Re: [ccp4bb]: map calculations

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***

Talal Gariani wrote:
> 
> ***  For details on how to be removed from this list visit the  ***
> ***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***
> 
> Hi there,
> I have a problem (explains why I am sending this cry for help).
> I am currently trying to find out water molecules that are in binding
> distance to my protein of interest.
> I used a combination of sfall, fft and overlapmap scripts to be able
> identify those molecules. Then comes the hitch. When I calculate the map
> from my pdb file, I end up with a map calculated in space group P1 (I
> have symm 18). I input the following grid of 110 240 100 to obtain a
> thin enough slicing of my map.
> Running fft to get the difference maps, I include the same grid as used
> for sfall (110 240 100), I get my maps (space group 18) and then try to
> run overlapmap to make a mask map. This is when I get the following
> error:
>   ***End of section does not match.***
> the section from my fc map is  110  100  240 (space group 1) and those
> from my difference maps is  110  100   61 (space group 18).
> I see that I have a discrepancy on the Y axis, however how can I get
> them to match ?Would this mean that I would have to change the grid
> whilst doing a fft, but then this would result in nasty problems when I
> will try to compare the maps. If I run fft in space group P1, then I
> will end up with incomplete data.....
> anyone has a suggestion(s)...?
> 
> Cheerios!!!
> 
> PS: here is a print out of the overlamap log :


 Use mapmask to trim the P1 map to the same volume as the SG18 one:
viz:  XYZLIM 0 109    0   99    0   60 and change the SYMMetry 
SYMM 18
END

 Then you will be OK 
Eleanor