Dear Thiyagarajan,
To get the peak heights, I would run a peak search on your final electron
density map, load the pdb file with the peaks along with the atomic model and
click on the peak closest to your spot of interest. If you use the program
peakmax, the peakheight is written in the B-factor position.
Concerning water/sodium/magnesium/chlorine, if refinement does not give
difference peaks you have to use common sense:
-Is the B-factor of the unknown ion similiar to B-factors in the neighborhood?
If it is similar, your choice of ion could be right, if it is much higher or
lower, you should try other ions.
-Are there charged residues nearby which would prefer to bind an ion of
opposite charge?
-What are the distances to nearby atoms (e.g. do they match the expected
hydrogen bond/contact distances for a particular ion or water?)
-Does the observed coordination geometry match that of the ion of your choice?
At 1.5 A resolution, you should be able to make a reasonable guess.
Good luck!
Herman Schreuder
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of
S. Thiyagarajan
Sent: Monday, April 20, 2009 12:48 PM
To: [email protected]
Subject: [ccp4bb] peak height at mouse click
Dear CCP4 users
Is there any easy way of calculating the peak height / number of electrons at a
given position, say a mouse click point in coot.
Is there any formula to calculate the number of electrons based on sigma level
and peak height, as given in difference map peaks in coot.
I have some peaks in my map which take water or sodium/magnesium or chlorine
atom with out giving out any positive or negative density upon further
refinement.
The asymmetric unit has about 425 residues and the data resolution is 1.5A.
Thanks and regards
S. Thiyagarajan
Department of Cell and Organism Biology
Lund University
Sölvegatan 35
Lund, Sweden
