Re: [COOT] problems of version 0.6

2009-05-06 Thread Maia Cherney
Thank you, Bernhard The buttons I like to change are internally assigned. For example, I would prefer to use key b to move backwards through residues of a chain. Right now you need two hands for that (shift-space). To drag the map, again, you need two hands (ctrl-left mouse). I would like to

Re: [COOT] merge water chains

2009-05-06 Thread Bernhard Lohkamp
Since I supposedly mentioned this (and I have made a script)... there is a python function to do so: use merge_solvent_chains(imol) or merge_water_chains(imol) alternatively you have to do it by hand, i.e. using Calculate-Change Chain ID (use residue range). B P.S. no corresponding scheme

Re: [COOT] problems of version 0.6

2009-05-06 Thread Bernhard Lohkamp
Thank you for your reply. The version number is 0.6-pre-1. .. and the revision number? Using $coot --version you get more information (which is useful for us, e.g. revision number, python yes or no). Also, in the Edit menu of this version I could not find preferences. I definitely need

Re: [COOT] RSR exploding RNA

2009-05-06 Thread Paul Emsley
CK wrote: I think perhaps I should clarify what I've been doing. I've been refining my structure using phenix.refine and had reached a fairly satisfactory point with suitably low R-factors (21/25) and very reasonable RMSDs for bonds and angles. At this point I ran my structure through the

Re: [COOT] RSR exploding RNA

2009-05-06 Thread CK
Fortunately, the molprobity server has an option for converting your PDB file back to v2.3 and this seems to have fixed almost everything. My RNA is no longer explosive and the hydrogens in the protein portions don't go wandering off. The only remaining issue is that the hydrogen on the