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273 discussions

model clustering
by damien.devos＠cos.uni-heidelberg.de 14 Aug '12

14 Aug '12

Hi, Is there a simple way in IMP to compare (all vs all) and then cluster the x% best models obtained after optimization and evaluation? Thanks Damien **************** Damien Devos Center of Organismal Studies Ruprecht-Karls-Universitat Im Neuenheimer Feld 230 69120 Heidelberg, Germany

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struggling to make structure predictions
by Adhikari, Badri (MU-Student) 07 Aug '12

07 Aug '12

Hello all, I am struggling to write a python program that takes protein sequence as input and produces some conformations as the output (with no any other input data). With the help of previous replies, I tried merging the examples: "structure_from_sequence.py", "charm_forcefield.py" and "basic_optimization.py" and wrote a script that is attached. This script runs and produces chimera python files that I can visualize through chimera. 1. Will the script that I have prepared work as an example to produce 3D structures with just sequence as input? OR have I made any fundamental/conceptual mistakes while merging them? 2. I can produce chimera python files for each of the predicted conformations. But I want pdb files. Is it possible to do that? Are there any examples? 3. Is it possible to add contacts restrain (distance between atoms as a restrain) moving forward with this approach? Sincerely, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri BAP54(a)mail.missouri.edu<mailto:BAP54@mail.missouri.edu>

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Boost <= 1.36
by Daniel Russel 07 Aug '12

07 Aug '12

Is anyone using the development version of IMP with boost <= 1.36? The easiest way to tell is to look at the boost/version.hpp header, probably in /usr/include/boost/version.hpp. Thanks.

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looking for ab initio structure prediction examples
by Adhikari, Badri (MU-Student) 24 Jul '12

24 Jul '12

Hello all, I have installed IMP nightly build and I can run all the examples. I am actually looking for an example that does ab initio protein structure prediction. The example http://www.salilab.org/~drussel/unstructured/imp_doc/atom_examples.html#str… does generate pdb files but I came to know that, this example does not actually do the structure prediction. It gives just the extended chain structures. Do we have any examples in which we can feed a sequence and get some models (probably pdb files)? Otherwise, what examples do we need to refer in order to do that? Once I do that, I plan to add other spatial restrains one by one and observe the changes in prediction after that. Sincerely, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri BAP54(a)mail.missouri.edu<mailto:BAP54@mail.missouri.edu>

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can generate structure from sequences. how to add contact information as restrain?
by Adhikari, Badri (MU-Student) 09 Jul '12

09 Jul '12

Hello imp users and experts, I am using edited version of http://www.salilab.org/~drussel/unstructured/imp_doc/atom_examples.html#str… to generate structures from amino-acid sequences. This example uses IMP.atom.CHARMMTopology. I would like to feed contact information as a restrain to guide the prediction process. 1. What should be the approach? Which classes/functions should be used? 2. Are there any such examples? Sincerely, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri BAP54(a)mail.missouri.edu<mailto:BAP54@mail.missouri.edu>

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distance restraint
by damien.devos＠cos.uni-heidelberg.de 30 Jun '12

30 Jun '12

Hi, I am so far using a distance restraint, which is satisfy if the particules are below the distance, down to 0, ie contact. Is that correct? Then what is the point of the std_dev if it is anything below distance that score lowest? So far, my code is something like <Distance> <Restraint name="mydist" distance="10" std_dev="1"> <Particle id="prt1"/> <Particle id="prt2"/> </Restraint> </Distance> However, I would like to have a function with a minimal score if the particules are at the give distance, with some stdev. I probably need to use the DistancePairScore function. But how to do that in XML format? Thanks for IMP and the support **************** Damien Devos Center of Organismal Studies Ruprecht-Karls-Universitat Im Neuenheimer Feld 230 69120 Heidelberg, Germany

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IMP issue regarding examples in web-ste: this is probably an expert level issue
by Adhikari, Badri (MU-Student) 03 May '12

