August 2012 - IMP-users

IMP.algebra.get_transformation_aligning_first_to_second
by unverdor＠biochem.mpg.de 30 Aug '12

30 Aug '12

Hi, we just stumbled across the same problem Ben had last year: get_transformation_aligning_first_to_second doesn't give the correct results. Can the resulting transformation be applied with get_transformed, like in the example? Or does anybody have an idea how we could get the transformation between two point sets in a different way? Thanks a lot! Carsten & Pia Date: Thu, 20 Oct 2011 10:29:14 +0200 From: Benjamin SCHWARZ <schwarz.ben(a)gmail.com> Reply-To: Help and discussion for users of IMP <imp-users(a)salilab.org> Subject: [IMP-users] does IMP.algebra.get_transformation_aligning_first_to_second minimize RMSD ? To: Help and discussion for users of IMP <imp-users(a)salilab.org> Hi list, Just confronted to something that looks like a bug, either in IMP or in my reading of the IMP manual. I'd expect the alignment of two sets of particles or vectors to minimize the RMD between the two sets, but in my case it appears the alignment produces a worse RMSD. See output underneath, and sample script attached. Considering 30 3D vectors natural rmsd between v1 and v2: 209.651290894 aligning v1 on v2... with resulting rmsd 220.458206177 running IMP version kernel SVN 10177 with Boost.FileSystem _______________________________________________ IMP-users mailing list IMP-users(a)salilab.org https://salilab.org/mailman/listinfo/imp-users

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rmf/hdf5 format
by Adhikari, Badri (MU-Student) 29 Aug '12

29 Aug '12

Hello all, While working on IMP, why do we have to use the rmf library/hdf5 file format? When do I know that I need to write my hierarchy to hdf5 file? Sincerely, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri BAP54(a)mail.missouri.edu<mailto:BAP54@mail.missouri.edu>

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pdb to restrains
by Adhikari, Badri (MU-Student) 28 Aug '12

28 Aug '12

Hello all, Can we read a pdb structure and extract restrains from the pdb? Is there a way by which we can convert pdb structures to restrain and then sample/construct structures back from just the restrains produced? Sincerely, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri BAP54(a)mail.missouri.edu<mailto:BAP54@mail.missouri.edu>

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No module named rmf
by Adhikari, Badri (MU-Student) 27 Aug '12

27 Aug '12

Following is the error I get while trying to execute the sample_0.py example. All other examples that do not use rmf module run smoothly. Everything was smooth while installing. Is there anything I missed during the installation? $../bin/python2.7 sample_0.py Traceback (most recent call last): File "sample_0.py", line 7, in <module> import IMP.rmf ImportError: No module named rmf Also that the rmf module is in the svn-trunk folder but not in the release folder. Please suggest what I should do. Sincerely, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri BAP54(a)mail.missouri.edu<mailto:BAP54@mail.missouri.edu>

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model clustering
by damien.devos＠cos.uni-heidelberg.de 14 Aug '12

14 Aug '12

Hi, Is there a simple way in IMP to compare (all vs all) and then cluster the x% best models obtained after optimization and evaluation? Thanks Damien **************** Damien Devos Center of Organismal Studies Ruprecht-Karls-Universitat Im Neuenheimer Feld 230 69120 Heidelberg, Germany

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struggling to make structure predictions
by Adhikari, Badri (MU-Student) 07 Aug '12

07 Aug '12

Hello all, I am struggling to write a python program that takes protein sequence as input and produces some conformations as the output (with no any other input data). With the help of previous replies, I tried merging the examples: "structure_from_sequence.py", "charm_forcefield.py" and "basic_optimization.py" and wrote a script that is attached. This script runs and produces chimera python files that I can visualize through chimera. 1. Will the script that I have prepared work as an example to produce 3D structures with just sequence as input? OR have I made any fundamental/conceptual mistakes while merging them? 2. I can produce chimera python files for each of the predicted conformations. But I want pdb files. Is it possible to do that? Are there any examples? 3. Is it possible to add contacts restrain (distance between atoms as a restrain) moving forward with this approach? Sincerely, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri BAP54(a)mail.missouri.edu<mailto:BAP54@mail.missouri.edu>

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Boost <= 1.36
by Daniel Russel 07 Aug '12

07 Aug '12

Is anyone using the development version of IMP with boost <= 1.36? The easiest way to tell is to look at the boost/version.hpp header, probably in /usr/include/boost/version.hpp. Thanks.

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