I just realized it's the "mapmask" program. Documentation at:
www.ccp4.ac.uk/dist/html/mapmask.html
The SCALE [SIGMA [c1 [c2]]] seems to be promising. I'll give that a
try.
Thanks,
-Andy
On 7/21/2010 10:34 AM, Andy Torelli wrote:
Kevin,
Thank you for the reply. Your suggestion works well.
As a follow-up question, I noticed that extending the map has changed
the sigma level that must be chosen in PyMOL in order to match the view
in COOT. Is this because the sigma level is defined based on the
distribution of electron density and by changing the extent of the map I
have changed the distribution of electron density peaks?
If so, I'd like to normalize the new map to the original map in order
to get the sigma contouring to match. I expect the program
documentation may help with this. Do you know which program is used for
the "Extend a map/mask file" function you mentioned?
Thank you very much for your time,
-Andy
On 7/21/2010 10:02 AM, Kevin Cowtan wrote:
The ccp4 program mapmask does what you want. From ccp4i, select:
Map and Mask Utilities/Edit-Rotate Map& Mask/Extend a map-mask file
Andy Torelli wrote:
Hi everyone,
I produced an NCS-averaged map in COOT that I would like to output
and load into PyMOL to make a figure. The map loads successfully into
PyMOL, but of course the density only covers a portion of my molecule
that is fully covered when viewed in COOT. I know/believe this is
because COOT generates maps with electron density that is only defined
explicitly for certain regions of the unit cell and dynamically displays
electron density (based on symmetry) for the regions that are not defined.
I e-mailed the PyMOLbb regarding this issue some time ago and
learned that symmetry-expansion was in the works, but it doesn't seem to
be working in version 1.2r3pre. I was wondering if there is any way to
tell COOT to output a map with electron density values explicitly
defined for a given region (e.g. a protein chain, defined region of
space or a ligand/ion).
Things I've tried:
- making a mask (Extensions->Maps->Mask Map by Atom Selection) and
loading that map into PyMOL based on a previous post suggestion, but the
(lack of) coverage was the same.
- loading the map into MAPMAN and converting to a different file
format. The map was too big to be loaded and I'm not sure if I can
re-define the area for which electron density will be defined.
Thanks for your help and suggestions,
-Andy Torelli
