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[ccp4bb]: map calculations
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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 :
##########################################################
##########################################################
##########################################################
### CCP PROGRAM SUITE: OVERLAPMAP VERSION 3.5: 18/02/99##
##########################################################
User: talal Run date: 27/11/00 Run time:17:38:19
Please reference: Collaborative Computational Project, Number 4. 1994.
"The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst.
D50, 760-763.
as well as any specific reference in the program write-up.
(Q)QOPEN allocated # 1
User: talal Logical Name: MAPIN1
Status: READONLY Filename: junk1.map
File name for input map file on unit 3 : junk1.map
file size =10561104 ; logical name
MAPIN1
Number of columns, rows, sections ............... 110 100
240
Map mode ........................................ 2
Start and stop points on columns, rows, sections 0
109 0 99 0 239
Grid sampling on x, y, z ........................ 100 240
110
Cell dimensions ................................. 68.73500
101.12900 42.53300 90.00000 90.00000 90.00000
Fast, medium, slow axes ......................... Z
X Y
Minimum density ................................. 0.00000
Maximum density ................................. 6.20626
Mean density .................................... 0.25032
Rms deviation from mean density ................. 0.38568
Space-group ..................................... 1
Number of titles ................................ 1
Titles :
A run of SFALL
(Q)QOPEN allocated # 2
User: talal Logical Name: MAPIN2
Status: READONLY Filename: fw_2fo-fc.map
File name for input map file on unit 4 : fw_2fo-fc.map
file size = 2685344 ; logical name
MAPIN2
Number of columns, rows, sections ............... 110 100
61
Map mode ........................................ 2
Start and stop points on columns, rows, sections 0
109 0 99 0 60
Grid sampling on x, y, z ........................ 100 240
110
Cell dimensions ................................. 68.73499
101.12900 42.53300 90.00000 90.00000 90.00000
Fast, medium, slow axes ......................... Z
X Y
Minimum density ................................. -1.38198
Maximum density ................................. 3.30944
Mean density .................................... 0.00026
Rms deviation from mean density ................. 0.37535
Space-group ..................................... 18
Number of titles ................................ 1
Titles :
Map from fft
***End of section does not match.***
OVERLAPMAP: Fatal Error
OVERLAPMAP: Fatal Error
--
Talal Gariani phone office: +46-90-785-6795
UCMP lab: +46-90-785-6794 / -6783
Umea University FAX: +46-90-778 007
S-901 87 Umea, Sweden e-mail: talal.gariani@ucmp.umu.se