ModPipe-users

modpipe-users@salilab.org

19 discussions

Mailman Hosting Services
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23 Nov '23

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ModPipe 2.3.1 release
by Ben Webb 27 Oct '23

27 Oct '23

ModPipe 2.3.1 is now available. This release contains minor updates, most notably support for Modeller 10. See https://salilab.org/modpipe/doc/changes.html for the full change log. Check it out at https://salilab.org/modpipe/ Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Modpipe download links broken
by Giulia Baggio 26 May '20

26 May '20

Hello, the two download link at https://salilab.org/modpipe/ don't work, probably because they link at https://salilab.org/modpipe/modpipe-2.3.3.tar.gz.asc instead of https://salilab.org/modpipe/modpipe-2.3.0.tar.gz.asc <https://salilab.org/modpipe/modpipe-2.3.3.tar.gz.asc> (which works). I didn't find any bug report forms,I hope using the mailing list was fine. Regards, Giulia

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ModPipe 2.3.0 release
by Ben Webb 14 May '20

14 May '20

ModPipe 2.3.0 is now available. This release contains major updates, most notably support for Python 3, new hits modes, and basic support for building models using multiple templates. See https://salilab.org/modpipe/doc/changes.html for the full change log. Check it out at https://salilab.org/modpipe/ Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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problem while running modpipe
by Vivek Junghare 11 Sep '19

11 Sep '19

Hi, I am trying to run a MODPIPE on my system. I am running it on Ubuntu 16.04LTS version. I have tried to run demo example on test sequence. This run was successful. However when I tried to run on different sequence there was error. Please help me with this. I have attached error message in png format as well as text format. The input sequence was - >gi|985561167|gb|AMD11804.1|TEM-224| class A beta-lactamase TEM-224 [Klebsiella pneumoniae] MSIKHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTF KVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMTDNTAANLLLTTI GGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWME ADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGA SLIKHW* Thanks & regards, Vivek J. Research Scholar, Dept. of Biotechnology, IIT Roorkee.

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Regarding the GatherModMP.py config file
by suresh satpati 27 Jul '18

27 Jul '18

Dear Sir/Madam, I have installed ModPipe in my Ubuntu platform and able to use ModPipe.pl to run & generate models from test sequences in the data folder (using demo part documentation: https://salilab.org/modpipe/doc/running.html). But to select the best model from these I am facing difficulty in running GatherModMP.py as it is asks for the GatherModMP.py config file that I didn't find anywhere in the demo or in the internet for what variables to define in it. If possible can you please send me the config file for GatherModMP.py and steps for selecting best model. Thanking you, Suresh -- Regards, Suresh Satpati, Ph.D. Research Associate Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka - 560012 India Mob. No. +91-9861138427

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Re: [ModPipe-users] ModPipe-users Digest, Vol 8, Issue 1
by jb ZHOU 10 Mar '16

10 Mar '16

Hello Ben, Thank you very much for you help,I changed `pwd` to "pwd" before, Sincerely, Zhoujb 2016-03-10 4:00 GMT+08:00 <modpipe-users-request(a)salilab.org>: > Send ModPipe-users mailing list submissions to > modpipe-users(a)salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/modpipe-users > or, via email, send a message with subject or body 'help' to > modpipe-users-request(a)salilab.org > > You can reach the person managing the list at > modpipe-users-owner(a)salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of ModPipe-users digest..." > > > Today's Topics: > > 1. Modpipe problem (jb ZHOU) > 2. Re: Modpipe problem (Ben Webb) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 9 Mar 2016 09:42:10 +0800 > From: jb ZHOU <zhoujb0920(a)gmail.com> > To: modpipe-users(a)salilab.org > Subject: [ModPipe-users] Modpipe problem > Message-ID: > < > CACTggG+RgtqZPqb0-vvJLXxpDTw08AuGZYMzh0GB8CVVoes5qw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear ModPipe community: > I installed modpipe in our system,but when I run the example of modpipe,I > get the following error,I don't know how to deal with it: > > $ ../main/ModPipe.pl --conf_file modpipe.conf --sequence_id > 97e075794f588a59e8a0fb8a945814b1MLGIKIKP > MPLib::MPModules::GetProfile__E> Sequence file not found: > > pwd/data/97e/97e075794f588a59e8a0fb8a945814b1MLGIKIKP/sequence/97e075794f588a59e8a0fb8a945814b1MLGIKIKP.fsa > ModPipe.pl__E> Failed to calculate BUILD_PROFILE profile > ModPipe.pl__E> Sequence: 97e075794f588a59e8a0fb8a945814b1MLGIKIKP > > Thanks for your help, > Zhoujb >