03 May '12

Hello IMP users and experts, IMP looks attractive to us. Thank you for all the active support. I am using IMP available at http://salilab.org/imp/get.php?pkg=1.0/download/imp-1.0.tar.gz Two interesting questions: 1. The example code at http://salilab.org/imp/nightly/doc/html/atom_examples.html#charmm_forcefiel… and the example at PREFIX/modules/atom/examples/charmm_forcefield.py are supposed to do the same thing, but the code are not exactly same. The web code uses functions that my IMP does not understand. Is this some IMP version issue? 2. The first example, access dope, in http://salilab.org/imp/nightly/doc/html/atom_examples.html tries to pick up 1fdx.B99990001.pdb which I don't find anywhere in any of the folders. So, how is this example supposed to run? Looks like this has something to do with my issues as well. Most importantly, please, help me find a version of code for http://salilab.org/imp/nightly/doc/html/atom_examples.html#structure_from_s… that is similar to the examples provided in the installation package. It looks like my version of IMP does not have functions like IMP.atom.get_all_atom_CHARMM_parameters(). I am not familiar enough with IMP's language to convert the code myself. I am desperately working on trying to generate some models from sequences. --------------------------------------------------------------------------------------------------- In case you think that it is some installation issues, here are the details: --------------------------------------------------------------------------------------------------- My IMP installation log is at http://web.missouri.edu/~bap54/IMPinstall.log I have installed IMP in two of our servers. I don't have root access in these machines. IMP seems to be working well for normal use because I can run almost all of the examples and test files. The list of programs that I can run are attached as list_of_programs_that_run_smoothly.txt However, I get error while executing some programs. The list is attached in programs_that_throw_error.txt Also, I cannot run examples at http://salilab.org/imp/nightly/doc/html/atom_examples.html#structure_from_s…. The errors that I receive are attached in errors_in_the_website_examples.txt The most important example that I need to run is http://salilab.org/imp/nightly/doc/html/atom_examples.html#structure_from_s…. And the error that I get while trying to run this example is: $python structure_from_sequence.py Traceback (most recent call last): File "../imp_examples/structure_from_sequence.py", line 4, in ? topology = IMP.atom.CHARMMTopology(IMP.atom.get_all_atom_CHARMM_parameters()) AttributeError: 'module' object has no attribute 'get_all_atom_CHARMM_parameters' * I have already tried in 3 different machines with different configurations, with no luck at all. In one virtual machine, I installed with root access as well. I get the same error everywhere. The interesting thing is: once installed nothing is written to share/doc/imp, so I need to manually copy the example files needed (like example_protein.pdb) to run the examples. * All required tools are installed properly. I worked hard to install all boost libraries. All the required programs are installed correctly. This can be seen in the IMPinstall.log at http://web.missouri.edu/~bap54/IMPinstall.log * I have single copy of IMP installed. No multiple copies. Sincerely, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri BAP54(a)mail.missouri.edu<mailto:BAP54@mail.missouri.edu>

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Regarding IMP run
by subhomoi borkotoky 26 Apr '12

26 Apr '12

Dear all, I have the IMP to my Ubuntu 11.10 system. But I don't know how to use it even though I looked into IMP<http://salilab.org/imp/nightly/doc/html/namespaceIMP.html>Documentation . Please let me know how can I run the example scripts. what command should I write in terminal. Please help me. -- Thanks and Regards, -------------------------- SUBHOMOI BORKOTOKY, Centre for Bioinformatics Pondicherry University Pondicherry

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protein structure from amino acid sequences with IMP
by Adhikari, Badri (MU-Student) 13 Apr '12

13 Apr '12

Hello all, I am configuring IMP as non-root user in 3 of our redhat servers. My goal, for now, is to generate extended chain structures from amino acid sequences. I am able to run the following test examples that come with the IMP installation (credit goes to Ben and Daniel): i) test_charmm_atom.py ii) test_charmm_parameters.py iii) test_charmm_topology.py However, I am unable to run the examples in http://salilab.org/imp/nightly/doc/html/atom_examples.html#charmm_forcefield The most useful example for me would be structure-from-sequence. I get the following errors: $ python /rose/space1/imp/examples/structure-from-sequence.py Traceback (most recent call last): File "/rose/space1/imp/examples/structure-from-sequence.py", line 4, in <module> topology = IMP.atom.CHARMMTopology(IMP.atom.get_all_atom_CHARMM_parameters()) AttributeError: 'module' object has no attribute 'get_all_atom_CHARMM_parameters' $ python /rose/space1/imp/examples/charm-forcefield.py Traceback (most recent call last): File "/rose/space1/imp/examples/charm-forcefield-atom.py", line 10, in <module> ff = IMP.atom.get_heavy_atom_CHARMM_parameters() AttributeError: 'module' object has no attribute 'get_heavy_atom_CHARMM_parameters' $ python /rose/space1/imp/examples/molecular-hierarchy.py residue #16 of name "LYS"Added particle for 0...1 It looks like we need to supply the charm forcefield related files as well. I am wondering on the following questions as google does not seem to be helpful. (1) What file/files and parameter file/files do we need to run these examples? (2) Where do we place the files? (3) How to generate those files for the sequences that I have? Sincerely, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri BAP54(a)mail.missouri.edu<mailto:BAP54@mail.missouri.edu>

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protein structure generation from sequences with IMP
by Adhikari, Badri (MU-Student) 10 Apr '12

10 Apr '12

Hello all, We are working on a project in which we need to generate protein models from the amino acid sequences, using IMP. After reading on the IMP website, I can see that this tool primarily deals with different data sources. But, still I believe that this tool could be useful for us as we might need to add more information later. Have you ever tried generating models (like pdb files) with just amino acid sequences using IMP? If you have anything that could be helpful to me please help. Warm Regards, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri BAP54(a)mail.missouri.edu<mailto:BAP54@mail.missouri.edu>

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