- modeller_usage - salilab.org

Heteroatom problem, message 2
by John Penniston 09 Nov '02

09 Nov '02

I've been trying for days to make a proper model of my large (1058 residue) membrane protein, PMCA. It needs to contain a calcium ion, but I can't get modeller to put it in. I'm sorry the attached files are so big, but it's a big molecule. I'm sending this as 2 messages, zipped up using Winzip; If I try to put it in a single message, it bounces, and I think all of these files are needed to diagnose the problem. I'm trying to model PMCA based on the only known homolog 1EUL. 1EUL contains 2 calcium ions, and I expect the PMCA version to contain only one of them, as indicated in the alignment file. No matter what I try, the PMCA file produced has the calcium removed. The file I have renamed as PMCA E1.pdb is the final file produced in the attempt enclosed here and described in the log file. I did this one using an MS-DOS box under Windows 98, but the same kinds of errors occur in Windows 2000. Thanks for your attention. John Penniston -- John T. Penniston, Ph.D. Dept. of Biochemistry and Molecular Biology Guggenheim 16, Mayo Clinic 200 First St. SW Rochester, MN 55905 USA

1 0

Loop Modeling
by Alex Brown 07 Nov '02

07 Nov '02

Dear Modellers, I have been running through the examples in the Fiser and Sali paper concerning the modeling of the loop in cpCN-V (circularly permuted cyanovirin). I used the given scripts, modifying it to allow the modeling of different linker lengths, from 6 to 12 residues, as suggested in the paper. 200 final models of each linker were obtained, the model with the lowest energy score (objective function) being selected in each case. This gave the following table of results: Length (aa) Residues Objective Function Model # File Name 6 49-54 21.6408 119 cpCN-V.BL06 7 48-54 12.1955 49 cpCN-V.BL07 7 49-55 33.0729 118 cpCN-V.BL07a 8 47-54 7.5401 153 cpCN-V.BL08 8 49-56 35.8842 152 cpCN-V.BL08a 8 48-55 31.0163 117 cpCN-V.BL08b 9 46-54 12.1449 95 cpCN-V.BL09 9 49-57 24.4132 39 cpCN-V.BL09a 9 47-55 29.1883 145 cpCN-V.BL09b 9 48-56 27.4328 115 cpCN-V.BL09c 10 46-55 28.5179 184 cpCN-V.BL10 10 47-56 29.004 199 cpCN-V.BL10a 10 48-57 31.8589 25 cpCN-V.BL10b 11 46-56 18.1581 109 cpCN-V.BL11 11 47-57 22.4939 189 cpCN-V.BL11a 12 46-57 27.0164 198 cpCN-V.BL12 My question is, can I take the 'best' loop model as being that with the lowest objective function (i.e. model cpCN-V.BL08, objective function 7.5401). I did wonder how my results compared with those obtained by Fiser and Sali, but I have been unable to find this. Cheers, Alex Brown PS. I'm running Modeller v6.2 on Mac OS X (Darwin). Each modeling run (200 loop models) took 6-10 hours !!!!

2 3

Re: problems
by Bozidar Yerkovich 01 Nov '02

01 Nov '02

Hi, Change: SET MD_LEVEL = 'refine1' To: SET MD_LEVEL = 'refine_1' Best, Bozidar > I wanted to use modeller6v2 with these attached files but I couldn't find > where is the problem. Would you help me please. I tested Modeller with the > file in the diretory examples/ and it worked well. So I couldn't understand... INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET MD_LEVEL = 'refine1' SET STARTING_MODEL=1 SET ENDING_MODEL=10 SET DEVIATION = 4.0 SET KNOWNS='1ORD' SET HETATM_IO = off SET WATER_IO = off SET HYDROGEN_IO = off SET ALIGNMENT_FORMAT = 'PIR' SET SEQUENCE='gadmid' SET ALNFILE='AligntPubli1.ali' CALL ROUTINE='model' > Thank you very much > > Violaine Moreau > Bozidar Yerkovich, PhD Rockefeller University New York, NY, 10021, USA 212-327-7206 bozidar(a)salilab.org http://salilab.org/modeller