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Modpipe problem
by jb ZHOU 09 Mar '16

09 Mar '16

Dear ModPipe community: I installed modpipe in our system,but when I run the example of modpipe,I get the following error,I don't know how to deal with it: $ ../main/ModPipe.pl --conf_file modpipe.conf --sequence_id 97e075794f588a59e8a0fb8a945814b1MLGIKIKP MPLib::MPModules::GetProfile__E> Sequence file not found: pwd/data/97e/97e075794f588a59e8a0fb8a945814b1MLGIKIKP/sequence/97e075794f588a59e8a0fb8a945814b1MLGIKIKP.fsa ModPipe.pl__E> Failed to calculate BUILD_PROFILE profile ModPipe.pl__E> Sequence: 97e075794f588a59e8a0fb8a945814b1MLGIKIKP Thanks for your help, Zhoujb

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H5Fopen() error
by Nadine Homeyer (Staff) 22 Feb '16

22 Feb '16

Dear all, I installed ModPipe and Modeller and would like to run a modelling job. I poceeded as discribed on the example page http://salilab.org/modpipe/doc/running.html#examples and the files provided in the command file (see attachment) all exist. Nevertheless I get the error: /main/ModPipe.pl --conf_file modpipe.conf --sequence_id daa1d2be76c627b54186fcf8869f3a2dGSHMPTRF \ --hits_mode 1100 MPLib::MPModules::GetProfile__M> No profile found for sequence MPLib::MPModules::GetProfile__M> Seqid : daa1d2be76c627b54186fcf8869f3a2dGSHMPTRF MPLib::MPModules::GetProfile__M> Profile: /local_homes/nhomeyer/work/chopin_testing/PKS13/AcylCarrier_PDB/daa/daa1d2be76c627b54186fcf8869f3a2dGSHMPTRF/sequence/daa1d2be76c627b54186fcf8869f3a2dGSHMPTRF-uniprot90.prf MPLib::MPModules::GetProfile__M> Will calculate a new profile MPLib::MPModules::GetProfile__M> Calculating profile for sequence: daa1d2be76c627b54186fcf8869f3a2dGSHMPTRF HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0: #000: H5F.c line 604 in H5Fopen(): unable to open file major: File accessibilty minor: Unable to open file #001: H5Fint.c line 1085 in H5F_open(): unable to read superblock major: File accessibilty minor: Read failed #002: H5Fsuper.c line 277 in H5F_super_read(): file signature not found major: File accessibilty minor: Not an HDF5 file Traceback (most recent call last): File "/local_homes/nhomeyer/src/modpipe-2.2.0/src/int/BuildProfile.py", line 157, in <module> main() File "/local_homes/nhomeyer/src/modpipe-2.2.0/src/int/BuildProfile.py", line 153, in main build_profile(env, sequence, database, opts) File "/local_homes/nhomeyer/src/modpipe-2.2.0/src/int/BuildProfile.py", line 119, in build_profile chains_list='ALL') File "/local_homes/nhomeyer/src/modpipe-2.2.0/ext/mod/modlib/modeller/sequence_db.py", line 69, in read minmax_db_seq_len) _modeller.ModellerError: hdf5err____E> unable to open file MPLib::MPModules::GetProfile__E> Failed to calculate a profile for sequence: daa1d2be76c627b54186fcf8869f3a2dGSHMPTRF MPLib::MPModules::GetProfile__E> /local_homes/nhomeyer/src/modpipe-2.2.0/src/BuildProfile.py -o daa1d2be76c627b54186fcf8869f3a2dGSHMPTRF-uniprot90.prf -F FASTA -i 5 daa1d2be76c627b54186fcf8869f3a2dGSHMPTRF.fsa uniprot90 MPLib::MPModules::GetProfile__E> Results message: 256 ModPipe.pl__E> Failed to calculate BUILD_PROFILE profile ModPipe.pl__E> Sequence: daa1d2be76c627b54186fcf8869f3a2dGSHMPTRF Any suggestions how to solve this are welcome. Kind regards, Nadine The University of Dundee is a registered Scottish Charity, No: SC015096

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Is it possible to calculate MPQS (ModPipe Quality Score) of models generated using MODELLER using MODpipe
by Su Datt Lam 13 Aug '15

13 Aug '15

Hey guys, I am a newbie in protein structure modelling. I have generated some protein models using MODELLER and I have been using GA341, normalized DOPE to find out how good the quality of my model. However, recently, I found out about MPQS and find it very interesting. Is it possible for me to assess the models that I have created using ModPipe without rebuilding the models again? Sincerely, Su

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