A pdb file (biological assembly of a virus capid) has 24 model and each model has 3 chains A,B and C. I am interested to keep only those models which are in contact with chain A of model 1. "Contact" means if distance between any two atoms is less than 4 Angstroms. Though I did with some python scripts, I am interested to know whether there is any handy way to do this job. Thank you for help.
You can try Chimera visualiser, there you can delete the chains which are beyond certain rmsd
Any molecular visualization software (PyMol, VMD, UCSF Chimera, etc.) allows making complex selections along the lines of: every atom/molecule/residue within X Angstroms of any of/all of atom/set of atoms/residue/molecule. I believe this can be done across multiple models in a PDB file, though I've never tried that. You'll need to learn the selection language for the particular software you want to use.
If you want to do this across many PDB files (e.g. you want to split every model into a separate file and ask in what fraction of them is a contact made), you'll either have to repeat the rather tedious "by hand" selection process or automate it through scripting. Both PyMol and VMD (and probably Chimera as well, though I've never used it) can be used in non-GUI mode to run scripts of this sort. Both can be scripted in python and in their own selection language (though this has more limited capabilities), and VMD can be scripted in Tcl/Tk. You'll have to learn the corresponding API, which can be complicated.
You can also script this using any of a number of molecular modeling software packages that are not tied to molecular visualization. The CSB Toolbox (https://csb.codeplex.com) and ProDy (http://prody.csb.pitt.edu) are two python packages that immediately come to mind, though there are plenty more in a variety of languages.
Thank you all for your suggestions. I was just looking a kind of 'cheap, dirty and quick' approach though I have used some visualization softwares and codes to solve my problem.
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