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
>>>
>>
>>
>>
>
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