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<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'>Hi<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'>I have been using <span class=SpellE>g_anaeig</span> with –<span
class=SpellE>extr</span> to generate a range of structures. As you know the set
is centered on an average structure and contains configurations extrapolated along
a given eigenvector.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'>I can do this for the first two eigenvectors, and I get
two sequences.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'>What I would really like to do now is generate a single
matrix of structures as follows<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span lang=FR style='font-size:
10.0pt;font-family:Verdana;mso-ansi-language:FR'>Structure(x,y)=average
structure + (x*eigenvector1) + (y*eigenvector 2)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span lang=FR style='font-size:
10.0pt;font-family:Verdana;mso-ansi-language:FR'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'>Where x and y are in the range -2,-1<span class=GramE>,0,1,2</span>
(or some scaled equivalent). Looking at it this way the current output of <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'><o:p> </o:p></span></font></p>
<p class=MsoNormal><span class=SpellE><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana'>g_anaeig</span></font></span><font
size=2 face=Verdana><span style='font-size:10.0pt;font-family:Verdana'> –<span
class=SpellE>extr</span> –first 1 –last 2 etc<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'><o:p> </o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana'>is</span></font></span><font
size=2 face=Verdana><span style='font-size:10.0pt;font-family:Verdana'> simply
the central row and central column of my matrix : [(-2:2),0]<span
style='mso-spacerun:yes'> </span>and [0,(-2:2)]. I want [(-2:2)<span
class=GramE>,(</span>-2:2)]<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-left:36.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo1;
tab-stops:list 36.0pt'><![if !supportLists]><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana;mso-fareast-font-family:Verdana;
mso-bidi-font-family:Verdana'><span style='mso-list:Ignore'>a)<font size=1
face="Times New Roman"><span style='font:7.0pt "Times New Roman"'>
</span></font></span></span></font><![endif]><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana'>Am I right in thinking that <span
class=SpellE>g_anaeig</span> cannot yet do this 2 eigenvector scan.<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:36.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo1;
tab-stops:list 36.0pt'><![if !supportLists]><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana;mso-fareast-font-family:Verdana;
mso-bidi-font-family:Verdana'><span style='mso-list:Ignore'>b)<font size=1
face="Times New Roman"><span style='font:7.0pt "Times New Roman"'>
</span></font></span></span></font><![endif]><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana'>If so: I have looked at the source
code for <span class=SpellE>g_anaeig</span> and am rather daunted to fiddle
with it. If anyone would be interested in implementing this scan I would be
very interested to try it. (Cheeky, I know!).<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:36.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo1;
tab-stops:list 36.0pt'><![if !supportLists]><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana;mso-fareast-font-family:Verdana;
mso-bidi-font-family:Verdana'><span style='mso-list:Ignore'>c)<font size=1
face="Times New Roman"><span style='font:7.0pt "Times New Roman"'>
</span></font></span></span></font><![endif]><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana'>Otherwise I think <span
class=SpellE>Im</span> going to have to extract the eigenvector data from <span
class=SpellE>eigenvec.trr</span> and make up my own analysis. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'>Any (polite!) comments welcome.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'>Paul<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana;mso-no-proof:yes'>Dr Paul Barrett</span></font><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt;mso-no-proof:yes'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana;mso-no-proof:yes'>[**PLEASE NOTE NEW PHONE NUMBER**]</span></font><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt;mso-no-proof:yes'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana;mso-no-proof:yes'>Laboratory of Molecular Biophysics</span></font><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana;mso-no-proof:yes'>Department of Biochemistry</span></font><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><st1:place><st1:PlaceType><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana;mso-no-proof:yes'>University</span></font></st1:PlaceType><font
size=2 face=Verdana><span style='font-size:10.0pt;font-family:Verdana;
mso-no-proof:yes'> of </span></font><st1:PlaceName><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana;mso-no-proof:yes'>Oxford</span></font></st1:PlaceName></st1:place><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><st1:City><st1:place><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana;mso-no-proof:yes'>Oxford</span></font></st1:place></st1:City><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana;mso-no-proof:yes'>OX1 3QU</span></font><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt;mso-no-proof:yes'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana;mso-no-proof:yes'>Tel 01865 275369</span></font><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana;mso-no-proof:yes'>Fax 01865 275182</span></font><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt;mso-no-proof:yes'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt;mso-no-proof:yes'><a href="mailto:barrett@biop.ox.ac.uk"><font size=2
face=Verdana><span style='font-size:10.0pt;font-family:Verdana'>barrett@biop.ox.ac.uk</span></font></a><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt;mso-no-proof:yes'><a href="mailto:hellopaul1@hotmail.com"><font size=2
face=Verdana><span style='font-size:10.0pt;font-family:Verdana'>hellopaul1@hotmail.com</span></font></a></span><o:p></o:p></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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