- modeller_usage - salilab.org

id_table, dendrogram
by springer＠SprSGI.med.harvard.edu 05 Apr '98

05 Apr '98

i ran your sample file for id_table modified for a group of 89 sequences. i used the HUGE binary. It appears DENDROGRAM failed. The program printed out all files, except the dendrogram did not appear in the log file. The program never terminated running after 45 minutes, i killed it. all other files were written within about 5 minutes. i send separately the full log file. i append here the top of the log file and the top file. i send separately the alignment file if you want (please do not make it public). Tim # Example for: ID_TABLE, SEQUENCE_COMPARISON, PRINCIPAL_COMPONENTS, DENDROGRAM # Pairwise sequence identity between sequences in the alignment. # Read all entries in this alignment: READ_ALIGNMENT FILE = 'ywtd89.ali' # Calculate pairwise sequence identities: ID_TABLE MATRIX_FILE = 'ywtd89_id.mat' # Calculate pairwise sequence similarities: SET RR_FILE = '$(LIB)/as1.sim.mat', MAX_GAPS_MATCH = 1 SEQUENCE_COMPARISON MATRIX_FILE = 'ywtd89.mat', VARIABILITY_FILE = 'ywtd89.var' # Do principal components clustering using sequence similarities: PRINCIPAL_COMPONENTS MATRIX_FILE = 'ywtd89.mat', FILE = 'ywtd89.princ' # Dendrogram in the log file: DENDROGRAM _______________________________________________________________________ MODELLER 4h, June 16, 1997 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS v Copyright(c) 1989-1997 Andrej Sali All Rights Reserved v Written by A. Sali, R. Sanchez & A. Badretdinov Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Array dimensions (!8/9/96!): Maximum number of residues : 1000 Maximum number of atoms : 16000 Maximum length of alignment : 1000 Maximum number of sequences in alignment : 101 Maximum number of restrained features : 160000 Maximum number of restraint parameters : 1600000 Maximum number of restraint atoms : 480000 Maximum number of non-bonded atom pairs : 90000 Maximum number of non-bonded restraint types : 1 Maximum number of non-bonded restraint type parms: 1 Maximum number of explicitly excluded pairs : 100 Maximum number of pseudo atoms : 200 Maximum optimization schedule length : 50 MODELLER is compiled in : single precision Job starting time : 05-Apr-98 11:39:55

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residues with non standard topology
by giulio＠unimo.it 05 Apr '98

05 Apr '98

Dear users, I would like to ask if somebody could explain and send some input files for the homology modeling of a protein that binds NADPH. How should I set the parameters of NADPH? Your help is very appreciated. Best regards Giulio Rastelli Dipartimento di Scienze Farmaceutiche Universita di Modena

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enormous-version for deck alpha?
by Oliver Hucke 31 Mar '98

31 Mar '98

Dear Modeller users/developers, what can I do, when I want model a protein with more than 1000 residues on a DECK-alpha computer? I could not find an enormous-executable for this machine type. Thanks Oliver. Oliver Hucke, <hucke(a)ruf.uni-freiburg.de> Institut fuer Physikalische Chemie Universitaet Freiburg Albertstr. 23a D-79104 Freiburg

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evaluation of models
by Timothy A. Springer Ph.D. 26 Mar '98

