AVER DOMAIN 1 should be followed by ROTA MATRIX and TRAN. What does "NCS
2 1" do? Is that in the documentation? I never saw that before, and I
don't see it now in blah/ccp4-6.1.3/doc/dm.doc . If you intend to refine
the NCS matrices, the instructions for that should be on the same line
with "AVER". If this were mine, I would try deleting the "NCS 2 1"
mystery keywords.
hope that helps,
Dan
David Schuller wrote:
CCP4 6.1.13
I am having trouble running dm. It complains with "Invalid keyword"
for each of my "AVER" lines, even though my script is modeled as
exactly as possible over the example in the documentation:
http://www.ccp4.ac.uk/dist/html/dm.html
---------My script:
#!/bin/csh -f
#
# single space group averaging
# as 2 separate domains
# also solv level and hist
#
#
dm \
HKLIN refm02.mtz \
HKLOUT dm1.mtz \
NCSIN1 A1.mask \
NCSIN2 A2.mask \
>dm1.out << 'EOF-squash'
MODE SOLV HIST AVER
COMBINE PERT
NCYCLE 50
SCHEME RES
SOLC 0.38
AVER DOMAIN 1
NCS 2 1
ROTA MATRIX 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
TRAN 0.0 0.0 0.0
AVER DOMAIN 1
ROTA MATRIX 0.10238 0.99474 0.00253 0.99468 -0.10234 -
-0.01160 -0.01128 0.00370 -0.99993
TRAN 55.22907 -55.55328 -47.53135
AVER DOMAIN 2
NCS 2 2
ROTA MATRIX 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
TRAN 0.0 0.0 0.0
AVER DOMAIN 2
ROTA MATRIX 0.08745 0.99616 0.00325 0.99616 -0.08743 -
-0.00509 -0.00479 0.00368 -0.99998
TRAN 55.30942 -54.99581 -47.74856
LABI FP=FP SIGFP=SIGFP PHIO=PHIC FOMO=FOM
LABO FDM=FDM PHIDM=PHIDM FOMDM=FOMDM
'EOF-squash'
#
-------- The output:
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<!--SUMMARY_END--></FONT></B>
<a name="dmdm"><h1>dm 2.1</h1></a>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
###############################################################
###############################################################
###############################################################
### CCP4 6.1: dm version 6.1 : ##
###############################################################
User: schuller Run date: 12/11/2010 Run time: 14:29:01
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.
<!--SUMMARY_END--></FONT></B>
</pre>
<a href="http://www.yorvic.york.ac.uk/~cowtan/dm/refs.html";>dm
reference:</a>
<blockquote>
K. Cowtan (1994),
dm: An automated procedure for phase improvement by density
modification.
Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 31,
p34-38.
</blockquote><p>
<a name="tocdm"><h2>Contents</h2></a>
<ul>
<li><a href="#commanddm">Command input</a>
<li><a href="#commentsdm">Comments</a>
<li><a href="#mtzindm">MTZ input</a>
<li><a href="#datachkdm">Data Checking</a>
<li><a href="#datascldm">Data Scaling</a>
<li><a href="#solmskdm">Solvent Mask</a>
<li><a href="#cyc0001dm">First Cycle</a>
<li><a href="#dataoutdm">Output</a>
</ul>
<a name="commanddm"><h2>Command Input</h2></a>
<pre>
Data line--- <a
href="/usr/local/xtal/ccp4_6.1.13_i386/html/dm.html#mode">MODE </a>
SOLV HIST AVER
Data line--- <a
href="/usr/local/xtal/ccp4_6.1.13_i386/html/dm.html#combine">COMBINE
</a> PERT
Data line--- <a
href="/usr/local/xtal/ccp4_6.1.13_i386/html/dm.html#ncycle">NCYCLE
</a> 50
Data line--- <a
href="/usr/local/xtal/ccp4_6.1.13_i386/html/dm.html#scheme">SCHEME
</a> RES
Data line--- <a
href="/usr/local/xtal/ccp4_6.1.13_i386/html/dm.html#solc">SOLCONT </a>
0.38
Data line--- <a
href="/usr/local/xtal/ccp4_6.1.13_i386/html/dm.html#average">AVERAGE
</a> DOMAIN 1
*** Warning
Invalid keyword
*** Warning
Invalid sub-keyword in position 2
*** Warning
Invalid sub-keyword in position 3
Data line--- <a
href="/usr/local/xtal/ccp4_6.1.13_i386/html/dm.html#average">ROTATION</a>
MATRIX 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
Data line--- <a
href="/usr/local/xtal/ccp4_6.1.13_i386/html/dm.html#average">TRANSLAT</a>
0.0 0.0 0.0
Data line--- <a
href="/usr/local/xtal/ccp4_6.1.13_i386/html/dm.html#average">AVERAGE
</a> DOMAIN 1
Data line--- <a
href="/usr/local/xtal/ccp4_6.1.13_i386/html/dm.html#average">ROTATION</a>
MATRIX 0.10238 0.99474 0.00253 0.99468 -0.10234 -0.01160 -0.01128
0.00370 -0.99993
Data line--- <a
href="/usr/local/xtal/ccp4_6.1.13_i386/html/dm.html#average">TRANSLAT</a>
55.22907 -55.55328 -47.53135
Data line--- <a
href="/usr/local/xtal/ccp4_6.1.13_i386/html/dm.html#average">AVERAGE
</a> DOMAIN 2
*** Warning
Invalid keyword
*** Warning
Invalid sub-keyword in position 2
*** Warning
Invalid sub-keyword in position 3
Data line--- <a
href="/usr/local/xtal/ccp4_6.1.13_i386/html/dm.html#average">ROTATION</a>
MATRIX 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
Data line--- <a
href="/usr/local/xtal/ccp4_6.1.13_i386/html/dm.html#average">TRANSLAT</a>
0.0 0.0 0.0
Data line--- <a
href="/usr/local/xtal/ccp4_6.1.13_i386/html/dm.html#average">AVERAGE
</a> DOMAIN 2
Data line--- <a
href="/usr/local/xtal/ccp4_6.1.13_i386/html/dm.html#average">ROTATION</a>
MATRIX 0.08745 0.99616 0.00325 0.99616 -0.08743 -0.00509 -0.00479
0.00368 -0.99998
Data line--- <a
href="/usr/local/xtal/ccp4_6.1.13_i386/html/dm.html#average">TRANSLAT</a>
55.30942 -54.99581 -47.74856
Data line--- <a
href="/usr/local/xtal/ccp4_6.1.13_i386/html/dm.html#labin">LABIN </a>
FP=FP SIGFP=SIGFP PHIO=PHIC FOMO=FOM
Data line--- <a
href="/usr/local/xtal/ccp4_6.1.13_i386/html/dm.html#labout">LABOUT
</a> FDM=FDM PHIDM=PHIDM FOMDM=FOMDM
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
dm: Input error (see above)
Times: User: 0.0s System: 0.0s Elapsed: 0:00
</pre>
</html>
<!--SUMMARY_END--></FONT></B>
