Forgot to also post this response to the BB. Randy
Begin forwarded message: > From: Randy Read <rj...@cam.ac.uk> > Date: 25 June 2010 12:59:12 GMT+01:00 > To: Yong Y Wang <wang_yon...@lilly.com> > Subject: Re: [ccp4bb] error in running Phaser NMA mode > > Dear Yong, > > Sorry about that! I suspect the example script in the documentation wasn't > updated when the syntax of the EIGEN command changed. You need to add a > subkey "READ", i.e. > > EIGEN READ test_nma.mat > > Actually, unless you're planning on doing a series of normal modes > calculations with different combinations of the lowest frequency modes, it's > easier to run a single job generating the PDB files, without writing the > eigenvectors out. > > You should also note that the example just shows, for illustration, that you > can combine any set of the lowest frequency modes. Modes 1-6 are > uninteresting (just rigid-body rotations and translations), and the first > thing you would normally try is just varying mode 7, or modes 7+8 or possibly > modes 7-9. You would only get to combinations of pairs like 7 and 10 if you > were doing a more exhaustive search of all the possibilities. > > I'll correct the documentation as soon as possible. > > All the best, > > Randy Read > > On 24 Jun 2010, at 19:12, Yong Y Wang wrote: > >> I am getting an error in running Phaser in NMA mode based on the usage in >> the Phaser document. >> <pre> >> <B><FONT COLOR="#FF0000"> >> <html><!-- CCP4 HTML LOGFILE --> >> <!--SUMMARY_BEGIN--> >> >> ##################################################################################### >> ##################################################################################### >> ##################################################################################### >> ### CCP4 PROGRAM SUITE: Phaser 2.1.4 ### >> ##################################################################################### >> User: rx36953 >> Run time: Thu Jun 24 14:01:32 2010 >> Version: 2.1.4 >> OS type: linux >> Release Date: Thu Nov 13 10:53:32 2008 >> >> If you use this software please cite: >> "Phaser Crystallographic Software" >> A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni & >> R.J. Read >> J. Appl. Cryst. (2007). 40, 658-674 >> >> <!--SUMMARY_END--> >> <!--END--></FONT></B> >> <!--SUMMARY_BEGIN--> >> >> ************************************************************************************* >> *** Phaser Module: PREPROCESSOR 2.1.4 *** >> ************************************************************************************* >> >> >> <!--SUMMARY_END--> >> ENTER KEYWORD INPUT FROM FILE OR FROM STANDARD INPUT >> <!--SUMMARY_BEGIN--> >> TITLe beta normal mode analysis pdb file generation >> MODE NMA >> ENSEmble test PDB protein_A_CRYST.pdb IDENtity 100 >> ROOT test_nma_pdb # not the default >> EIGEn test_nma.mat >> NMAPdb MODE 7 MODE 10 RMS 0.5 FORWARD >> <!--SUMMARY_END--> >> -------------------- >> EXIT STATUS: SUCCESS >> -------------------- >> >> CPU Time: 0 days 0 hrs 0 mins 0.00 secs (0.00 secs) >> Finished: Thu Jun 24 14:01:32 2010 >> >> </pre> >> </html> >> <pre> >> <B><FONT COLOR="#FF0000"> >> <html><!-- CCP4 HTML LOGFILE --> >> >> ##################################################################################### >> ##################################################################################### >> ##################################################################################### >> ### CCP4 PROGRAM SUITE: Phaser 2.1.4 ### >> ##################################################################################### >> User: rx36953 >> Run time: Thu Jun 24 14:01:32 2010 >> Version: 2.1.4 >> OS type: linux >> Release Date: Thu Nov 13 10:53:32 2008 >> >> If you use this software please cite: >> "Phaser Crystallographic Software" >> A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni & >> R.J. Read >> J. Appl. Cryst. (2007). 40, 658-674 >> >> <!--END--></FONT></B> >> >> <!--SUMMARY_BEGIN--> >> ************************************************************************************* >> *** Phaser Module: NORMAL MODE ANALYSIS 2.1.4 *** >> ************************************************************************************* >> >> TITLe beta normal mode analysis pdb file generation >> ENSEmble test PDB protein_A_CRYST.pdb IDENtity 100 >> ROOT test_nma_pdb # not the default >> EIGEn test_nma.mat >> >> <B><FONT COLOR="#FF8800"> >> -------------------------------- >> SYNTAX ERROR: Use READ or WRITE >> -------------------------------- >> </FONT></B> >> >> <!--SUMMARY_END--> >> -------------------- >> EXIT STATUS: FAILURE >> -------------------- >> >> CPU Time: 0 days 0 hrs 0 mins 0.00 secs (0.00 secs) >> Finished: Thu Jun 24 14:01:32 2010 >> >> </pre> >> </html> >> >> Anyone knows how to use the NMA mode? Is the document not up-to-date? >> >> Thanks, >> >> Yong > > ------ > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: + 44 1223 336500 > Wellcome Trust/MRC Building Fax: + 44 1223 336827 > Hills Road E-mail: rj...@cam.ac.uk > Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