26 Mar '98

Dear Andrej, I have a few questions I would highly value your opinions on, and below a status report on what I am doing on evaluating fold models and my opinions on the methods I am using. My models are based on fold predictions, not sequence homology. Questions. 1. I am going to objectively evaluate my models, and for this I need some homology models and some incorrect, misthreaded refined or highly refined models to compare to. If you could send me about 100 pdb files of each type, that vary in length and include lengths in the 100-400 range, that would be extremely helpful. 2. Where can I get other models to evaluate? I can find some homology models at Brookhaven, can you refer me elsewhere? 3. Please comment on my evaluation plan. I will calculate the z-scores of combined energy using the zscore command of Prosa II from Sippl's group or nqachk from Whatif. ProsaII comes with pre-calculated z-scores for a database of proteins, and shows plots of z-score versus length. I want to add points for 1) my models, 2) "correct" homology models, and 3) misthreaded, but well energy minimized, misthreaded models. My hope is that my models will lie in the range of the homology models, and be intermediate between the real structures and the misthreaded models, and clearly better than the misthreaded models. I would dearly love to have a statistical test showing the model is correctly threaded, i.e. significantly reject the null hypothesis of a misthreaded model. Comments. I have compared the structure evaluation tools of Prosa and Whatif. Whatif has a second generation quality control feature called nqachk (new quachk). Prosa and nqachk appear to better discriminate models from xray structures than quachk. z-scores for both Prosa and nqachk are dependent on the length of the protein. My models are n11, d11, and r11. They are compared to two templates, mo6_s2 and 1tbgB. The latter both have native scores. My models do well on surface potentials, but have sc-sc and bb-sc contacts that lower their pairwise z scores and nqachk values. My models are better than any of the modules in the polyprotein of ProsaII, ranking first for combined energy in all cases. ProsaII (Sippl) output Hide & Seek on polyprotein pII3.0.short.ply - selection of parameters molecule seq-l zp-comb zp-pair zp-surf rk-comb rk-pair rk-surf ep-comb ep-pair ep-surf n11 265 -5.48 -2.33 -5.17 1 191 1 -3.34 11.72 -6.41 d11 264 -5.34 -2.65 -4.42 1 56 1 7.33 4.88 1.13 r11 260 -5.71 -2.42 -5.11 1 125 1 -11.04 6.57 -9.05 mo6_s2 257 -9.74 -6.26 -6.68 1 1 1 116.35 -65.75 -26.03 1tbgB 296 -9.67 -5.79 -7.25 1 1 1 112.59 -53.15 -30.41 Whatif (Vriend) output ("Average for range" is quachk, "All contacts" and following 4 lines are nqachk) n11.pdb.txt Average for range 1 - 265 : -1.032 All contacts : Average = -0.685 Z-score = -4.37 BB-BB contacts : Average = -0.066 Z-score = -0.46 BB-SC contacts : Average = -0.968 Z-score = -5.24 SC-BB contacts : Average = -0.156 Z-score = -0.78 SC-SC contacts : Average = -0.695 Z-score = -3.51 d11.pdb.txt Average for range 1 - 264 : -0.569 All contacts : Average = -0.576 Z-score = -3.65 BB-BB contacts : Average = 0.026 Z-score = 0.20 BB-SC contacts : Average = -0.946 Z-score = -5.12 SC-BB contacts : Average = -0.039 Z-score = -0.07 SC-SC contacts : Average = -0.580 Z-score = -2.88 r11.pdb.txt Average for range 1 - 260 : -0.743 All contacts : Average = -0.551 Z-score = -3.49 BB-BB contacts : Average = 0.038 Z-score = 0.28 BB-SC contacts : Average = -0.868 Z-score = -4.69 SC-BB contacts : Average = -0.131 Z-score = -0.63 SC-SC contacts : Average = -0.537 Z-score = -2.64 ******************************************************************************* * Timothy A. Springer, Ph.D. * * Latham Family Professor of Pathology * * Harvard Medical School e-mail: springer(a)sprsgi.med.harvard.edu * * Center for Blood Research phone: 617-278-3200 * * 200 Longwood Ave. Room 251 fax: 617-278-3232 * * Boston MA 02115 * *******************************************************************************

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Again MALIGN
by deb＠cmb2.saha.ernet.in 25 Mar '98

25 Mar '98

Dear Azat, Yes, the program can read maximum 5 sequences as input at a time. Ok, now I'm trying to do multiple structure alignment. With only 2 structures as input, the alignment is really good, but it's failing with 3 or more. It's giving following message: "............... openf5___> file does not exist: /disk2/pdb/pdb.ent/List.ent (do not worry about this one) Multiple dynamic programming alignment (MALIGN): Residue-residue metric : /usr2/people/deb/exec/modeller4/modlib//as1.sim.mat Gap introduction penalty: -600.0000 Gap extension penalty : -400.0000 Length of alignment : 556 malign3d_> Alignment: 1 # Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 1atu 1bbi 1hia # ====================================== 1 1.142 0.274 L 112 T 55 D 98 fit2xyz_E> number of equivalent positions < 3: 1 recover__> MODELLER_STATUS >= STOP_ON_ERROR: 1 1 ...................." Hope this time I'm not doing the same mistake as before. 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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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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