modeller_usage

modeller_usage@salilab.org

4 participants
3146 discussions

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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Modeller 4 help!
by Nick Glover 02 Feb '98

02 Feb '98

Modeller users: As a neophyte, both to homology modeling and to the program Modeller-4, I am somewhat confused by the protocol to follow in order to generate a model of my target enzyme. I would be very grateful if the Modeller user community could help get me going! I have the sequence of my target, and five .pdb files of enzymes that belong to the same family, and share between 30 - 50% sequence similarity to the target. I want to get a 'good' model of the target - CPU time is not a problem, I would prefer to be thorough and get better results. Can anybody suggest the procedure I should follow, from the beginning! What file do I begin with? Do I write this myself? What is it called? How do I obtain an alignment file? MALIGN-3D? then CHECK_ALIGNMENT? Which script files should I run? mod model-default? How do I account for the error noted in the newsgroup archives? Any suggestions appreciated! Similarly, if anyone has modified the basic script files to good effect, I would appreciate a copy! Thanks in advance, Nick ---------- Nick Glover Department of Chemistry Simon Fraser University 8888 University Drive Burnaby, BC V5A 1S6 Canada

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O2 IRIX 6.3
by sali＠piano 28 Jan '98

28 Jan '98

The mod_iris4d executable works on our O2 IRIX 6.3. Andrej -- -- 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: Hydrogen problems with Modeller4
by Andrew Martin 26 Jan '98

26 Jan '98

> Dear Andrew and Brian! > > please replace BUILD_MODEL INITIALIZE_XYZ = off > to BUILD_MODEL INITIALIZE_XYZ = off, BUILD_METHOD = > 'INTERNAL_COORDINATES' > > in file $MODINSTALL/scripts/__generate_model.top ^^^^^^^ bin - not scripts > > and > SET TOPLIB = '${LIB}/top_allh.lib' > in your .top file. > > Happy landings! > > Yours, > > Azat > Excellent! That's certainly fixed it... But wouldn't this have been a problem affecting everybody using Modeller for straightforward homology modelling??? I haven't used the SET TOPLIB as I was not reading hydrogens, so it is taking the default SET TOPLIB = '${LIB}/top_heav.lib' I was seeing the problem with this. As far as I can see it's not really related to the hydrogens issue. My .top file was quite simply: INCLUDE SET ATOM_FILES_DIRECTORY = './:/data/pdb/' SET PDB_EXT = '.pdb' SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 SET DEVIATION = 0 SET KNOWNS = 'xyz' SET HETATM_IO = off SET WATER_IO = off SET HYDROGEN_IO = off SET MD_LEVEL = 'refine1' SET ALIGNMENT_FORMAT = 'PIR' SET SEQUENCE = 'abc' SET ALNFILE = 'align.pir' CALL ROUTINE = 'model' Any thoughts??? Andrew ---------------------------------------------------------------------------- Dr. Andrew C.R. Martin University College London EMAIL: (Work) martin(a)biochem.ucl.ac.uk (Home) andrew(a)stagleys.demon.co.uk URL: http://www.biochem.ucl.ac.uk/~martin Tel: (Work) +44(0)171 419 3890 (Home) +44(0)1372 275775

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Re: Hydrogen problems with Modeller4
by Andrew Martin 23 Jan '98

23 Jan '98

I have had very similar problems with Modeller4: huge numbers of violations and gaps in the backbone even without hydrogens. However, my .top files (generated by my MINT program) contain the command SET HYDROGEN_IO=off I haven't had time to analyse exactly what's going on yet (for the moment I've gone back to Modeller3). I'll try to take another look in the next few days. I too have assumed I've been doing something stupid and have just downloaded Modeller4 again to try installing from scratch again. Andrew > What you did should work. Can you please email the input files to > azat(a)salilab.org, so that Azat can take a closer look. > > Thanks, Andrej > > > Brian Marsden wrote: > > > > I'm having a bit of a torrid time trying to get Modeller4 to cope with > > hydrogens. Here's the scenario: > > > > I have a template pdb file (directly from the Brookhaven PDB databank) > > which contains an NMR structure and therefore contains all hydrogens. > > Looking at the FAQ in Modeller's documentation I find that I probably > > need to add the following lines to get-model.top: > > > > SET HYDROGEN_IO=on > > SET TOPOLOGY_MODEL=1 > > SET TOPLIB = '${LIB}/top.lib' > > SET PARLIB = '${LIB}/par.lib' > > > > I then run Modeller in the usual way and end up with models with a huge > > number of violations, and whopping great big gaps in the backbone. > > ---------------------------------------------------------------------------- Dr. Andrew C.R. Martin University College London EMAIL: (Work) martin(a)biochem.ucl.ac.uk (Home) andrew(a)stagleys.demon.co.uk URL: http://www.biochem.ucl.ac.uk/~martin Tel: (Work) +44(0)171 419 3890 (Home) +44(0)1372 275775

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Hydrogen problems with Modeller4
by Brian Marsden 21 Jan '98

21 Jan '98

I'm having a bit of a torrid time trying to get Modeller4 to cope with hydrogens. Here's the scenario: I have a template pdb file (directly from the Brookhaven PDB databank) which contains an NMR structure and therefore contains all hydrogens. Looking at the FAQ in Modeller's documentation I find that I probably need to add the following lines to get-model.top: SET HYDROGEN_IO=on SET TOPOLOGY_MODEL=1 SET TOPLIB = '${LIB}/top.lib' SET PARLIB = '${LIB}/par.lib' I then run Modeller in the usual way and end up with models with a huge number of violations, and whopping great big gaps in the backbone. Strangely, if I strip the pdb file of all its hydrogens, remove the SET HYDROGEN_IO=on and put TOPOLOGY_MODEL to 3 everything is fine - a nice model is made, but, of course, without any hydrogens. I'm probably doing something daft - can anyone out there point me in the direction? Many thanks. Brian. --------------------------------------------------------------------- Brian Marsden marsden(a)bioch.ox.ac.uk Home: +44 1865 552696 OCMS, Oxford Fax: +44 1865 275253 Work: +44 1865 275720 ---------------------------------------------------------------------

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[Fwd: [Fwd: Segmentation Fault : Core Dumped]]
by Azat Badretdinov 21 Jan '98

21 Jan '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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modeller_usage