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19 discussions

GA341 from models.fin parsing
by strumillo 14 Nov '14

14 Nov '14

Hello, while parsing the final file from modpipe, models.fin, I'd like to select the models, which has GA341 over 0.7 as suggested - while the line looks like this: ga341: !<GA341> {combined:-6.4202000000000004,compactness:0.1792,distance:-201.07679999999999,surface_area: -14.8515, total: 1, z_combined:-9.6105999999999998, z_distance: -7.7803000000000004,z_surface_area: -6.8894000000000002} whatever the values in this specific example are, which one should I check? combined, total,z_combined? all best, m.

2 1

Modpipe installation and testing
by Sammy Desilva 22 Sep '14

22 Sep '14

Hi, could someone please post a basic guide to install/configure and use modpipe on Ubuntu?

2 1

MODELLER bug report
by Marco Galardini 11 Jun '14

11 Jun '14

Dear ModPipe community I managed to install modpipe in our system, but I'm struggling to test it. If I try to run the demo sequence using mode 0010 (providing the missing databases in the configuration file) I get the following error: $ ../main/ModPipe.pl --conf_file modpipe.conf --sequence_id 97e075794f588a59e8a0fb8a945814b1MLGIKIKP --hits_mode 0010 --score_by_tsvmod OFF MPLib::MPModules::GetProfile__M> Found profile for sequence MPLib::MPModules::GetProfile__M> Seqid : 97e075794f588a59e8a0fb8a945814b1MLGIKIKP MPLib::MPModules::GetProfile__M> Profile: /nfs/[...]/modpipe-2.2.0/demo//data/97e/97e075794f588a59e8a0fb8a945814b1MLGIKIKP/sequence/97e075794f588a59e8a0fb8a945814b1MLGIKIKP-uniprot90.prf MPLib::MPModules::GetProfile__M> Will use the above profile MPLib::MPModules::GetProfile__M> PRFUPDATE: OFF MPLib::MPUtils::CopyXPRFDB__M> No. of structure profiles in database: 39330 *PLLib::Modeller::RunModeller__E> MODELLER failed: exited with value 1** **HitsPrfPrf.pl__E> MODELLER failed on profile: 97e075794f588a59e8a0fb8a945814b1MLGIKIKP-uniprot90.prf** **MPLib::MPModules::GetHitsPP__E> Failed to calculate hits (0010): 97e075794f588a59e8a0fb8a945814b1MLGIKIKP** *MPLib::MPModules::GetHitsPP__E> /nfs/[...]/modpipe-2.2.0/src/HitsPrfPrf.pl --alignment_basename 97e075794f588a59e8a0fb8a945814b1MLGIKIKP-prfprf-0010 --set_score_statistics ON --output_alidir 97e075794f588a59e8a0fb8a945814b1MLGIKIKP-prfprf-0010-ali --hitfile_name 97e075794f588a59e8a0fb8a945814b1MLGIKIKP-prfprf-0010.hits --ccmatrix_offset -100 --profile_list /nfs/[...]/modpipe-2.2.0/dbs/pdb95/db/pdb95_prf.list --pdb_repository /nfs/[...]/modpipe-2.2.0/demo//db/pdb --target_profile 97e075794f588a59e8a0fb8a945814b1MLGIKIKP-uniprot90.prf --score_type CCMAT --gap_extend_cost -70 --custom_tag "MODELLER Prf-Prf (0010)" --profile_pssmdb /nfs/[...]/modpipe-2.2.0/dbs/pdb95/db/pdb95_prf.pssm --target_code 97e075794f588a59e8a0fb8a945814b1MLGIKIKP --summary_file 97e075794f588a59e8a0fb8a945814b1MLGIKIKP-prfprf-0010.sum --gap_open_cost -700 --e_value 1 ModPipe.pl__E> Failed to get Prf-Prf hits (0010): 97e075794f588a59e8a0fb8a945814b1MLGIKIKP When running the modeller command from the tmp directory the following ABNORMAL TERMINATION error appears: $ /nfs/[...]/modpipe-2.2.0/ext/mod/bin/modpy.sh /nfs/[...]/bin/python2 97e075794f588a59e8a0fb8a945814b1MLGIKIKP-prfprf.py MODELLER 9.13, 2014/02/12, r9876 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2014 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux [...] 2.6.32-358.14.1.el6.x86_64 x86_64 Date and time of compilation : 2014/02/11 22:46:42 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2014/06/05 13:57:11 *alloc_p_215E> Dynamic memory allocation failed.** ** Routine, variable, status: ipssm 3** ***** ABNORMAL TERMINATION of Modeller. This is a bug** ** in Modeller. Please report it to the Modeller** ** developers, including any input files necessary** ** to reproduce the problem.* Directory names and hostname have been redacted. The configuration file that has been used it's identical as the one provided in the modpipe website as an example, with the addition of the XPRF_LIST and XPRF_PSSMDB variables. Thanks for your help, Marco -- Marco Galardini Postdoctoral Fellow EMBL-EBI - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK Phone: +44 (0)1223 49 2547

