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> -- ======================================================================= All Things Serve the Beam ======================================================================= David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [log in to unmask]