- IMP-dev - salilab.org

[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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[Bug 107] New: TextInput reports mismatched arguments rather than failure to open file
by bugzilla-daemon＠salilab.org 30 Jul '10

30 Jul '10

https://salilab.org/imp/bugs/show_bug.cgi?id=107 Summary: TextInput reports mismatched arguments rather than failure to open file Product: IMP Version: unspecified Platform: All OS/Version: All Status: NEW Severity: minor Priority: P5 Component: kernel AssignedTo: drussel(a)SALILAB.ORG ReportedBy: drussel(a)SALILAB.ORG CC: imp-dev(a)salilab.org Estimated Hours: 0.0 Swig eats the I/O exception and reports it as an argument mismatch. -- 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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[Bug 64] Need a comprehensive solution for symmetry in models
by bugzilla-daemon＠salilab.org 30 Jul '10

30 Jul '10

https://salilab.org/imp/bugs/show_bug.cgi?id=64 --- Comment #1 from Daniel <drussel(a)SALILAB.ORG> 2010-07-30 10:32:53 PDT --- *** Bug 110 has been marked as a duplicate of this bug. *** -- 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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[Bug 110] New: Add periodic boundary conditions
by bugzilla-daemon＠salilab.org 30 Jul '10

30 Jul '10

https://salilab.org/imp/bugs/show_bug.cgi?id=110 Summary: Add periodic boundary conditions Product: IMP Version: unspecified Platform: All OS/Version: All 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 Initially just have a special purpose close pairs restraint and a class to wrap things at the boundary. See if bounding box sweep can work with circular boundary? Seems unlikely. Grid might be best. -- 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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[Bug 108] New: NetCDF I/O
by bugzilla-daemon＠salilab.org 30 Jul '10

30 Jul '10

https://salilab.org/imp/bugs/show_bug.cgi?id=108 Summary: NetCDF I/O Product: IMP Version: unspecified Platform: All OS/Version: All Status: NEW Severity: enhancement Priority: P5 Component: kernel AssignedTo: drussel(a)SALILAB.ORG ReportedBy: drussel(a)SALILAB.ORG CC: imp-dev(a)salilab.org Estimated Hours: 0.0 It would be nice to have a write_model_binary/read_model_binary using NetCDF to go along with the current text versions. There is a standard for writing series of molecule structures to a file, but it would be also good, for maximimal compactness to have an option to just write optimized attributes. -- 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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Just for fun
by Daniel Russel 28 Jul '10

28 Jul '10

Here are stats extracted from the svn logs <http://www.salilab.org/~drussel/imp_stats/>. It excludes data files and commits made before they were connected to usernames.

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Restraint::get_is_part_of_model() and ScoreState::get_has_model()
by Daniel Russel 22 Jul '10

22 Jul '10

do the same thing. I propose to rename the first to be like the second.

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