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External dependencies
by Marco Galardini 19 May '14

19 May '14

Dear ModPipe community, I'm interested in running a local instance of modpipe, but some of the external dependencies are a bit tricky to be found; in particular: - JESS - CE (maybe available here? http://cl.sdsc.edu/jfatcatserver/download.jsp) - SEG They are listed when running ./Setup -h, but not in the online wiki (http://salilab.org/modpipe/doc/install-ext.html#install-ext) Thanks for your help, kind regards, Marco -- Marco Galardini Postdoctoral Fellow EMBL-EBI - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK Phone: +44 (0)1223 49 2547

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Re: [ModPipe-users] [modeller_usage] Fwd: Installation Issues
by Modeller Caretaker 21 Oct '13

21 Oct '13

On 10/18/2013 01:12 PM, Amjad Farooq wrote: > However, when I run a test under /tests, I get the following error: > > make > ************************************************************************** > cd unit && ../../int/runscript.sh python run-all-tests.py -v > /dev/null > /bin/sh: ../../int/runscript.sh: No such file or directory > make: *** [unit] Error 127 > ************************************************************************** > > Where is this ../../int/runscript.sh script? The /int directory is empty! It looks like you forgot to run the Setup script. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

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Installation Issues
by Amjad Farooq 18 Oct '13

18 Oct '13

Dear Ben, How does one install MODELLER 9.12 inside ModPipe? I have MODELLER 9.12 installed on a linux machine and it runs fine. But, I am having some issues with installing MODELLER 9.12 inside ModPipe. According to the instructions, one should make changes to the $MODPIPE/ext/mod/bin/modXXX executable: http://salilab.org/modpipe/doc/install-ext.html#install-ext But, I do not see modXXX under the bin/ directory in MODELLER 9.12? The only scripts available under the bin/ in MODELLER 9.12 appear to be: mod9.12_i386-intel8 modpy.sh.in modslave.py Is there a way to tell ModPipe to read in automatically pre-installed MODELLER 9.12 at another location instead of installing it again under $MODPIPE/ext/mod/ on the same machine? Can you please help?! Thanks very much, Amjad *AMJAD FAROOQ PhD DIC | Associate Professor Dept of Biochemistry & Molecular Biology | Miller School of Medicine | University of Miami | Miami | FL 33136 Located @ Gautier Building #217 | Mail @ 1011 NW 15th Street #217, Miami , FL 33136 amjad(a)farooqlab.net | off 305-243-2429 | lab 305-243-9799 | fax 305-243-3955 | www.farooqlab.net*

3 2

Use of external programs and NRSQEDB tag in modPipe
by Dimitrije Jevremovic 12 Jul '12

