On 15 May 2002, Gareth Stockwell wrote: > First let me say that PyMol is the most useful and powerful open-source > software I have come across.
> 1. There appears to be a bug in the isomesh routine (see comment > submitted to the Sourceforge bugtracker). I haven't tried the latest > CVS version though. Okay, thanks for the heads-up. > 2. Some suggestions for improvements to PyMol: Great! > a) Automatic creation of sub-objects for protein structures > After loading in a structure (e.g. a PDB protein file), would it be > possible to have the option of automatically breaking it into an object > for each chain, and one for each ligand present in the structure, so > that the user could quickly click on/off the required components? > (This could be extended into a heirarchical tree-structure, in which > chains, residues, atoms would all be available via the object list on > the control panel) Something like this can be easily constructed using a Python program with the API. I don't have time to do this myself right now, but I'd encourage you (or someone else) to attempt it and then submit it for inclusion. > b) Graphical summary of density distribution for map data > A feature which popped-up a histogram of density values, which could > alter an isomesh contour value by clicking on it, would be extremely > useful. Hmm, neat idea! Very easy to implement, but how to do it with the current GUI isn't so obvious... > Also, is there a way to have a '.pymolrc' file containing commands which > are run whenever PyMol starts? Absolutely, all you need to do is create ".pymolrc" and place it in your home directory. Alternatively, you can instead create ".pymolrc.py" which contains actual Python code instead of just PyMOL commands. Cheers, Warren
