Re: [COOT] how to set the refinement map

[Seth Harris]

Thanks Paul,

Actually I do have a map button. But I'd rather write something in a script
somewhere once than click the button and confirm the click EVERY time I
start the program!

Hmmm, I had tried the (set-imol-refinement-map 1) in my .coot but obviously
the problem was the map did not yet exist. So close! A monkey in the
wrench... but it works beautifully if I put the (set-imol-refinement-map 1)
into a coot_refinement_map.scm file and then my script adds the --script
coot_refinement_map.scm option to the command line launching the program
(at the end, I guess, to be sure the map is already loaded by then).

A small thing, but it felt time to get it right!

Much gratitude (especially after building up a few new proteins and feeling
that tangible time savings from coot's nice tools and keyboard shortcuts!),
Seth



On Mon, May 10, 2010 at 3:23 PM, Paul Emsley paul.ems...@bioch.ox.ac.ukwrote:

 Seth Harris wrote:

 Hello,

 After what felt like a reasonable amount of poking about, I can't find how
 to set the refinement map (yes, I tried 'set-refinement-map') although I did
 find that guess-refinement-map returns a good guess but doesn't seem to
 stop the Oops! Must Select Map to fit to! box from bothering me.


 Wow.  It now strikes me that this is a pain if you don't have a Map
 button - which I guess you don't.  Which makes me think that you are using
 the gtk1 version.  OK, time for that to die out.


  (It could at least open the map selection dialog like what happens when
 you do Validate  Check/Delete waters without first specifying a map.) Seems
 a bit perverse to be able to determine I very likely want to refine against
 map 1, but not to actually set it for me. I am usually launching coot from a
 script-generated command, so my maps are always in the same order and I can
 reliably set the refinement map to imol #1, so I'd like to do that on
 startup.


 In that case, I would have thought that (set-imol-refinement-map nnn) would
 do the trick (nnn is 1, in this case presumably).

 (you can only do that if map number nnn exists at the time).


  Is there any real danger in coot just going ahead with a guessed
 refinement map instead of the halting dialog? (Given the subsequent
 confirmation screen and the possibility to undo.) Or likely I am missing
 something everyone else has figured out?


 Maybe most others are using gtk2 version.

 Paul.

Re: [COOT] how to set the refinement map

[Paul Emsley]

Seth Harris wrote:


Actually I do have a map button.


Hmm... I see.

But I'd rather write something in a script somewhere once than click 
the button and confirm the click EVERY time I start the program!


OK, I'm not understanding you then.  If you start from fresh and you 
read in more than one map before refining anything, then of course Coot 
will not know which map to use.  Understandable it seems to me.  And 
typically one does not do that very often - certainly not every time.


If you use the state script, the state script contains the setting for 
the refinement map.


If you write your *own* script then you can easily set the refinement 
map as you read in your interesting mtz file:


(set-imol-refinement-map (make-and-draw-map x.mtz 2FOFCWT 
PH2FOFCWT  0 0))




Hmmm, I had tried the (set-imol-refinement-map 1) in my .coot but 
obviously the problem was the map did not yet exist.


indeed.

So close! A monkey in the wrench... but it works beautifully if I put 
the (set-imol-refinement-map 1) into a coot_refinement_map.scm file 
and then my script adds the --script coot_refinement_map.scm option 
to the command line launching the program (at the end, I guess, to be 
sure the map is already loaded by then).


That will do then?



A small thing, but it felt time to get it right!


It is not clear to me if you need to get it right or you have 
succeeded in getting it right...


Paul.