February 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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CHECK_ALIGNMENT
by Nick Glover 14 Feb '98

14 Feb '98

Modeller users: When analyzing your alignment file using CHECK_ALIGNMENT, how critical is it to eliminate all of the following errors: chkaln___> Checking pairwise structural superpositions: Equivalent CA pairs with distance difference larger than 6.0 angstroms: chkaln___> Checking structure-sequence alignments: Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: Should you keep refining the alignment until all of these errors are eliminated, or are one or two acceptable (i.e. 6.2 ang., 8.4 ang... ) Nick ---------- Nick Glover Department of Chemistry Simon Fraser University 8888 University Drive Burnaby, BC V5A 1S6 Canada

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[Fwd: MODELLER Manual]
by Andrej Sali 13 Feb '98

13 Feb '98

-- 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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[Fwd: MODELLER Manual]
by Andrej Sali 13 Feb '98

13 Feb '98

-- 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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Re: MODELLER Manual
by Andrej Sali 13 Feb '98

13 Feb '98

Hi, Yes, I am aware o this, but do not know what the problem/solution is. It prints ok on our HP LaserJet 5MP and previews fine with our version of ghostscript. Maybe you can try to use ghostscript to convert the PS file into another format that can be printerd on your prtiner (such as PCL for HPs'). I hope this problem will go away in version 5, we got a new version of TeX. I will generate a new PS file with this version of latex and email it to you. Thanks for reporting the problem, Andrej J.W. Bizzaro wrote: > > Andrej, > > The file "manual.ps" appears to have a problem in that I can only print > 12 pages of the manual. Thanks. > > Jeff > bizzaro(a)bc.edu -- 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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[Fwd: alignment queries..]
by Azat Badretdinov 10 Feb '98

10 Feb '98

-- - Dr. Azat Badretdinov - The Rockefeller Univ, Box 270 - 1230 York Ave, New York NY 10021, USA - Phone: (212) 327 7206 - Fax: (212) 327 7540 - E-mail: azat(a)salilab.org - WWW/URL: http://salilab.org/~azat

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alignment queries..
by Nick Glover 05 Feb '98

05 Feb '98

modeller users: Question 1: What is considered to be the minimum length of a sequence motif necessary to derive meaningful constraints from the alignment to use in modeling.. one, two, three, or more? i.e. template -K- -YI- -EEE- -YSIG- -DIDAP- target -x- -xx- -xxx- -xxxx- -xxxxx- The Modeller routines tend to pick out longer motifs than Meme, Matchbox, PIMA, BLOCKS, etc. Smallest motif I have had picked out for my sequences using these alternative methods is three a.a.'s... what would be the effect of only matching two, or even just one residue on the modeling? which brings me to my next query.. Question 2: how rigorous must one be with the alignment? given an template of, say, IPSDC would it be okay to match VPGCC, etc.. trying, in general, to keep acidic matched to acidic, basic to basic, rings to rings and hydrophobic to hydrophobic, bulky to small, as shown in (A).. is this the right method - be less worried about the *exact* nature of the match, as long as they are physically/chemically similar.. else, is it best to mix and match among templates, as illustrated in (B) (A) is this acceptable? template 1 LPSDC template 2 VQSAC template 3 IPSEC template 4 VPGCC target IPSDC (B) or should I break it up like this? template 1 L-P-S-D-C template 2 V--QS--AC template 3 -IP-S--EC template 4 V-P--G-CC target -IP-S-D-C I believe that this is the critical step in the whole procedure, so your comments would be greatly appreciated! Nick ---------- Nick Glover Department of Chemistry Simon Fraser University 8888 University Drive Burnaby, BC V5A 1S6 Canada

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modeller running under IRIX6.3
by Yi Liu 05 Feb '98

05 Feb '98

Dear Andrej, I tried eveything you suggested. My system is R10000 with IRIX6.3. mod_r10000-IRIX6.2 won't run under IRIX6.3. When I tried mod_iris4d, it worked under both IRIX5.3 and IRIX6.3. If it is compiled under IRIX5.3, will it not be efficient under IRIX6.3? Thank you very much Yi

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Re: Problem including substrate and heme
by Azat Badretdinov 03 Feb '98

03 Feb '98

The problem is that there is no MYR entry in the top_heav.lib or other top*.lib libraries in the standard distribution. Please check all the times that the entry of the molecule is present in BOTH restyp.lib and top*.lib corresponding to your model (all atoms, heavy atoms only, etc.). Azat. Jeffrey P. Jones wrote: > > Thanks for your reply. Both of these residues are in the library files, h & 5 > are the default single letter descriptors. Any other suggestions? > > Azat Badretdinov wrote: > > > Hi, Jeffrey! > > > > Jeffrey P. Jones wrote: > > > > > > I am wondering what the format is for input in the alignment file of two > > > molecules say heme (h) and myristic acid (5) distinct from the protein > > > of interest. > > > > > > My guess is: > > > > > > AATLCLL(protein sequence)GT/h/5* > > > > Please read the corresponding example in FAQ in the manual, how to deal > > with small molecules of non-aminoacid nature. > > > > The format is oK, but you have to specify in some library file what h > > and 5 is (Hem is probably present in the standard library). > > > > Yours, > > Azat. > > > > > > > > The order they appear in the pdb file is AA/heme/myristate. > > > > > > Is this the format? When I use it the myristic acid input is ignored. > > > > > > Jeff > > > > > > -- > > > Jeffrey P. Jones, Ph.D. > > > Associate Professor of Pharmacology, Physiology > > > Biochemistry and Biophysics > > > (716)275-5371, http://cyp.medicine.rochester.edu/~jpj/jones_group.html > > > jpj(a)cyp.medicine.rochester.edu > > > > -- > > - Dr. Azat Badretdinov > > - The Rockefeller Univ, Box 270 > > - 1230 York Ave, New York NY 10021, USA > > - Phone: (212) 327 7206 > > - Fax: (212) 327 7540 > > - E-mail: azat(a)salilab.org > > - WWW/URL: http://salilab.org/~azat > > -- > Jeffrey P. Jones, Ph.D. > Associate Professor of Pharmacology, Physiology > Biochemistry and Biophysics > (716)275-5371, http://cyp.medicine.rochester.edu/~jpj/jones_group.html > jpj(a)cyp.medicine.rochester.edu -- - Dr. Azat Badretdinov - The Rockefeller Univ, Box 270 - 1230 York Ave, New York NY 10021, USA - Phone: (212) 327 7206 - Fax: (212) 327 7540 - E-mail: azat(a)salilab.org - WWW/URL: http://salilab.org/~azat

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Problem including substrate and heme
by Jeffrey P. Jones 03 Feb '98

03 Feb '98

I am wondering what the format is for input in the alignment file of two molecules say heme (h) and myristic acid (5) distinct from the protein of interest. My guess is: AATLCLL(protein sequence)GT/h/5* The order they appear in the pdb file is AA/heme/myristate. Is this the format? When I use it the myristic acid input is ignored. Jeff -- Jeffrey P. Jones, Ph.D. Associate Professor of Pharmacology, Physiology Biochemistry and Biophysics (716)275-5371, http://cyp.medicine.rochester.edu/~jpj/jones_group.html jpj(a)cyp.medicine.rochester.edu

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