IMP-users November 2015

imp-users@salilab.org

7 participants
5 discussions

how do I build working pmi rnapolii examples ?
by Isabelle Phan 25 Mar '16

25 Mar '16

Hello Ben, How do I install working examples for pmi rnapolii? I need to run the analysis on my model and could not match the IMP tutorial for rnapolii with my old code. They had diverged too much. So I installed 2.4.0 stable release. This does not seem to have working examples for rnapolii. The code only has modules/pmi/broken-examples/rnapolii I tried pulling from the development version, but that does not seem to include working examples either. Am grateful for any help, Isabelle

3 4

Failed to build 1e6v example with multifit
by Mateusz Koryciński 02 Dec '15

02 Dec '15

Dear All, Was anyone able to build 1e6v example? I was trying to model complex I am currently working on, however with no luck. To test the software I've tried to model example 1e6v, provided along with the source code. Multifit align step produced asmb.combinations file with "NO SOLUTIONS FOUND". Shouldn't example produce results? I was following the same instructions as in the 3sfd tutorial, which works. Looking forward to hearing from you. Best regards, Mateusz Korycinski

3 3

installation issue: cgal version 10.dylib missing
by John Robinson 14 Nov '15

14 Nov '15

After installation of IMP via homebrew, 'import IMP' fails because it can’t find /usr/local/lib/libCGAL.10.dylib I have verison 11.dylib installed. ls /usr/local/lib/libCGAL* produces /usr/local/lib/libCGAL.11.0.0.dylib /usr/local/lib/libCGAL.11.dylib /usr/local/lib/libCGAL.dylib /usr/local/lib/libCGAL_Core.11.0.0.dylib /usr/local/lib/libCGAL_Core.11.dylib /usr/local/lib/libCGAL_Core.dylib And suggestions would be helpful. Thanks, ~John Robinson

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Conjugate Gradient optimizer with rigid bodies
by Karine VOLTZ 10 Nov '15

10 Nov '15

Dear all, I have a system consisting of several sub-units all represented as rigid bodies (even sub-units containing only one domain). I have tried a MC sampling with a simple set of restraints on the system and it's working fine. Now I would like to use the IMP.core.MonteCarloWithLocalOptimization() using a CG optimizer but it does not seem to work: monitoring the energies at each MC step shows always the same energy. I wanted to know if it's actually possible to use the function IMP.core.MonteCarloWithLocalOptimization() with rigid bodies? Thank you in advance for your help, Karine

2 1

question about PMI included.None.xl.db file
by Jason Schmidberger 02 Nov '15

02 Nov '15

Hello, I have been running IMP::pmi with a protein complex we are working on in our lab. I have managed to adapt the PMI online example (RNA pol) to work for my example. A series of files are output in the execution directory: included.None.xl.db, excluded.None.xl.db, missing.None.xl.db In my "included.None.xl.db file" I only have the following two lines; {'res2': '155', 'prot1': 'mol3', 'prot2': 'mol5', 'res1': '160'} {'res2': '155', 'prot1': 'mol3', 'prot2': 'mol5', 'res1': '154'} I include more than 30 x-link restraints in my set up. When I compare this to the same file as output with the worked RNA pol example, that file has many more entries. QUESTION: what is the meaning behind this file? Does it mean most of my x-link restraints were thrown out? Cheers, Jason

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IMP-users November 2015