November 1998 - modeller_usage

problem!
by Paola D'Alessio 15 Jun '01

15 Jun '01

Dear users, I am trying to produce a chimeric model for my protein. The first thing I want to do is to check the alignment I have. When I tell Modeller to execute the "check_alignment" command, I get the following message: rdpir___E> alignment sequence not found in PDB file: 1 ./pXXXX.pdb ####################################################################################################################################### The alignment I have is: >P1;pXXXX structureX:pXXXX:.::.::::: CKPMSNFRF-GENHAIMGVAFTWVMALACAAPPLVGWS--RYIPEGMQC-SCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTH--------QGSDFGPIFMTIPAFFAKTSAVYNPVIYIMM* >P1;pAveM structure:pAveM:2::211::::: -----------VRWAKLYSLVIWGCTLLLSSPMLV-----------------------------EVFTNMLLNVVGFLLPLSVITFCTMQ---------------------ERRATVLVLVVLLLFIICWLPFQISTFLDTL----------------VITQIASFMAYSNSCLNPLVYVIV* >P1;Ali2 sequence:Ali2:::::::: VKTMSMGRMRGVRWAKLYSLVIWGCTLLLSSPMLVFRTMKEYSDEGHNVTACVISYPSL---IWEVFTNMLLNVVGFLLPLSVITFCTMQIMQVLRNNEMQKFKEIQT---ERRATVLVLVVLLLFIICWLPFQISTFLDTLHRLGILSSCQDERIIDVITQIASFMAYSNSCLNPLVYVIV* ####################################################################################################################################### Perhaps, something is wrong with file names or PDB codes.(I stored the pdb files as pXXXX.pdb) Can somebody help me? Thank you very much, Paola -- dott. Paola D'Alessio (PhD student) Universita' degli Studi di Salerno Dipartimento Scienze Farmaceutiche via Ponte Don Melillo, 84084 Fisciano (Sa), Italy tel.+39 089 962822; e-mail: pdalessio(a)unisa.it

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Use of the linux version
by Nigel Lindsey 20 Nov '98

20 Nov '98

I have using the linux small version of modeller with some sucess but have recently tried to convert to the version that allows 10 templates. However when I try to use it appears to see mod4 but fails to see the mod_i486-linux file. This is also the case if I use the Which command. Any help would be gratefully received ---------------------- Nigel Lindsey Department of Biomedical Sciences University of Bradford Bradford BD7 1DP 01274 383567 N.J.Lindsey(a)bradford.ac.uk

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building models strategy
by Gulshat Ibragimova 19 Nov '98

19 Nov '98

Dear Modellers, what could be the best strategy for building models (especially when one has to build lot of them -:)? The "search_sequence" procedure gives a list of proteins with similar sequences. However, their structures are generally misaligned. So this very diverse structural information might lead to bad models. Perhaps, it would make sense to find out structural relatives of the most identical protein (using the FSSP, at example) and to use them for building models despite their (relatives') low sequence similarity? Thanking for any comments, Gulshat --------------------------------------------------------------------- Gulshat Ibragimova, Ph.D. EMBL, Postfach 102209 69012 Heidelberg, FRG Tel: +49 (0)6221 387466, Fax: +49 (0)6221 387517

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Executable file for Silicon Graphics O2
by chunhua yuan 16 Nov '98

16 Nov '98

Hi, Dear MODELLER users: Our Silicon Graphics is O2, which has operating system IRIX Release 6.3 and CPU MIPS R5000, Rev 2.1. Can anybody tell me which executable file should I download besides the modeller4-data.tar.Z? and what is the "HOSTTYPE" for O2 computer? Thank you very much. Best Regards, Chunhua Yuan

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Loop modelling in a large system
by Graham tyrrell 05 Nov '98

05 Nov '98

Dear Modellers, I am attempting to use Modeller to model a number of loops into a very large protein system, and am having a few problems. (I am relatively new to Modeller so please excuse any dumb questions) I have 4 suitable structures which I wish to use as templates for the missing loop regions in my main structure. The problem I have is that I want to constrain the coordinates of my model to a greater extent towards that of the template which has the loops missing, I then want to use the remaining templates to build in the loops. This seems a similar problem to one described in the FAQ: ('5. I don't want to use one region of a template for construction of my model') however, due to the large number of loops missing, and the length of my sequence (~1000 residues) this would be extremely laborious, with plenty of room for error. I was wondering if anyone had any similar experience, and could advise me as to an appropriate strategy. Regards, Graham Tyrrell -- ---------------------------------------------------------------------- Graham Tyrrell Email (Work) : tyrrell(a)yorvic.york.ac.uk (Personal) : gpt103(a)york.ac.uk Telephone : (01904) 432550 -----------------------------------------------------------------------

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Re: gt5templatesonPC
by sali＠rockvax 03 Nov '98

03 Nov '98

Hi, I will compile a Linux version that allows more templates. Please look for it on our ftp site a little later today. You will probably need to increase your swap space size and possibly also do 'limit stacksize 256000' as root and run it as root ... I agree with you that Linux on PCs is the way to go! Version 5, due in a couple of weeks, has dynamic memory allocation and does not have such size problems. Best, Andrej > Dear Sali, > > I m very interested to run modeler with 6 or seven templates on a PC with > LINUX. > Is there a possibility to do this. (I have seen only the number 5 for PCs > and and a higher number for SGIs > in your handbook, but I think to use a PC for the modelerjob is very > usefull, bacause I tested, that a PII 450MHz has nearly double the speed of > a SGI R10000 O2 in calculating with modeler). > > Your help is welcome. > > Yours Volker > -- -- Andrej Sali, Assistant Professor The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 e-mail sali(a)rockvax.rockefeller.edu; http://salilab.org

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What is MPRMCNS?
by Susan Crennell 03 Nov '98

03 Nov '98

Hello, I am a new Modeller user and I've managed to read my sequence alignment in and CHECK it using the model-default.top script, Modeller even writes out a .ini initial model, but then stops saying: mkspline_E> too many parameters, increase MPRMCNS Please could you tell me how to do this, or how I can get round this problem? Thank you, Susan Crennell

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