Hello,
I used this script once just to have a look
at some NMA-moved structures:
---
#!/bin/bash
if [ "$#" -ne "1" ] ; then
# 0 1
echo "usage: phaser_nma.sh INPUT.PDB"
exit 1
fi
name=`echo $1 | sed "s/\.pdb$//g"`
phaser << EOF
TITLE moved by some low frequency normal modes
MODE NMA
ENSEMBLE 1 PDB $1 IDENTITY 100
EIGEN WRITE ON
ROOT $name
NMAPDB MODE 7 MODE 8 RMS 0.5 FORWARD MAXRMS 3
EOF
---
It produced some PDBs (I did not tried MR
on them after, I was just curious about the NMA
induced moves).
Regards,
F.
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
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