On 29/03/2020 10:04, Clemens Vonrhein wrote:
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:
That was not the plan - the Hydrogen atoms are used for interactions and
geometry optimization, not fitting to density.
I seem to have a hard time in dragging/pulling
things around as efficiently as if I was working without those
hydrogens.
Yes, me too.
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?
You are not using Coot 0.9, that, I would say, is mostly the problem.
FWIW, I want to make a YouTube video about how great it is to drag on
Hydrogen atoms for ligand fitting :-)
(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?
After you've added your ligand, you can, at the touch of a key-press set
the occupancy and remove the Hydrogen atoms.
Doing that automatically is a bit more difficult - I think that it's
doable, but I am not sure without digging into some code. Let's write
that script later.
(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 State"
* why is it not automatically stay in the working directory in the
same way as "File -> Save Coordinates -> Select Filename" or
"Draw -> Screenshot -> Simple"? I always have to go to the
directory explicitly in my file browser ... odd.
That is the Gtk way? I think now that even the coordinate dialog doesn't
start in the same directory.
* 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.
:-) I've done that too. I treat quick save as (Ctrl-S) state files are
treated as ephemeral. If I want to save it, I have to copy it.
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.
yes, I think --no-guano means no state script.
(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?
They are saved in the views save file. There is no key bindings to these
functions, but you could make one. A worked example might be educational?
Sorry for the delay - my folder didn't light up blue - I don't know why.
Regards,
Paul.
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