Hailiang Zhang wrote:
Dear Edward:
I generated two maps in the same way, load them in MAPMAN, then normalize
them and PE VA them. I think after normalization, the out put electron
density value at each atom should be equal to the sigma.
That was fast!
Yes, normalization should give the readout in sigma's.
Now the problem is, the output denisty values seems "squeezed" in the pdb
file format, so some lengthy values were not printed correctly. Do you
think there is a way we could avoid it?
To get around the squeezed format, you could first normalize and then
multiply the map by 0.1. (another mapman command)
Then the readout will be in units of 10 sigma.
Only if you have peaks >99 sigma, or <-9.9?
By the way, can MAPMAN automatically read all the paramters at the same
time so that I can run them at background? Or I have to enter MAPMAN
interface and type each comman one by one?
yes- something like:
#!/bin/csh -f
mapman -b <<eof
re m1 $MAPIN ccp4
norm m1
peak val m1 pdb.pdb
quit
eof
either put it in a file or just copy and paste the script into the window each
time
( -b tells mapman it is not interactive or something)
Look into peek sphere and cube also- might give better value for residue from CA if that
is what you are doing.
Thanks a lot!
Best Regards, Hailiang
If you already have your map, or if you can calculate the map in CCP4,
you can print out density at atoms using the Uppsala program MAPMAN,
function PEEK:
http://xray.bmc.uu.se/usf/mapman_man.html#S30
hth
Hailiang Zhang wrote:
Hi,
Phenix.model_vs_data offers a great function which prints out the sigma
level of the electron density at each residue or atom center. This is
very
useful comparing the relative density between two maps at the given
region, however, it is running a little bit slow. I am just wondering
whether some CCP4 subroutines also provides the similar function (didn't
find in overlapmap). Thanks a lot!
Best Regards, Hailiang