1 0

Usage
by Lewis, John 01 Nov '02

01 Nov '02

Very new here any help would be great! When I get this figured out I am going to do some documentation for dummies on this. When I run 'mod sequence_search' I get an error "fullfn__230E> File not found: very-short-for-test.cod" What is the .cod file? Here is a copy of my script. # Example for: SEQUENCE_SEARCH # This will search the MODELLER database of representative protein chains # for chains similar to the specified sequence. SET OUTPUT_CONTROL = 1 1 1 1 1 SET SEARCH_RANDOMIZATIONS = 20 # should use 100 in real life; SET GAP_PENALTIES_1D = -800 -400 SET SEARCH_CHAINS_LIST = 'very-short-for-test.cod' SEQUENCE_SEARCH FILE = 'P450.ali', ALIGN_CODES = '1nbt' MALIGN WRITE_ALIGNMENT FILE = 'toxin-search.pap', ALIGNMENT_FORMAT = 'PAP' So I made a file called "very-short-for-test.cod" I then get an error in this log: Date and time of compilation : 07/19/2002 11:38:41 Job starting time (YY/MM/DD HH:MM:SS): 2002/10/15 14:49:24.094 Dynamically allocated memory at amaxseq [B,kB,MB]: 2200483 2148.909 2.099 TOP_________> 2 2 SET SEARCH_RANDOMIZATIONS = 20 TOP_________> 3 3 SET GAP_PENALTIES_1D = -800 -400 TOP_________> 4 4 SET SEARCH_CHAINS_LIST = 'very-short-for-test.cod' TOP_________> 5 5 SEQUENCE_SEARCH FILE = 'P450.ali', ALIGN_CODES = '1nbt' openf5__224_> Open 11 OLD SEQUENTIAL very-short-for-test.cod amaxchn_215E> Dynamic memory allocation failed. Routine, variable, status: iseqdb 3 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2200483 2148.909 2.099 Starting time : 2002/10/15 14:49:24.094 Closing time : 2002/10/15 14:49:28.614 Total CPU time [seconds] : 4.36 thank you for any help!

2 1

Putting in a heteroatom
by John Penniston 31 Oct '02

31 Oct '02

I have modeled a large protein (1058 residues) based on the Xray structure of a homologous protein. The homologous protein (1EUL) has two Calcium ions, while the homologue I have modeled should have one Calcium ion, in the position corresponding to one of the Calciums in 1EUL. I can't figure out how to introduce this Calcium ion into my model. Can anyone advise me? Thanks, John -- John T. Penniston, Ph.D. Dept. of Biochemistry and Molecular Biology Guggenheim 16, Mayo Clinic 200 First St. SW Rochester, MN 55905 USA

1 0

Re: FW: Query
by owner-modeller_usage＠salilab.org 30 Oct '02

30 Oct '02

��Content-Class: urn:content-classes:message pvheader: ILIOzXjMrNvHW6rTHeh3A+XaY5en5xj/gAIH4csCZqQQ0dmkk0/0sTm2C9l5pBC6CUpUK6V3k8WhCTv0LPpuzvqJJQV4VgSDgxiWe1xUnyXp11gUw2A+h1SBGVVWJI3VPAMp/t2zypSf5s98LhgC4w== Message-ID: <017801c28044$944e8320$5204010a(a)diversa.com> From: "Andras Fiser" <andras(a)salilab.org> Date: Wed, 30 Oct 2002 10:45:55 -0800 Organization: ru Sender: <owner-modeller_usage(a)salilab.org> Precedence: bulk Return-Path: <owner-modeller_usage(a)salilab.org> hello, If one decides to use models as templates for modeling, must ensure that a good quality model has been built on the first place. This is often not a trivial task. however a good quality model is usually implies a reasonably closely related experimental structure as a template. Consequently this experimental structure is probably a better starting point than the model itself for future modeling studies. So, in general I would not consider models as templates, because either they have a highly similar experimental structure or they do not, but in that latter case their quality is highly questionable. best wishes, Andras please address your future questions to our discussion forum, many other people could share their experience: http://salilab.org/modeller/discussion_forum.shtml Andrej Sali wrote: > > -- > Andrej Sali, Associate Professor > Rockefeller University > 1230 York Avenue > New York, NY 10021, USA. > tel: +1 212 327 7550; fax 7540; secretary 7050; labs 7206, 7216 > sali(a)rockefeller.edu; http://salilab.org > > -----Original Message----- > From: yasabnis(a)olemiss.edu [mailto:yasabnis@olemiss.edu] > Sent: Tuesday, October 29, 2002 11:41 AM > To: sali(a)mail.rockefeller.edu > Subject: Query > > Dear Prof. Sali, > > I am a student at the University of Mississippi and an > active Modeller user. I had a small doubt about comparative protein > structure modeling and I thought you might be the perfect person to ask > a small doubt that I have. > > Can theoretical models published in PDB be used as one of > the homologs among other crystal structures to build a > homology model? > > If yes, are you aware of any articles where they have > actually used theoretical models as homologs along with > known crystal structures? > > Thank you in advance for your willingness to help. > > Sincerely, > > Yogesh Sabnis > Graduate Research Assistant Tel:(662)915-1286 > Dept. of Medicinal Chemistry Fax:(662)915-5638 > University of Mississippi > E-mail:yasabnis@olemiss.edu -- , Andras Fiser, PhD # phone: (212) 327 7216 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras

