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273 discussions

combine IMP.atom.Selectors ?
by Benjamin SCHWARZ 15 Jul '10

15 Jul '10

Hello list, I am very new to IMP, thus probably coming with a bunch of fairly naive question. Today I am wondering if it is possible to combine Selectors in order, for instance to select only ATOMS of chain A from a pdb file. If this is not directly possible what would you suggest to achieve the task ? thanks a lot for any time spent to answer me --Ben

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fail optimization
by Harianto Tjong 19 Apr '10

19 Apr '10

Dear imp users & developers, I am playing IMP with a large numbers of particles, e.g. > 10^5 and fail to optimize due to memoryError even though I still have enough VMEM and MEM. An example: -------------- Setting up score state for container ListSingletonContainer 0 Model(Model, kernel 1.0)127482 particles 0 restraints 1 score states Setting up score state for container ListSingletonContainer 3 Setting up score state for container ClosePairContainer Setting up score state for container MovedSingletonContainer Restraint SingletonsRestraint 0 has weight 1 Restraint PairsRestraint 1 has weight 1 Traceback (most recent call last): File "test.py", line 180, in <module> o.optimize(1000) File "/home/htjong/bin/imp-1.0/build/lib/IMP/core/__init__.py", line 665, in optimize def optimize(self, *args): return _IMP_core.ConjugateGradients_optimize(self, *args) MemoryError: std::bad_alloc -------------- I suppose I have to increase the memory usage limit during compilation. How is the proper way to do it? Thanks. Harianto.

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error while loading shared libraries: libimp_saxs.so:
by prabhakar g 12 Apr '10

12 Apr '10

Sir, We are a group working in solution x-ray scattering in KAIST, South Korea. We installed IMP from the Source code tarball<http://salilab.org/imp/1.0/download/imp-1.0.tar.gz>in Fedora 8, using the below procedure as given in your webpage scons prefix=/opt/imp/ all scons prefix=/opt/imp/ install but when we try to run the foxs binary we are get the below error ./foxs: error while loading shared libraries: libimp_saxs.so: cannot open shared object file: No such file or directory hope you could give some suggestions. sincerely prabha

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