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