12 Jul '12

Greetings, I have been using modPipe for the past 2 weeks and I have three (two questions + one comment) specific questions to ask: 1) When I downloaded and installed modPipe, I connected it according to instructions to MODELLER and some other external tools such as BLAST. First question is about external programs. Can all ten external programs mentioned at the end of the introduction page at http://salilab.org/modpipe/doc/intro.html be installed or just the four external programs described with instructions at the page http://salilab.org/modpipe/doc/install-ext.html (MODELLER, BLAST, CD-HIT and PROCHECK) ? 2) My introduction to modPipe was through the demo example described at http://salilab.org/modpipe/doc/running.html. This example executed relatively quickly for default given settings in modpipe.conf. However, when I compare the modpipe.conf file with the modpipe.conf file given at http://salilab.org/modpipe/doc/modpipe.conf I see that the content of NRSEQDB tag is different. The NRSEQDB tag in demo/modpipe.conf points to demo/db/testdb.hdf5 (~4.5MB) while the NRSEQDB tag in http://salilab.org/modpipe/doc/modpipe.conf points to binary form of file uniprot90 (which is > 2GB if downloaded from http://salilab.org/modeller/downloads/uniprot90.gz). It is taking awfully long to get the results for a single protein in 1100 or 1000 hits mode if non-redundant sequence database is set to be the entire uniprot90 binary database file. Should the NRSEQDB tag point to uniprot90.hdf5 file obtained by compressing the Uniprot90 FASTA file, or is there some more compact and smaller representation for the non-redundant sequence database which could be used to get the results faster? 3) This question is partially in connection with question 2). I see that the NRSEQDB and some other databases given in modpipe.conf tags during execution are copied in local tmp/sequence_id/ directory for every protein sequence separately. In the case of request for large number of proteins to be processes this may quickly eat up disk space (unprot90 binary file is larger than 2GB). Other than the above three issues, I think that I have setup modPipe correctly for execution. Thank you and my best regards, ----------------- Dimitrije Jevremovic intern at Bioinformatics & Computational Biology Department

2 1

TSVMod program
by Romain Studer 18 May '11

18 May '11

Dear Modpipe developers, I cannot find the program TSVMod. In changelog: "- Introduced flag to disable TSVMod calculation if needed - TSVMod scores are incorporated into ModPipe. Scores will be calculated for all structures. Additionally, when chosen as a gathering option, models with a predicted no35>0.4 will be selected. " In the doc/modpipe.conf: "# - TSVMod executables TSVMODEXE /netapp/sali/ModPipe/database/TSVMod/programs/main/score_tsvmod.pl" But I cannot find any "score_tsvmod.pl" in neither modpipe-2.2.0 nor modeller-9.9. I tried to set it to OFF in my modpipe.conf: # - TSVMod executables TSVMODEXE OFF But it still printing warnings: "MPLib::MPModules::GetModels__M> Number of alignments to process: 2 MPLib::MPModules::GetModels__M> Number of models calculated: 1 MPLib::MPModules::GetModels__M> Number of models calculated: 1 PLLib::TSVModUtils::ExecTSVMod__E> Could not find TSVMod executable: PLLib::TSVModUtils::ExecTSVMod__E> Could not find TSVMod executable: " Where I can find the TSVMod program? Or how I can set it to off to not use it? Thank you for your answer. Best regards, Romain

2 1

Threshold to select the best alignment?
by Romain Studer 17 May '11

17 May '11

Dear Modpipe developers, In the documentation: "Hits (input sequence to template structure matches) with an E-value better than a specified cut-off value are selected" I would like to know if we can tell Modpipe to select anotehr specific E-value threshold, or a percentage of identity? For example, I am able now to select the structures with ID>40% using the file *.mod (so after modelling), but it would be even better if I can avoid unecessary modelling with structure alignment lower than 40%. Thank you in advance for your help. Best regards, Romain Studer

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