.502 -37.344 1.00999.99 1SG3650 HETATM 3650 CAC BLK 455 -54.149 4.182 -34.765 1.00999.99 1SG3651 HETATM 3651 CBC BLK 455 -53.972 4.970 -35.805 1.00999.99 1SG3652 HETATM 3652 ND BLK 455 -54.923 0.052 -31.560 1.00999.99 1SG3653 HETATM 3653 C1D BLK 455 -54.874 1.432 -31.525 1.00999.99 1SG3654 HETATM 3654 C2D BLK 455 -55.330 1.916 -30.258 1.00999.99 1SG3655 HETATM 3655 C3D BLK 455 -55.681 0.681 -29.488 1.00999.99 1SG3656 HETATM 3656 C4D BLK 455 -55.392 -0.425 -30.350 1.00999.99 1SG3657 HETATM 3657 CMD BLK 455 -55.447 3.379 -29.780 1.00999.99 1SG3658 HETATM 3658 CAD BLK 455 -56.248 0.648 -28.080 1.00999.99 1SG3659 HETATM 3659 CBD BLK 455 -57.738 0.802 -28.197 1.00999.99 1SG3660 HETATM 3660 CGD BLK 455 -58.352 0.774 -26.836 1.00999.99 1SG3661 HETATM 3661 O1D BLK 455 -59.545 1.081 -26.729 1.00999.99 1SG3662 HETATM 3662 O2D BLK 455 -57.669 0.458 -25.858 1.00999.99 1SG3663 Thank you for your advice. Bo --- On Tue, 11/4/08, Rubben Torella <rubben.torella(a)gmail.com> wrote: From: Rubben Torella <rubben.torella(a)gmail.com> Subject: Heme To: n62star(a)yahoo.com Date: Tuesday, November 4, 2008, 1:01 AM Hi,Bo! What do you use in the alignment for heme? dot (.) or (*)? Because if you use (.), heme is considered as a block, while (*) consider heme as a co-factor. But you see heme and you can't see iron, or you can't see anything? I'm sorry if I don't understand your question. Rubben Torella

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Modelling an oligomer
by Lucas Bleicher 17 Oct '08

17 Oct '08

I want to model a heterotrimer consisting of proteins A, B and C, where the structure of the A:B complex is already known, and C should be modelled. There is a known structure of another structure made of proteins D, E and F, where D and E are homologous to A:B (and can be easily spatially superposed) and F is homologous to C. Do I have to work with restraints or is there a way to set a PIR file using the A:B and D:E:F complexes as "knowns" so that Modeller can assume that it must build an A:B:C complex so that A:B would be in the equivalent positions to D:E (but should of course be nearly identical to the A:B x-ray structure more than the D:E structure, since A:B is the real thing) and C must be modelled using F as template and be in the position it would occupy in the D:E:F structure? To add insult to injury, although C and F are homologous, there is a better template, G, for it in terms of identity and alignment size. So the ideal solution to the problem would be: A trimer consisting of A:B:C where A and B are knowns, C is modelled against G, and the A:B is positioned against D:E and the C model against G is positioned against F in the known D:E:F structure. I hope my message is not too confusing... Lucas P.S.: I already tried to separately model only the protein C against G and then using SSM to superpose the C model against F and the A:B complex against D:E, but that would produce some serious clashes, so I really need to build the whole thing on modeller. Novos endereços, o Yahoo! que você conhece. Crie um email novo com a sua cara @ymail.com ou @rocketmail.com. http://br.new.mail.yahoo.com/addresses

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Modeller 9v5 release
by Modeller Caretaker 16 Oct '08

16 Oct '08

The new version of Modeller, 9v5, 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 9v5 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9v5 is primarily a bugfix release relative to the last public release (9v4). Major user-visible changes include: # New normalized DOPE assessment method, which returns a Z-score, and is thus comparable between different proteins. # PDB atom files are now also looked for in PDB-style subdirectories (the first two characters after the digit); e.g. 1abc is searched for in the 'ab' subdirectory, pdb4xyz.ent in the 'xy' subdirectory. # Libraries updated to correctly read and write remediated RNA and DNA, some other HETATMs (e.g. ions) and to use the new hydrogen names, in PDB v3. # Modeller now outputs new-style PDBs, with the element in columns 77 and 78, rather than older-style PDB which has a sequence number in this position. See the Modeller manual for a full change log: http://salilab.org/modeller/9v5/manual/node38.html If you encounter bugs in Modeller 9v5, please see http://salilab.org/modeller/9v5/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply reply to this email and let us know. 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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