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Thanks Eric!!<br>
It works very well!! Is it also possible to save the alignment file
without omitting the all-gap columns?<br>
<br>
Thanks again<br>
Tiziano<br>
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<p class="MsoNormal" style=""><span
style="font-size: 10pt;">+++++++++++++++++++++++++++++++++++++<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt;">Tiziano <span
class="SpellE">Tuccinardi</span>, <span
class="SpellE">PhD</span><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt;">Dip. Scienze
Farmaceutiche<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt;">Via <span
class="SpellE">Bonanno</span> 6,<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt;">56126 PISA<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt;">Tel ++39 050 2219595<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt;">Fax ++39 050 2219605<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt;">E-mail <a
href="mailto:tuccinardi@farm.unipi.it">tuccinardi@farm.unipi.it</a><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt;"><a
href="http://www.mmvsl.farm.unipi.it/staff/tiziano-tuccinardi/">http://www.mmvsl.farm.unipi.it/staff/tiziano-tuccinardi/</a><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt;"><o:p> </o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt;" lang="EN-GB">Adjunct
Assistant
Professor<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span class="SpellE"><span
style="font-size: 10pt;" lang="EN-GB">Sbarro</span></span><span
style="font-size: 10pt;" lang="EN-GB"> Institute
for
Cancer Research and Molecular Medicine<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span class="SpellE"><span
style="font-size: 10pt;" lang="EN-GB">Center</span></span><span
style="font-size: 10pt;" lang="EN-GB"> for
Biotechnology<o:p></o:p></span></p>
<p class="MsoNormal" style=""><st1:place w:st="on"><st1:placetype
w:st="on"><span style="font-size: 10pt;"
lang="EN-GB">Temple</span></st1:placetype><span
style="font-size: 10pt;" lang="EN-GB"> <st1:placetype
w:st="on">University</st1:placetype></span></st1:place><span
style="font-size: 10pt;" lang="EN-GB"> <o:p></o:p></span></p>
<p class="MsoNormal" style=""><st1:city w:st="on"><span
style="font-size: 10pt;" lang="EN-GB">Philadelphia</span></st1:city><span
style="font-size: 10pt;" lang="EN-GB"> <st1:state
w:st="on">PA</st1:state>
<st1:postalcode w:st="on">19122</st1:postalcode>
(<st1:country-region w:st="on"><st1:place
w:st="on">USA</st1:place></st1:country-region>)<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt;" lang="EN-GB">+++++++++++++++++++++++++++++++++++++<o:p></o:p></span></p>
<p class="MsoNormal"><span style="" lang="EN-GB"><o:p> </o:p></span></p>
</div>
</o:smarttagtype></o:smarttagtype></o:smarttagtype></o:smarttagtype></o:smarttagtype></o:smarttagtype></div>
<br>
Il 16/03/2011 22.23, Eric Pettersen ha scritto:
<blockquote
cite="mid:2535818E-6CAD-4B61-92BF-C438C6C4BD4B@cgl.ucsf.edu"
type="cite">
<div>
<div>On Mar 16, 2011, at 6:30 AM, Tiziano Tuccinardi wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite"><span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0);
font-family: Helvetica; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal;
line-height: normal; orphans: 2; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; font-size: medium;">
<div bgcolor="#ffffff" text="#000000">Dear all,<br>
I am using MatchMaker for aligning about 100 structures,
and it works very well!!<br>
Is it possible to automatically save the pairwise
alignment without opening the MultAlignViewer? Due to the
large number of structures, I cannot use the Match-Align
tool but it would be enough to save the pairwise
alignments</div>
</span></blockquote>
<br>
</div>
<div>Hi Tiziano,</div>
<div><span class="Apple-tab-span" style="white-space: pre;"> </span>Sorry
about Match-Align not being practical for large numbers of
structures. It's written entirely in Python and it would be
nice if I could move it to C++, but it's pretty complicated and
there are always many other priorities...</div>
<div><span class="Apple-tab-span" style="white-space: pre;"> </span>And
then there's MultAlign Viewer, which was written many moons ago
before we realized how important it was to have command line
access to all parts of Chimera. So you can get the end result
you want but you do have to open an MAV for each pairing and
then run a script after all the pairings are done that will get
each of those MultAlign Viewer instances to save their
alignment. I have attached a script file for that. You run the
script with the "runscript" command, specifying the folder where
you want the alignments saved, and the alignment format. You
run it like this:</div>
<div><br>
</div>
<div><span class="Apple-tab-span" style="white-space: pre;"> </span>runscript
<folder-with-script>/save-alignments.py save-folder-path
"Clustal ALN"</div>
<div><br>
</div>
<div>The possible alignment formats are listed in the "Sequence
Alignments" table here:</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html</a></div>
<br>
<div>--Eric</div>
<br>
<div apple-content-edited="true"> <span class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color:
rgb(0, 0, 0); font-family: Helvetica; font-size: 16px;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; text-indent: 0px;
text-transform: none; orphans: 2; white-space: normal; widows:
2; word-spacing: 0px;">
<div style="word-wrap: break-word;">
<p style="margin: 0px;"><font style="font: 16px Helvetica;"
size="5" face="Helvetica"><span
class="Apple-converted-space"> <span
class="Apple-converted-space"> </span></span>Eric
Pettersen</font></p>
<p style="margin: 0px;"><font style="font: 16px Helvetica;"
size="5" face="Helvetica"><span
class="Apple-converted-space"> <span
class="Apple-converted-space"> </span></span>UCSF
Computer Graphics Lab</font></p>
<p style="margin: 0px;"><font style="font: 16px Helvetica;"
size="5" face="Helvetica"><span
class="Apple-converted-space"> </span><a
moz-do-not-send="true" href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p>
<p style="margin: 0px;"><font style="font: 16px Helvetica;"
size="5" face="Helvetica"><br>
</font></p>
<p style="margin: 0px;"><font style="font: 16px Helvetica;"
size="5" face="Helvetica">P.S. Right now the runscript
command doesn't handle "~"-expansion-to-home-dir
correctly, but will in the next daily build and in the
upcoming 1.5.3 release.</font></p>
<p style="margin: 0px;"><font style="font: 16px Helvetica;"
size="5" face="Helvetica"><br>
</font></p>
<p style="margin: 0px;"><font style="font: 16px Helvetica;"
size="5" face="Helvetica"><br>
</font></p>
</div>
</span></div>
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