- modeller_usage - salilab.org

Post-modeller refinement
by Nick Glover 01 Mar '98

01 Mar '98

Modellers: I have built a model, and submitted it to what I believe is a fairly rigorous optimization schedule (comments?): SET LIBRARY_SCHEDULE = 1 SET MAX_VAR_ITERATIONS = 500 SET MD_LEVEL = 'refine1' SET REFINE_HOT_ONLY = 0 SET RSTRS_REFINED = 2 SET REPEAT_OPTIMIZATION = 5 However, having checked the model with the Biotech Collaboration on-line validation tools I note several errors in my structure, notably in terms of VDW overlaps, bond angles, and unfulfilled buried h-bond formation, consistent with ENERGY evaluation which indicates a number of 'serious non-bonded atom clashes' and other violations. Ramachandran plots confirm the good stereochemistry of the model. Now, looking through Dr Sali's various papers I note that he performs no post-model refinement.. however, I wonder whether the community would care to comment on their own experiences in terms of model evaluation, and whether they have performed post-minimization or MD to relieve poor contacts, etc. My suggestion: in-vacuo steepest descents minimization followed by conjugate gradients to less than 0.1 kcal/ang., performed with a restraining potential on the backbone to preserve the backbone fold of the model, while allowing the sidechains to re-orient and relieve any bad contacts.. obviously, this is a fairly tame refinement, and could be performed in a solvated shell, etc. Suggestions and comments appreciated... a few words from those who have built and evaluated models would be very beneficial to those new to this methodology! Nick ---------------- NB: for interested parties.. The validation suite (Procheck, what-if, etc,) is available for on-line model verification: http://biotech.embl-heidelberg.de:8400 ---------- Nick Glover Department of Chemistry Simon Fraser University 8888 University Drive Burnaby, BC V5A 1S6 Canada

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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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