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shivesh kumar wrote:
Dear all,
I am trying to make good electron density picture in pymol for
publication.The problem is that I am unable to remove the extra
electron density of the symmetry related molecule which is coming
along with the region which I have chosen even at low sigma(1).What
should I do???thanx...
Shivesh
Hi Shivesh,
not sure what the equivalent command in Pymol is, but there must be a
carve option.
in Dino (www.dino3d.org) this would be the following:
load yourpdb.pdb -name myresidues
.myresidues new -name all -sel rnum=1:20,37:40
load mymap_in_ccp4_format.map -name ,fofc_cns
.fofc_cns new -name m -set center=[.myresidues.all[,level=1.5s,size=80
.fofc_cns.m renew -sel 3<>.myresidues.all
//here you define show only density which is in 3A around my defined atoms
you can write out a povray file with the option
write mysuperpicture.pov -v35
and then render it in povray to any desired resolution. Most Journals
require 600 dpi for your image, so for a 90 mm width image you'll need
2126 pixels and y pixels in height.
As somebody else pointed out it's a waste of time to calculate an image
multiple times. Go for the highest ever required resolution e.g. a
poster size image e.g. 10 inch @300 dpi save that image with the ending
_big or _large etc. For your presentation in Keynote or if you need to
use Powerpoint fire up Photoshop or any other tool e.g. image tricks (on
the Mac completely for free) and resize the image before adding it to
your presentation. Although most people still use 1024x768 for their
presentation time has moved on and we see more and more often higher
quality projectors which are capable of e.g. 1440x900 or even HD. But
you will most likely not use full size images in your presentations -
some decorative text and a title eat up a few pixels and you can safe
memory for your presentation in this way. Unless you have 2GB of RAM in
your laptop it will slow down your presentation if you add the original
images into your slides :-)
I wouldn't try to attempt removing extra or unwished density with
Photoshop, takes too much time and is often not very easy e.g. in stereo
figures.
One more thing I didn't mention. Rerun FFT and increase the grid to
something that looks nicer e.g. double the default values for your
setting. Of course the maps get larger and sometimes more difficult to
handle on a slow machine, but it's definitely worth the effort for a
nicer representation.
Good luck,
Jürgen
--
Jürgen Bosch
Howard Hughes Medical Institute and
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
