November 2002 - modeller_usage

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

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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 !!!!

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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

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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!

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