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pdb parser issue in IMP.atom.read_pdb
by Benjamin SCHWARZ 20 Jul '10

20 Jul '10

You probably know it, but some atom names would simply result in read_pdb to fail. This behavior seems a bit drastic too me. Maybe it would be possible to build a hierarchy containing atoms that could be recognized, and provide some warnings, or give access to the number of encountered errors or ignored atoms when building the hierarchy; leaving the final choice to the user to play with its structure or to reject it. As an example : pdb code 1E1Q mh = IMP.atom.read_pdb(pdbFilePath,m) _IMP.ValueException: Illegal character in atom name, only A-Z, 0-9, " "allowed. Got "HET: O5'"

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IMP.atom.read_pdb confusing error message when not finding file
by Benjamin SCHWARZ 20 Jul '10

20 Jul '10

When trying to read a pdb file that does not exist on my disk I get a puzzling message : mh = IMP.atom.read_pdb(pdbFilePath,m,sel) NotImplementedError: Wrong number of arguments for overloaded function 'read_pdb'. Possible C/C++ prototypes are: IMP::atom::read_pdb(IMP::TextInput,IMP::Model *) IMP::atom::read_pdb(IMP::TextInput,IMP::Model *,IMP::atom::PDBSelector const &,bool) IMP::atom::read_pdb(IMP::TextInput,IMP::Model *,IMP::atom::PDBSelector const &)

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Binary installation of IMP 1.0 on Macbook Pro OSX 10.6.3 snowleopard
by Benjamin SCHWARZ 19 Jul '10

19 Jul '10

>> By the way, would you be interested in any testimony with regard to IMP installation ? If so, I could open a thread here just for that. > Of course, please do. So be it. The installation in itself was OK, though I found the "Installation successful" messages a bit disconcerting. Maybe you should consider an installation log file or a longer message to tell what exactly was installed, in which directory, and suggest some starting points for beginners. Concerning the utilization now : I have two python 2.6 installed on my computer though I do not remember nor why nor how. The default python (the one that runs when typing "python" on the command line) links to /Library/Frameworks/Python.framework/Versions/2.6/bin/python (it claims to be a v2.6.4 compiled with gcc 4.0.1 ) My second python dwells in /usr/bin and claims to be a v2.6.1 compiled with gcc 4.2.1 With the first interpreter, IMP is not automatically found and I have to modify the PYTHONPATH (therefore the localization of IMP in the installation message could be of interest.). When this is done, the package is found but any attempt to use it results in an error : Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/local/lib/python2.6/site-packages/IMP/__init__.py", line 25, in <module> _IMP = swig_import_helper() File "/usr/local/lib/python2.6/site-packages/IMP/__init__.py", line 17, in swig_import_helper import _IMP ImportError: dlopen(/usr/local/lib/python2.6/site-packages/_IMP.so, 2): no suitable image found. Did find: /usr/local/lib/python2.6/site-packages/_IMP.so: mach-o, but wrong architecture With /usr/bin/python the IMP package is automatically detected, and everything runs fine. In order to explain the problem observed with the default interpreter, I firstly suspected it had something to do with the gcc version, but now I rather think it is a 32bits/64bits conflict : > file /usr/local/lib/python2.6/site-packages/_IMP.so /usr/local/lib/python2.6/site-packages/_IMP.so: Mach-O 64-bit bundle x86_64 > file /Library/Frameworks/Python.framework/Versions/2.6/bin/python /Library/Frameworks/Python.framework/Versions/2.6/bin/python: Mach-O universal binary with 2 architectures /Library/Frameworks/Python.framework/Versions/2.6/bin/python (for architecture ppc): Mach-O executable ppc /Library/Frameworks/Python.framework/Versions/2.6/bin/python (for architecture i386): Mach-O executable i386 > file /usr/bin/python /usr/bin/python: Mach-O universal binary with 3 architectures /usr/bin/python (for architecture x86_64): Mach-O 64-bit executable x86_64 /usr/bin/python (for architecture i386): Mach-O executable i386 /usr/bin/python (for architecture ppc7400): Mach-O executable ppc

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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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