Dear all, given that nearly everything seems to be possible with Coot (apart from making a good cup of coffee ... but who knows), maybe someone could help me out here.
(1) When working with a hydrogenated molecule (not riding hydrogens!) in Coot it seems as if the real-space refinement takes those full-occupancy hydrogens into account during fitting as if they are normal atoms: I seem to have a hard time in dragging/pulling things around as efficiently as if I was working without those hydrogens. So is there a way of telling Coot to have those hydrogens as "riding hydrogens" during real-space refinement, i.e. ignore them for the actual refinement but move them along with the rest of the heavy atoms during fitting? I don't want to delete them first and then having to add them back on (which will be tricky for those parts of the structure where I modified the model). Also: "over-dragging" a heavy atom leaves those hydrogens back - which makes it feel much less effective e.g. for methyl groups and such. Or am I missing something? (2) Another thing maybe for the script gurus: have you ever felt the need to a simplification of adding buffer molecules? I want to add e.g. DMS and then have the following steps done automatically for me at the same time: remove hydrogens, merge with current molecule, remove the initialy added molecule and set occ of the new residue to 0.99 (to have a marker for subsequent occupancy refinement). This must be a fairly common sequence of commands for a lot of people - so maybe someone has already put that functionality somewhere? (3) I'm often caught out when trying to save a certain view (to later produce nicely aligned pictures e.g. of refinement progress) when using "File -> Save Stave" * why is it not automatically stay in the working directory in the same wy as "File -> Save Coordinates -> Select Filename" or "Draw -> Screenshot -> Simple"? I always have to go to the directory explicitly in my file browser ... odd. * after saving the state file I have to remember to save the state again into a differently named file before exiting: otherwise the default state file created (normally) by coot will overwrite the last explicitly saved state file ... losing what I was trying to achieve along the way. There are also some problems with --no-state-script and/or --no-guano (need to check again) that prevents me from saving a state explicitely in the first place. (4) are there already existing key-bindings for adding, editing and deleting 3D annotations? And how do I automatically save/load those upong startup/exiting? Sorry if these questions are already answered somewhere else ... any pointer/hint would be very much apreciated! Cheers Clemens -- *-------------------------------------------------------------- * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * Global Phasing Ltd., Sheraton House, Castle Park * Cambridge CB3 0AX, UK www.globalphasing.com *-------------------------------------------------------------- ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1