August 2010 - IMP-dev

em2D to em2d rename and possible issues on mac os
by Daniel Russel 31 Aug '10

31 Aug '10

The em2D module has been renamed em2d as certain scripts assume module names are lower case. If you get an error on a mac (which has a case-insensitive file system and so tends to get confused about this sort of thing), delete modules/em2D, do svn update and build again.

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Recent and coming changes in IMP
by Daniel Russel 27 Aug '10

27 Aug '10

I haven't sent such an email in a while. Here is a summary of some of the interesting recent changes: - Javi added his 2D EM scoring functionality as IMP::em2D - some new ways to speed up scons have been added. See IMP::core::HarmonicDistancePairScore, IMP::core::SoftSpherePairScore and, for C++ users, the generic restraint support IMP::container::create_restraint() and IMP::core::create_restraint(). These each offer between 2x and 1.2x speedup when using simple scores (like harmonics on distances). In addition, a function IMP::container::get_slack_estimate() has been added which will estimate the correct slack to use with a IMP::container::ClosePairContainer. This will be extended to support IMP::core::ExcludedVolumeRestraint eventually. - support for dense and sparse grids have been added to IMP::algebra. See the IMP::algebra module page (I'm still working on how to make the docs clearer). - all write functions now have associated IMP::OptimizerState and IMP::FailureHandler classes. For examples, see IMP::WriteOptimizerState, IMP::WriteBinaryOptimizerState, IMP::WriteFailureHandler, IMP::atom::WritePDBOptimizerState etc. - functions IMP::write_binary_model(), IMP::read_binary_model() and IMP::read_configurations() have been added to support space and filesystem efficient storage of model configurations. Multiple configuration can be written to a single file. This functionality requires NetCDF be installed (NetCDF is a standard library for reading and writing binary data). - domino2 has been added. It provides a simpler interface on Keren's domino optimize as well as a number of new optimization and hooks for customizing the optimization process - a better explaination of how to use reference counted pointers has been added to IMP::Pointer. - all simple, planar polygons are now supported for display when CGAL is present Some of the future changes: - The IMP::algebra::Grid3D will be used to store EM grids and many of the computational kernels for EM will be moved to algebra so that density maps can be used in core and statistics. - the excluded volume restraint is likely to get faster (and produce better derivatives) as Keren is working on an implementation using grids rather than zillions of atoms

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[Bug 114] New: Use directions from higher up in the tree when doing EV on rigid bodies
by bugzilla-daemon＠salilab.org 06 Aug '10

06 Aug '10

https://salilab.org/imp/bugs/show_bug.cgi?id=114 Summary: Use directions from higher up in the tree when doing EV on rigid bodies Product: IMP Version: unspecified Platform: PC OS/Version: Linux Status: NEW Severity: enhancement Priority: P5 Component: core AssignedTo: drussel(a)SALILAB.ORG ReportedBy: drussel(a)SALILAB.ORG CC: imp-dev(a)salilab.org Estimated Hours: 0.0 Don't use a harmonic on them at all. -- Configure bugmail: https://salilab.org/imp/bugs/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

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Re: [IMP-dev] removing get_fixed_[xyz]*_from_rotation
by Keren 06 Aug '10

06 Aug '10

Needed for converting external transformations ( as those from gamb ) to imp Daniel Russel <drussel(a)gmail.com> wrote: >Javi proposed getting rid of the get_fixed_[xyz]*_from_rotation() functions as they are unlikely to be used by anyone and potentially confusing. Anyone using them or planning on using them? >_______________________________________________ >IMP-dev mailing list >IMP-dev(a)salilab.org >https://salilab.org/mailman/listinfo/imp-dev

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removing get_fixed_[xyz]*_from_rotation
by Daniel Russel 06 Aug '10

06 Aug '10

Javi proposed getting rid of the get_fixed_[xyz]*_from_rotation() functions as they are unlikely to be used by anyone and potentially confusing. Anyone using them or planning on using them?

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[Bug 113] New: ExcludedVolumeRestraint with one particle
by bugzilla-daemon＠salilab.org 02 Aug '10

02 Aug '10

https://salilab.org/imp/bugs/show_bug.cgi?id=113 Summary: ExcludedVolumeRestraint with one particle Product: IMP Version: unspecified Platform: PC OS/Version: Linux Status: NEW Severity: enhancement Priority: P5 Component: core AssignedTo: drussel(a)SALILAB.ORG ReportedBy: drussel(a)SALILAB.ORG CC: imp-dev(a)salilab.org Estimated Hours: 0.0 Provide a warning if only a single particle or rigid body is passed to the EVR. -- Configure bugmail: https://salilab.org/imp/bugs/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

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