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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