1 0

Re: FW: Query
by Andras Fiser 29 Oct '02

29 Oct '02

hello, If one decides to use models as templates for modeling, must ensure that a good quality model has been built on the first place. This is often not a trivial task. however a good quality model is usually implies a reasonably closely related experimental structure as a template. Consequently this experimental structure is probably a better starting point than the model itself for future modeling studies. So, in general I would not consider models as templates, because either they have a highly similar experimental structure or they do not, but in that latter case their quality is highly questionable. best wishes, Andras please address your future questions to our discussion forum, many other people could share their experience: http://salilab.org/modeller/discussion_forum.shtml Andrej Sali wrote: > > -- > Andrej Sali, Associate Professor > Rockefeller University > 1230 York Avenue > New York, NY 10021, USA. > tel: +1 212 327 7550; fax 7540; secretary 7050; labs 7206, 7216 > sali(a)rockefeller.edu; http://salilab.org > > -----Original Message----- > From: yasabnis(a)olemiss.edu [mailto:yasabnis@olemiss.edu] > Sent: Tuesday, October 29, 2002 11:41 AM > To: sali(a)mail.rockefeller.edu > Subject: Query > > Dear Prof. Sali, > > I am a student at the University of Mississippi and an > active Modeller user. I had a small doubt about comparative protein > structure modeling and I thought you might be the perfect person to ask > a small doubt that I have. > > Can theoretical models published in PDB be used as one of > the homologs among other crystal structures to build a > homology model? > > If yes, are you aware of any articles where they have > actually used theoretical models as homologs along with > known crystal structures? > > Thank you in advance for your willingness to help. > > Sincerely, > > Yogesh Sabnis > Graduate Research Assistant Tel:(662)915-1286 > Dept. of Medicinal Chemistry Fax:(662)915-5638 > University of Mississippi > E-mail:yasabnis@olemiss.edu -- , Andras Fiser, PhD # phone: (212) 327 7216 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras

1 0

Modelling domains
by Satyan Sharma 29 Oct '02

29 Oct '02

Hi, I have a protein with two domainswhich i would like to model. I have 3 template structures. One template (T1) has both the domains but with not good homology, which I would like to use for the orientation of the 2 domains. The 2 structures are of 2 individual domains with very high homology. I have tried to model my protein using template 1 (T1)and use the ".ini" file from it to further refine the 2 domains. Now is there a way how can i put these 2 back. Any suggestions. Or is there a better approach. Thanx, Satyan Sharma

2 1

(no subject)
by Andrej Sali 29 Oct '02

29 Oct '02

First, thanks to the users who suggested a MODELLER meeting. How can we help? Of course, we love to facilitate and support the use of MODELLER as much as we can. Perhaps at some point we will try to organize a modeller users meeting ourselves, but right now is not a good time for our group, because we are distracted by our move from the Rockefeller University to UCSF next spring. Still, if somebody else were willing to take the initiative to organize a meeting soon, I am confident some of us would attend to help. We are planning a major new release of MODELLER in January 2003, and, as part of this new release, Bozidar Yerkovich is making sure that the manual is complete and useful. An important source of ideas and suggestions for the new manual is this modeller users' mailing list. We would be most grateful if people sent as many of their suggestions to Bozidar, so that he can incorporate them into the manual. Maybe we should have a "Users Section" of the manual were pieces from the users are given verbatim? How to organize the modeller web site better? How to make sure that everybody benefits from the experience of the contributors? How to encourage contributions to the users list, the manual, the examples, and MODELLER? How to improve the manual and the examples? In the meantime, the simplest working examples are probably here http://salilab.org/modeller/user_manual.shtml. Thanks again, Andrej -- Andrej Sali, Associate Professor Rockefeller University 1230 York Avenue New York, NY 10021, USA. tel: +1 212 327 7550; fax 7540; secretary 7050; labs 7206, 7216 sali(a)rockefeller.edu; http://salilab.org

1 0

Lets Get Together
by Lewis, John 29 Oct '02

29 Oct '02

This is a good idea. I am in the St. Louis area. We are strugelling also with it. A lot of it has to do with the documentation. And the examples. I have gotten it to work but basicly one needs to change every thing from the directions. atm files are actually pdb so get your structure from the pdb blast and then change the file to a .atm. Then creat your own atom directory. Any how once we figured that out it has gotten a lot easyer. But I think we could get a hold of some one to meet at University of Ill. In Champaign Urbana. Its a good half way point. between Chicago and STL. And a lot of people there would use it too. And at SIUE carbon dale. We already work with U of Ill. here at the danforth center. And Wash U. Heck people at Monsanto has asked me about this. There is a lot of people that could benefit from a get together. then we can do a better documentatin. danforthcenter.org jlewis(a)danforthcenter.org

2 1