Hi Manas Sule,
this is a bit more complicated:
For PyMOL, you usually calculate an electron density map covering your
molecule. As far as I understand PyMOL, the sigma is taken directly from
your input map.
For Coot, this is completely different. Coot tries to reconstruct from
your input map the complete map for the unit cell taking the
crystallographic symmetry into account (using it for displaying an
"infinite" map), and calculates the sigma from the unit cell map. This
already might be different to the sigma within the box that you used to
cover your molecule. However, if the reconstruction fails, either
because the symmetry of your map is wrong (i.e., P1), or the input box
is too small to allow reconstruction of the whole unit cell, the rest of
the unit cell is filled with "0", resulting in much smaller sigma values!
If this happens, you have to display the input map at a much higher
sigma level in Coot to get the same absolute electron density value and
thus appearance. Apparently, this is the case for your map.
To get the sigma value right, you should calculate a map covering either
the asymmetric unit with the right symmetry or covering the whole unit
cell. Then, run a peak search program, like CCP4 peakmax, or play
visually with the sigma value using that map - it should be same in
PyMOL and in Coot, then.
Best regards,
Dirk.
Am 06.12.11 15:12, schrieb Manas Sule:
Is there a difference in the sigma values assigned by pymol and coot????
I am able to see the density at 8 sigma in coot for the Fo-Fc map but
can go to maximum at 4.5 sigma in pymol after which it disappears....
On Mon, Dec 5, 2011 at 11:33 PM, Roger Rowlett <rrowl...@colgate.edu
<mailto:rrowl...@colgate.edu>> wrote:
I think the isomesh command will let you set whatever contour
level you wish, e.g.:
isomesh map, mymap.map, X.X, maparea
Where map is the name of the mesh object, mymap.map is the map
file name, X.X is the desired contour level, and maparea, is the
selection about which you would like to see the electron density
mesh. I haven't tested the contour limits, but it's larger than 10.
_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu <mailto:rrowl...@colgate.edu>
On 12/5/2011 12:49 PM, Manas Sule wrote:
I have tried that...but i can see the density in coot at even 8
sigma.. however the maximum i can go to in pymol is 4.5 simga on
a F0-Fc map
Can u suggest any method to see the same density at 6 sigma
Manas
On Mon, Dec 5, 2011 at 11:14 PM, Pete Meyer <pame...@mcw.edu
<mailto:pame...@mcw.edu>> wrote:
isomesh [mesh name], [map name], 6.0
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