Hi Michael,
I have an alternative way to visualize CNS composite omit maps with coot, using a modified version of Joel Bard's script, found on the coot FAQ page.
I'm pasting it below, the usage is:
cns-omit2coot.com omit.coeff model.pdb
where omit.coeff is the file you get by setting the write_coeff flag in the composite omit input file to "true".
This will generate an mtz file which you can open in coot with the "auto open mtz" command thus having the map displayed automatically.
Here's the script,
hth
Sebastiano
----------------------------------------------------------------------------
#!/bin/csh
if ( ${#argv} != 2 ) then
endif
set MAP1=`echo $1 | awk -F. '{print $1}'`
set CELL=`awk '/CRYST1/ {printf "%.3f %.3f %.3f %.3f %.3f %.3f\n", $2, $3, $4, $5, $6, $7 }' $2`
#have to go through all sorts of hoops because sometimes we might
#get P 21 and sometimes we might get P 1 21 1 for example
#sftools needs P21, can't handle P1211
#that being said - there must be a better way
set SYMM1=`awk 'BEGIN { FIELDWIDTHS="55 11 4" } /CRYST1/ {gsub(" ","",$2); printf "%s\n", $2}' $2`
pdbset xyzin $2 xyzout ${MAP1}_tmp.pdb << eof1
cell $CELL
spacegroup $SYMM1
eof1
set SYMM2=`awk 'BEGIN { FIELDWIDTHS="55 11 4" } /CRYST1/ {printf "%s\n", $2}' ${MAP1}_tmp.pdb`
echo $SYMM2
set SYMM=`grep "'${SYMM2}'" $CCP4/lib/data/symop.lib | awk '{print $4}'`
grep "'${SYMM2}'" $CCP4/lib/data/symop.lib | awk '{print $4}'
if( $? == 1 ) then
endif
echo "Space group is $SYMM"
if ( -e ${MAP1}.mtz ) then
endif
sftools << eof
read $1
cns
$CELL
$SYMM
END
W
P
R
SET LABELS
FOM
PHIC
SCALE
DELFWT
PHDELWT
WRITE ${MAP1}.mtz
STOP
eof
rm ${MAP1}_tmp.pdb
------------------------------------------------------------------------------------------------------
At 02:53 PM 11/2/2006 -0500, you wrote:
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
Hi Everyone,
I'm trying to convert a CNS composite omit map to CCP4 format for use in Coot, but when I attempt to do so using "xdlmapman" (version 1.0.4) I get an error message that says my map exceeds the maximum file size for reading into xdlmapman. Anyone know how to fix this? Reducing the map grid size is not desirable, although I do reallize that it may "fix" the problem. Seems like one should be able to increase the memory or something like that. Any help will be appreciated. Thanks.
MSM
_________________________________________________________________
Find a local pizza place, music store, museum and more then map the best route! http://local.live.com?FORM=MGA001
--
Sebastiano Pasqualato, PhD
IFOM
Istituto FIRC di Oncologia Molecolare
via Adamello, 16
20139 Milano
Italy
tel +39 02 574 303 325
fax +39 02 574 303 310
