November 2009 - IMP-dev

Last week in IMP
by Daniel Russel 30 Nov '09

30 Nov '09

- imp.xcodeproj was moved into tools and updated accordingly - the bin directory finally went away - IMP::display::ChimeraWriter now supports the latest version of Chimera - IMP::display::CGOWriter was renamed to IMP::display::PymolWriter as it can do more than just CGO. - IMP::VectorOfRefCounted::operator[] can now be used for assignments just like a normal vector. No more need to use the IMP::VectorOfRefCounted::set() method. - the IMP::atom::Hierarchy constructor from an IMP::Particle* is now explicit (as were the ther decorator constructors)

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No imp-dev meeting today
by Daniel Russel 10 Nov '09

10 Nov '09

Too many people away/busy and nothing too pressing. Sorry about the late notice. But everyone please make sure that they are progressing towards the various deadlines. Upcoming ones include: DOPE Examples and docs for IMP.domino Examples and docs for IMP.saxs Nup84-based example Multifit Addition of gmm code and cleanup of existing code to IMP.statistics A figure comparing rep and data for 26S and Nup84 Text on 26S ring ordering. Keren will resume with Domino next week. --Daniel

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problem linking helper module outside of IMP
by Keren Lasker 09 Nov '09

09 Nov '09

hi, Compiling an external exe, I am getting an error in the linkage stage, basically saying that helper can not see misc: /usr/bin/ld: warning: libimp_misc.so, needed by /viola1/home/kerenl/ bioinformatics/projects/imp/build/lib/libi\ mp_helper.so, not found (try using -rpath or -rpath-link) /viola1/home/kerenl/bioinformatics/projects/imp/build/lib/ libimp_helper.so: undefined reference to `IMP::misc:\ :get_module_version_info()' /viola1/home/kerenl/bioinformatics/projects/imp/build/lib/ libimp_helper.so: undefined reference to `IMP::misc:\ :LowestRefinedPairScore::LowestRefinedPairScore(IMP::Refiner*, IMP::PairScore*)' collect2: ld returned 1 exit status scons: *** [bin/clustering_coefficient] Error 1 I tried changing the dependency order in the SCons files, but did not succeed - can someone help ? thanks, Keren.

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This week in IMP
by Daniel Russel 06 Nov '09

06 Nov '09

There is a new method IMP::display::create_writer() which creates the appropriate writer based on the file name passed. - You can now add members to rigid bodies via IMP::core::RigidBody::add_member(). These members can be other rigid bodies (although this functionality is only lightly tested). - The code to get bounding volumes for IMP::atom::Hierarchy has been moved to the atom module, as as the clone and destroy code. They can be found at IMP::atom::clone(), IMP::atom::destroy(), IMP::atom::get_bounding_box(). - Added IMP::core::VolumeRestraint. - Several functions have been added to helper in creating restraints. They are create_simple_connectivity_on_rigid_bodies(), create_simple_connectivitiy_on_molecules(), create_simple_distance(), create_simple_diameter(), create_simple_em_fit(), and create_simple_excluded_volume_on_rigid_bodies(). Functions load_em_density_map() and set_rigid_bodies() are added as well. See IMP::helper for more information. - IMP::ScoreStates are further hidden. Namely, IMP::core::RigidBody constructs the needed score states internally, doing away with the need for the create functions (which have been done away with). In addition there are new decorators IMP::core::Cover and IMP::core::Centroid which manage their respective score states, further doing away with more create methods. The hierarchy-based create method for rigid bodies has been moved to the atom module and is called IMP::atom::rigid_body_setup_hierarchy(). - IMP::em::read_map() will figure out the file type to use automatically from the extension. Other such methods should follow suite. - A class IMP::core::StructureSet has been added to provide a convenient way to manage solutions of optimization runs. - IMP::core::RigidBodyMover now takes its angle argument in radians and is documented as such. - IMP::core::ClosePairsScoreState and IMP::core::CloseBipartitePairsScoreState have been replaced by IMP::core::ClosePairContainer and IMP::core::CloseBipartitePairContainer. The score states have been marked as deprecated and are mostly still there, but are more limited than they were. - IMP::core::AllPairsPairContainer has been renamed to IMP::core::AllPairContainer and a bipartite version has been added.

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scripts/utils directory
by Keren Lasker 04 Nov '09

04 Nov '09

hi, I would like to add various python scripts to the DOMINO module. These scripts would have functionalities such as junction tree construction etc. Currently we have a global helper module, but I think it makes sense to add helper directory also within a module for more specific setup scripts. so calling junction tree construction would be: IMP.domino.helper.create_junction_tree() does it make sense ? Keren.

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helper cleanup
by Daniel Russel 02 Nov '09

02 Nov '09

The helper module contains various atom.Hierarchy-specific code (get_bounding_box, clone, destroy, and the functions for creating simplified versions). Externally, this doesn't make much sense, but code is there since some of it internally uses em for computations. In addition, Elina's new code for simplified restraint management forms a nice, coherent set of functionality which could take over the helper module by itself. As a result, I propose - helper.get_bound_box, helper.clone and helper.destroy be moved to atom. - the helper.create_simplified function be renamed em.create_simplified_from_density putting it in the em module and making it more clear why it is there (there current name is too vague anyway). It should also create the rigid bodies it needs internally. - helper.create_simplified_by_residue needs to be thought about since its current method of asigning radii doesn't make sense for anything other than density based restraints (so it may make sense to move it to em). I don't think any of the code is too widely used, so changing things now should be minimally disruptive. Thoughts?

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Curious Error and PDBs with more than 1 model
by Javier Ángel Velázquez Muriel 02 Nov '09

02 Nov '09

Hi. I'm testing IMP with a PDB file that has 3 models inside, and is quite big: ~900 kDa, 60 chains. I was expecting problems with reading more than one model, but I'm also getting this: ERROR: Can only allocate 150000 particles. Yell at Daniel. 1) Can IMP read multi-model PDBs now ? The code seems that it can. 2) How are the models treated? One IMP model per PDB model ? I would like to have all the PDB models into the IMP model in this case. 3) How does IMP identify chains internally? How can I access chain 54, for example, given that it's name is repeated in the PDB file? (The PDB has 3 models, 20 chains each, repeated name). Btw ... the PDB file was valid enough to be part of RCSB. Cheers.

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problem evaluating restraints
by Keren Lasker 01 Nov '09

01 Nov '09

hi, I think something is wrong now with calling to restraint evaluation. After adding the restraint to the model, I am keep getting the message: ERROR: ---------------------------------------------------------------------- Traceback (most recent call last): File "simple_test.py", line 49, in test_ev print r.evaluate(None) File "/viola1/home/kerenl/bioinformatics/projects/imp/build/lib/IMP/ __init__.py", line 1193, in evaluate def evaluate(self, *args): return _IMP.Restraint_evaluate(self, *args) ValueError: Restraint::evaluate() cannot be called during model evaluatio I think the attached test case should work and I am not sure why it does not ..... thanks, Keren.

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