cool!
Daniel - I assume that most people just gave up on reading this entire tread (I know I almost did ...) , as it is too long with many brunches that were never resolved. It would be a good idea to send on Monday a remainder with the topics for discussion and the proposed solutions, even better as a wiki page so others can add their solutions as well.
I will add the low-res perspective once you will post your ideas :)
Keren. On Oct 8, 2009, at 9:59 PM, Daniel Russel wrote:
> > On Oct 8, 2009, at 9:21 PM, Dina Schneidman wrote: > >> completely agree. these are resolved much faster by talking :) > I'm not entirely sure I agree (witness the last developers > meeting :-). But am ambivalent. It could be structured better though > which would help things converge faster. > > That said, we have several outstanding questions: > - do we have PROTEINs which can contain CHAINs or just PROTEINS > (which are chains). This we should probably just find something > authorative and use it. I don't much care either way. > > - what are the most useful things for one or more read_pdb functions > to return? For this we should come up with standard usage cases. I > would propose a couple here: > - someone is running through lots of PDB files and wants to load > one protein from each file. To do this, it would be nice to have a > function which loads a protein from the pdb and returns a hierarchy > containing only that protein. Whether this protein has one or more > chains depends on the answer to the first question > - load the whole structure from a pdb complete with many proteins > and ligands and other molecules. For this it is useful to be able to > read everything from one PDB model record. > - take one piece of the pdb and use it (such as a chain or > ligand). For this it is nice not to have to dissect a hierarchy. > - load a bunch of model records from a single pdb and deal with > all the molecules in each record. > > Any other cases? Think about it and we will discuss it on Tuesday. > > A proposal to think which handles the above cases is: > - one function which reads a protein from a pdb > - one function which reads everything from one model record in a pdb > and returns it in a list/vector > > > Good night. > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev