<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
  <head>
    <meta content="text/html; charset=ISO-8859-1"
      http-equiv="Content-Type">
  </head>
  <body bgcolor="#ffffff" text="#000000">
    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>
    <div class="moz-signature">
      <meta http-equiv="Content-Type" content="text/html;
        charset=ISO-8859-1">
      <meta name="ProgId" content="Word.Document">
      <meta name="Generator" content="Microsoft Word 11">
      <meta name="Originator" content="Microsoft Word 11">
      <link rel="File-List" href="firma_file/filelist.xml">
      <title>sign</title>
      <o:smarttagtype
        namespaceuri="urn:schemas-microsoft-com:office:smarttags"
        name="PostalCode">
        <o:smarttagtype
          namespaceuri="urn:schemas-microsoft-com:office:smarttags"
          name="country-region">
          <o:smarttagtype
            namespaceuri="urn:schemas-microsoft-com:office:smarttags"
            name="State">
            <o:smarttagtype
              namespaceuri="urn:schemas-microsoft-com:office:smarttags"
              name="City">
              <o:smarttagtype
                namespaceuri="urn:schemas-microsoft-com:office:smarttags"
                name="PlaceType">
                <o:smarttagtype
                  namespaceuri="urn:schemas-microsoft-com:office:smarttags"
                  name="place">
                  <!--[if gte mso 9]><xml>
 <o:DocumentProperties>
  <o:Author>Tiziano Tuccinardi</o:Author>
  <o:LastAuthor>Tiziano Tuccinardi</o:LastAuthor>
  <o:Revision>2</o:Revision>
  <o:TotalTime>8</o:TotalTime>
  <o:Created>2009-02-10T13:32:00Z</o:Created>
  <o:LastSaved>2009-02-10T13:40:00Z</o:LastSaved>
  <o:Pages>1</o:Pages>
  <o:Words>84</o:Words>
  <o:Characters>485</o:Characters>
  <o:Company>Dip. Scienze Farmaceutiche</o:Company>
  <o:Lines>4</o:Lines>
  <o:Paragraphs>1</o:Paragraphs>
  <o:CharactersWithSpaces>568</o:CharactersWithSpaces>
  <o:Version>11.9999</o:Version>
 </o:DocumentProperties>
</xml><![endif]--><!--[if gte mso 9]><xml>
 <w:WordDocument>
  <w:SpellingState>Clean</w:SpellingState>
  <w:GrammarState>Clean</w:GrammarState>
  <w:HyphenationZone>14</w:HyphenationZone>
  <w:PunctuationKerning/>
  <w:ValidateAgainstSchemas/>
  <w:SaveIfXMLInvalid>false</w:SaveIfXMLInvalid>
  <w:IgnoreMixedContent>false</w:IgnoreMixedContent>
  <w:AlwaysShowPlaceholderText>false</w:AlwaysShowPlaceholderText>
  <w:Compatibility>
   <w:BreakWrappedTables/>
   <w:SnapToGridInCell/>
   <w:WrapTextWithPunct/>
   <w:UseAsianBreakRules/>
   <w:DontGrowAutofit/>
  </w:Compatibility>
  <w:BrowserLevel>MicrosoftInternetExplorer4</w:BrowserLevel>
 </w:WordDocument>
</xml><![endif]--><!--[if gte mso 9]><xml>
 <w:LatentStyles DefLockedState="false" LatentStyleCount="156">
 </w:LatentStyles>
</xml><![endif]--><!--[if !mso]><object
 classid="clsid:38481807-CA0E-42D2-BF39-B33AF135CC4D" id=ieooui></object>
<style>
st1\:*{behavior:url(#ieooui) }
</style>
<![endif]-->
                  <style>
<!--
 /* Style Definitions */
 p.MsoNormal, li.MsoNormal, div.MsoNormal
        {mso-style-parent:"";
        margin:0cm;
        margin-bottom:.0001pt;
        mso-pagination:widow-orphan;
        font-size:12.0pt;
        font-family:"Times New Roman";
        mso-fareast-font-family:"Times New Roman";}
a:link, span.MsoHyperlink
        {color:blue;
        text-decoration:underline;
        text-underline:single;}
a:visited, span.MsoHyperlinkFollowed
        {color:purple;
        text-decoration:underline;
        text-underline:single;}
span.SpellE
        {mso-style-name:"";
        mso-spl-e:yes;}
@page Section1
        {size:612.0pt 792.0pt;
        margin:70.85pt 2.0cm 2.0cm 2.0cm;
        mso-header-margin:36.0pt;
        mso-footer-margin:36.0pt;
        mso-paper-source:0;}
div.Section1
        {page:Section1;}
-->
</style><!--[if gte mso 10]>
<style>
 /* Style Definitions */
 table.MsoNormalTable
        {mso-style-name:"Tabella normale";
        mso-tstyle-rowband-size:0;
        mso-tstyle-colband-size:0;
        mso-style-noshow:yes;
        mso-style-parent:"";
        mso-padding-alt:0cm 5.4pt 0cm 5.4pt;
        mso-para-margin:0cm;
        mso-para-margin-bottom:.0001pt;
        mso-pagination:widow-orphan;
        font-size:10.0pt;
        font-family:"Times New Roman";
        mso-ansi-language:#0400;
        mso-fareast-language:#0400;
        mso-bidi-language:#0400;}
</style>
<![endif]--><!--[if gte mso 9]><xml>
 <o:shapedefaults v:ext="edit" spidmax="2050"/>
</xml><![endif]--><!--[if gte mso 9]><xml>
 <o:shapelayout v:ext="edit">
  <o:idmap v:ext="edit" data="1"/>
 </o:shapelayout></xml><![endif]-->
                  <div class="Section1">
                    <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>
      <br>
      <fieldset class="mimeAttachmentHeader"></fieldset>
      <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;"></span> </div>
      <br>
      <pre wrap="">
<fieldset class="mimeAttachmentHeader"></fieldset>
_______________________________________________
Chimera-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a>
<a class="moz-txt-link-freetext" href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a>
</pre>
    </blockquote>
  </body>
</html>