Paul, OK maybe I did a bit of loose interpretation of the documentation on 'Extensions -> Modelling -> Replace Residue...' and did a bit of extrapolation to '... -> Monomer from dictionary' but whether you intended it or not, it certainly works in the way I described and very handy it is too! It's great watching a programmer's face when you tell him that his software has nice features that weren't intended - almost like machine intelligence! Anyway, we don't use ccp4i a great deal (at least it's not linked with our LIMS), and a soft link would require changes to be made to the Coot installation which is what I'm trying to avoid, and anyway I've no idea if soft links work in the same way in Windows (I believe they're called 'shortcuts') as in Linux. Specifically it would require the existing files in 'examples' (which admittedly only consist of an Rnase MTZ & PDB file) to be moved to my personal area each time I install a new Coot. Somewhere in your software you must either have set an environment variable or you have the 'examples' directory hard-wired for the 'Replace Residue' and 'Monomer from dictionary' functions (and maybe others too), or maybe you're even searching the whole installation tree for CIF files, otherwise how does it know where to find my files? I certainly haven't told it anywhere that they're in the 'examples' directory.
If there isn't such an environment variable already defined, I can live with that (for now ;-) ). Cheers -- Ian On Thu, Mar 4, 2010 at 1:57 PM, Paul Emsley <[email protected]> wrote: > Ian Tickle wrote: >> >> Quick question: is there an environment variable in WinCoot which >> points to the directory where 'Extensions->Modelling->Monomer from >> dictionary' gets its files? This is the '%COOT_PREFIX%/examples' >> directory by default. I couldn't see anything relevant in the >> documentation (e.g. section 1.5 'Environment variables'). >> >> If I start runwincoot.bat from a link I can specify a 'Start in' >> directory in Properties to be anywhere I like, but I'd like to do the >> same from inside runwincoot.bat. This will save me having to copy my >> private collection of monomer dictionaries every time a new version of >> Coot comes along. >> >> >> > > I had to look up what this function actually does :) > > OK, so it presumes that you have read in a cif file that contains > coordinates typically (a fragment of) the Chemical Component Library. > That's why there is no dictionary, because the data come from your file. So > much I guess you know. > > Perhaps I am misunderstanding you, but it seems that you suggest that if you > put cif files COOT_PREFIX/examples and use > > Extensions->Modelling->Monomer from dictionary... > > then coot will automatically load files from that directory? That is > suprising/cool/undocumented. > > I don't know about COOT_PREFIX/examples (perhaps that is Bernhard's > addition). Thus, I don't understand the need for copying cif files. If I > had a directory with a personal collection of cifs, I'd use a soft link or a > ccp4i project. > > Paul. >
