Hi to all:
I just made modeller work!!!!
I still don`t know what my problem was, but as I can run the examples just fine, I figured the problem were my files. Briefly, I just delete my old files and created them from scratch with nedit... My final files looked like this:
(model.top, my script):
INCLUDE # Include the predefined TOP routines SET ALNFILE = 'aln.ali' # alignment filename SET KNOWNS = '1cx1' # codes of the templates SET SEQUENCE = '1dnj' # code of the target SET ATOM_FILES_DIRECTORY = '../bin/modeller6v2/examples/atom_files/' # directories SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 2 # index of the last model # (determines how many models to calculate) SET DEVIATION = 4.0 # have to be >0 if more than 1 model SET RAND_SEED = -12312 # to have different models from another TOP file CALL ROUTINE = 'model' # do homology modelling
(aln.ali, my alignment file) C; First alignment >P1;1cx1 structureX:1cx1:FIRST:A:LAST:A:template:HCV: 2.50:-1.00 GSVVIVGRIILSGSGSITAYSQQTRGLLGCIITSLTGRDKNQVEGEVQVVSTATQSFLATCVNGVCWTVYHGAGSK TLAG PKGPITQMYTNVDQDLVGWQAPPGARSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLS-------PRPVSYL KGSS GGPLLCPSGHAVGIFRAAVCTRGVAKAVDFVPVESMETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVP AAYA AQGYKVLVLNPSVAATLGFGAYMSKAHGID------PNIRTGVRTITTGAPVTYSTYGKFLADGGCSGGAYDIIIC DECH STDSTTILGIGTVLDQAETAGARLVVLATATPPGSVTVPHPNIEEVALSNTGEIPFYGKAIPIEAI--RGGRHLIF CHSK KKCDELAAKLSGLGINAVAYYRGLDVSVIPT---IGDVVVVATDALMTGYTGDFDSVIDCNTCVTQTVDFSLDPTF TIET TTVPQDAVSRSQRRGRTGRGRRGIYRFVTPGERPSGMFDSSVLCECYDAGCAWYELTPAETSVRLRAYLNTPGLPV CQDH LEFWESVFTGLTH-IDAHFLSQTKQAGDNFPYLVAYQATVCARAQAPPPSWDQMWKCLIRLKPTLH---GPTPLLY RLGA VQNEVTLTHPITKYIMACMSADLEVVT*
>P1;1dnj sequence:1dnj:FIRST:@:LAST:@:model:dengue: 2.50:-1.00 GSSPILSITISEGSGS----AGVLWDVPSPPPVGKAELEDGAYRIKQRGILGYSQIGAGVYKEGTFHTMWHVTRGA VLMH KGKRIEPSWADVKKDLISYGG---GWKLEGEWKEGEEVQVLALE-PGKNPRAVQ-TKPGLFKTNTGTIGAVSLDFS PGTS GSPIVDRKGKVVGLYGNGVVTRSGAYVSAIAQTEKSIEDNPEIEDD-------IFRKKRLTIMDLHPGAGKTKRYL PAIV REAIKRGLRTLILAPTRVVAAEMEEALRGLPIRYQTPAIRAEHTGREIVDLMCHATFTMRLLSPV-RVPNYNLIIM DEAH FTDPASIAARGYISTRVEMGE-AAGIFMTATPPGSRDPFPQ-SNAPIMDEEREIPERSWNSGHEWVTDFKGKTVWF VPSI KAGNDIAACLRKNGKKVIQLSRKTFDSEYVKTRANDWDFVVTTDISEMGANFKAERVIDPRRCMKPVILT-DGEER VILA GPMPVTHSSAAQRRGRIGRNPKNENDQYI---------YMGEPLENDEDCAHWKEAKMLLDNINTPEGIIPSMFEP EREK VDAIDGEYRLRGEARKTFVDLMRRG---DLPVWLAYRVAAEGINYADRRWCFDGIKNNQILEE-NVEVEIWTKEGE RKKL KPRWLDARIYSDPLALKEFKEFAAGRK*
Hope this helps, Holton...
And thanks to all for your help!!!!
Luis
Luis & all Modellers -
OK, now that you've 'fixed' your problem, I think I've seen this before as well. In my case, it happened when I had moved my template PDB files from a PC to my SGI system, and MODELLER did not like the DOS format of the files. With nedit, if you open the file and then click "File" and "Save As", it will have a checkmark by MS-DOS Format if that is the case. Simply click that option OFF and save the file to remove the DOS formatting.
PS - I'm still curious about a simple way to set up an MD annealing run on a final model without any remaining restraints from the template. Can the developers point me to an example or guidelines in the manual?
Thanks & Happy Modelling,
Tom -- Thomas M Duncan Research Associate Professor Dept Biochemistry & Molecular Biology Institute for Human Performance, Rm 4311 SUNY Upstate Medical University 750 E Adams St Syracuse, NY 13210
Hi. I thought I would just 'de-lurk' to make a suggestion here :
On Thursday 27 February 2003 15:29, Tom Duncan wrote: <snip> > PS - I'm still curious about a simple way to set up an MD annealing run > on a final model without any remaining restraints from the template. Can > the developers point me to an example or guidelines in the manual?
Doesn't the 'optimize.top' script (in ${MODELLER_HOME}/examples/commands/) do something like this ? Given an initial structure (ie an initial model), local gradient descent or a variety of all-atom MD can be used via the 'OPTIMIZE' function. I'm afraid I couldn't say what default constraints might be applied, but I believe the function can be redefined (as all MODELLER functions can be) to select appropriate topologies, parameter files and ranges.
j.
Jim Procter Biomolekulare Modellierung / Zentrum Fur Bioinformatik / University of Hamburg
I do not think there are examples exactly for your query in the manual. But it should not be a problem to do it. There are several ways, one is outlined here:
You could set the weights of all homology derived restraints to 0 using the SCHEDULE_SCALE variable in SUBROUTINE ROUTINE = 'refine' or even 'refine_1' or 'refine_3' (whichever you are using) (just copy it from $MODINSTALL6v2/bin/__refine.top to the end of the main top file and edit it accordingly).
I have not tried this, so please be careful since there may be 'little' details lurking somewhere that can make your run go wrong ;-)
Best, Andrej
-- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 Email sali@salilab.org; Web http://salilab.org
> -----Original Message----- > From: owner-modeller_usage@salilab.org > [mailto:owner-modeller_usage@salilab.org] On Behalf Of Tom Duncan > Sent: Thursday, February 27, 2003 6:29 AM > To: Luis Rosales; Modeller_Usage > Subject: Re: It`s alive!!! > > > Luis & all Modellers - > > OK, now that you've 'fixed' your problem, I think I've seen > this before as well. In my case, it happened when I had moved > my template PDB files from a PC to my SGI system, and > MODELLER did not like the DOS format of the files. With > nedit, if you open the file and then click "File" and "Save > As", it will have a checkmark by MS-DOS Format if that is the > case. Simply click that option OFF and save the file to > remove the DOS formatting. > > PS - I'm still curious about a simple way to set up an MD > annealing run on a final model without any remaining > restraints from the template. Can the developers point me to > an example or guidelines in the manual? > > Thanks & Happy Modelling, > > Tom > -- > Thomas M Duncan > Research Associate Professor > Dept Biochemistry & Molecular Biology > Institute for Human Performance, Rm 4311 > SUNY Upstate Medical University > 750 E Adams St > Syracuse, NY 13210 > >
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Andrej Sali -
Jim Procter -
Luis Rosales -
Tom Duncan