Forgot to also post this response to the BB.
Randy
Begin forwarded message:
> From: Randy Read <[log in to unmask]>
> Date: 25 June 2010 12:59:12 GMT+01:00
> To: Yong Y Wang <[log in to unmask]>
> 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: [log in to unmask]
> 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: [log in to unmask]
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
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