modeller_usage

modeller_usage@salilab.org

1 participants
3147 discussions

Problem with MALIGN
by deb＠cmb2.saha.ernet.in 24 Mar '98

24 Mar '98

Hi All, I am presently trying to run MALIGN for 15 sequences, taking them from their respective PDB co-ordinates. With upto 5 sequences (taken at random)the multiple alignment is working all right, but it is failing for 6 or more inputs. Here is the .log file "................... openf5___> file does not exist: /disk2/pdb/pdb.ent/List.ent (do not worry about this one) rdpir___E> increase MAXSEQ openf5__E> error openning file rdpir___E> alignment sequence not found in PDB file: 1 ./ ............................" I've tried several Gap Penalty combinations. Please help me as I'm not sure where the mistake is. Debashis. ------------------------------------------------------------------------------ ("`-''-/").___..--''"`-._ `6_ 6 ) `-. ( ).`-.__.`) Debashis Mukhopadhyay (_Y_.)' ._ ) `._ `. ``-..-' Research Fellow,C&MB Div., _..`--'_..-_/ /--'_.' ,' Saha Institute Of Nuclear Physics, (il).-'' (li).' ((!.-' 1/AF, Bidhannagar,Calcutta-700 064. India. deb(a)cmb2.saha.ernet.in ------------------------------------------------------------------------------

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Test by marcius
by Marc A MARTI-RENOM 11 Mar '98

11 Mar '98

TEST OF MODELLER_USAGE LIST SERVER

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MODELLER for phylogenetics
by deb＠cmb2.saha.ernet.in 10 Mar '98

10 Mar '98

Hi All, I am here with some problems which are not directly related to modelling. I want to use the MODELLER to draw Phylogenetic trees of some proteins from their struc tural comparisons. These proteins supposedly belong to a superfamily having less than 10% sequence identity. My problems are following: 1)Is there any ready script to achieve the above? 2)As an input to Phylip I need an alignment file after structural comparison where no target consensus sequence is needed. How to get that? 3)The structural comparison suggested here-is it a multifeatured one? If so, is there any literature reference containing a list of comparison parameters? Please help. Debashis. ------------------------------------------------------------------------------ ("`-''-/").___..--''"`-._ `6_ 6 ) `-. ( ).`-.__.`) Debashis Mukhopadhyay (_Y_.)' ._ ) `._ `. ``-..-' Research Fellow,C&MB Div., _..`--'_..-_/ /--'_.' ,' Saha Institute Of Nuclear Physics, (il).-'' (li).' ((!.-' 1/AF, Bidhannagar,Calcutta-700 064. India. deb(a)cmb2.saha.ernet.in ------------------------------------------------------------------------------

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SET WRITE_INTERMEDIATES = 1
by Nick Glover 09 Mar '98

09 Mar '98

Modellers: If SET WRITE_INTERMEDIATES = 1, how often are the intermediates written out? Is there some variable that can be set to control the level of intermediate output, i.e. every 1000 iterations? Nick _______________ Nicholas Glover Department of Chemistry Simon Fraser University 8888 University Drive Burnaby, BC V5A 1S6 Canada Tel: (604) 291-4531 Fax: (604) 291-3765 email: nglover(a)sfu.ca

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OPTIMIZATION
by Nick Glover 08 Mar '98

08 Mar '98

Modellers: When setting up an optimization, how does one define a different number of iterations for the conjugate graidents and MD stages? In one of the scripts provided with the program I see the variable: SET MAX_VAR_ITERATIONS = 500 ..which I presume sets the number of iterations for the CG stage - so is there a corresponding variable MAX_??_ITERATIONS for MD stage? or does setting MAX_ITERATIONS set the number of MD iterations? i.e. will.. SET MAX_VAR_ITERATIONS = 500 SET MAX_ITERATIONS = 1000 ..in my modelling script do 500 steps of CG followed by 1000 steps of MD? I see no note of MAX_VAR_ITERATIONS in the Index.. also, is it common to SET MD_RETURN = MINIMAL, or to FINAL? I presume MINIMAL? Further, in the default _model script is equilibration (INIT_VELOCITIES) set to ON? In the _defs script it is not defined, so is it on by default, and what effect may this have on optimization? Last, what effect does running the MD stage at high temperatures have on the model? Presumably, more conformational space is sampled, and if the MINIMAL model is chosen, perhaps this may be of lower PDF than if a lower temperature was chosen? Thanks in advance, Nick ____________________ Nicholas Glover Department of Chemistry Simon Fraser University 8888 University Drive Burnaby, BC V5A 1S6 Canada Tel: (604) 291-4531 Fax: (604) 291-3765 email: nglover(a)sfu.ca

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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

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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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modeller_usage