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*To*: Talal Gariani <talal.gariani@ucmp.umu.se>*Subject*: Re: [ccp4bb]: map calculations*From*: "Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>*Date*: Mon, 27 Nov 2000 17:08:21 +0000*CC*: ccp4bb@dl.ac.uk*Organization*: Structural Biology Lab. , Dep. Of Chemistry, University of York*References*: <Pine.SOL.3.96.1001124111211.6624A-100000@post.its.mcw.edu> <3A2290F9.BEAF3860@ucmp.umu.se>*Reply-To*: E.Dodson@ysbl.york.ac.uk*Sender*: owner-ccp4bb@dl.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

**References**:**Re: [ccp4bb]: maps***From:*Paul Hubbard <phubbard@post.its.mcw.edu>

**[ccp4bb]: map calculations***From:*Talal Gariani <talal.gariani@ucmp.umu.se>

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