March 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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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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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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