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<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><font size="3"><font face="Calibri">To whom this may concern,
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<o:p></o:p></font></font></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><font size="3"><font face="Calibri">I’m an undergraduate student doing some research at KSTATE this summer and I’ve been assigned to work on a project that utilizes Chimera.<o:p></o:p></font></font></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><font size="3"><font face="Calibri">My professor is unavailable a lot of the time and I’ve been struggling a bit with a problem.
<o:p></o:p></font></font></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><font size="3"><font face="Calibri">I’ve been successful at opening up the following PDB files:<o:p></o:p></font></font></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><font size="3"><font face="Calibri">1DHK<span style="mso-spacerun: yes">
</span>1DPX<span style="mso-spacerun: yes"> </span>1HYL<span style="mso-spacerun: yes">
</span>2CAU <span style="mso-spacerun: yes"> </span>3BLG<span style="mso-spacerun: yes">
</span>1OA6<span style="mso-spacerun: yes"> </span>1JBC<span style="mso-spacerun: yes">
</span>1OA5<o:p></o:p></font></font></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><font face="Calibri"><font size="3">I’m able to open up the .pdb files, proceed to use the commands “del solvent” and “del @ .b” in the command line.
<o:p></o:p></font></font></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><font size="3"><font face="Calibri">I’m also able to go to Tools</font><span style="FONT-FAMILY: Wingdings; mso-ascii-font-family: Calibri; mso-ascii-theme-font: minor-latin; mso-hansi-font-family: Calibri; mso-hansi-theme-font: minor-latin; mso-char-type: symbol; mso-symbol-font-family: Wingdings"><span style="mso-char-type: symbol; mso-symbol-font-family: Wingdings">à</span></span><font face="Calibri">Higher
Order Structure </font><span style="FONT-FAMILY: Wingdings; mso-ascii-font-family: Calibri; mso-ascii-theme-font: minor-latin; mso-hansi-font-family: Calibri; mso-hansi-theme-font: minor-latin; mso-char-type: symbol; mso-symbol-font-family: Wingdings"><span style="mso-char-type: symbol; mso-symbol-font-family: Wingdings">à</span></span><font face="Calibri">
Crystal Contacts before changing the contact distance from 1.0 to 4.0 and check mark the create copies of contacting molecules.<o:p></o:p></font></font></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><font size="3"><font face="Calibri">However when I attempt to do the following actions for the rest of the proteins I run into a variety of issues:<o:p></o:p></font></font></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><font size="3"><font face="Calibri">For example 2CAU:<o:p></o:p></font></font></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><font size="3"><font face="Calibri">When I attempt to “measure buried area #0 # 2-7,” I get the following response in my reply log:<o:p></o:p></font></font></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">#0, chain A: JACK BEAN vicilin<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">6 pairs of NCS asymmetric units of 2CAU contact at distance 1.0 A<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri"><span style="mso-spacerun: yes">
</span>Atoms<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes">
</span>MTRIX<span style="mso-tab-count: 1"> </span>SMTRY<span style="mso-tab-count: 1">
</span>Unit cell<span style="mso-tab-count: 1"> </span>MTRIXref<span style="mso-tab-count: 1">
</span><span style="mso-spacerun: yes"> </span>Copies<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri"><span style="mso-spacerun: yes">
</span>1<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes">
</span>0<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes">
</span>4<span style="mso-tab-count: 1"> </span>0<span style="mso-spacerun: yes">
</span>0<span style="mso-spacerun: yes"> </span>0 <span style="mso-tab-count: 1">
</span><span style="mso-spacerun: yes"> </span>0<span style="mso-tab-count: 1">
</span><span style="mso-spacerun: yes"> </span>1<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri"><span style="mso-spacerun: yes">
</span>1<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes">
</span>0<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes">
</span>5<span style="mso-tab-count: 1"> </span>0<span style="mso-spacerun: yes">
</span>0<span style="mso-spacerun: yes"> </span>0 <span style="mso-tab-count: 1">
</span><span style="mso-spacerun: yes"> </span>0<span style="mso-tab-count: 1">
</span><span style="mso-spacerun: yes"> </span>1<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri"><span style="mso-spacerun: yes">
</span>1<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes">
</span>0<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes">
</span>6<span style="mso-tab-count: 1"> </span>-1<span style="mso-spacerun: yes">
</span>0 -1 <span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes"> </span>0<span style="mso-tab-count: 1">
</span><span style="mso-spacerun: yes"> </span>1<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri"><span style="mso-spacerun: yes">
</span>1<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes">
</span>0<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes">
</span>8<span style="mso-tab-count: 1"> </span>0<span style="mso-spacerun: yes">
</span>0<span style="mso-spacerun: yes"> </span>0 <span style="mso-tab-count: 1">
</span><span style="mso-spacerun: yes"> </span>0<span style="mso-tab-count: 1">
</span><span style="mso-spacerun: yes"> </span>1<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri"><span style="mso-spacerun: yes">
</span>1<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes">
</span>0<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes">
</span>9<span style="mso-tab-count: 1"> </span>0<span style="mso-spacerun: yes">
</span>0 -1 <span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes"> </span>0<span style="mso-tab-count: 1">
</span><span style="mso-spacerun: yes"> </span>1<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri"><span style="mso-spacerun: yes">
</span>1<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes">
</span>0<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes">
</span>11<span style="mso-tab-count: 1"> </span>0<span style="mso-spacerun: yes">
</span>0 -1 <span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes"> </span>0<span style="mso-tab-count: 1">
</span><span style="mso-spacerun: yes"> </span>1<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 1<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">MSMSLIB 1.3 started on Local PC<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">Copyright M.F. Sanner (March 2000)<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">Compilation flags<span style="mso-spacerun: yes">
</span><o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 1<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">MSMSLIB 1.3 started on Local PC<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">Copyright M.F. Sanner (March 2000)<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">Compilation flags<span style="mso-spacerun: yes">
</span><o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 1<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">MSMSLIB 1.3 started on Local PC<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">Copyright M.F. Sanner (March 2000)<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">Compilation flags<span style="mso-spacerun: yes">
</span><o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 0<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">MSMSLIB 1.3 started on Local PC<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">Copyright M.F. Sanner (March 2000)<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">Compilation flags<span style="mso-spacerun: yes">
</span><o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 0<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">MSMSLIB 1.3 started on Local PC<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">Copyright M.F. Sanner (March 2000)<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">Compilation flags<span style="mso-spacerun: yes">
</span><o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 0<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">MSMSLIB 1.3 started on Local PC<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><o:p><font face="Calibri"> </font></o:p></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">Copyright M.F. Sanner (March 2000)<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">Compilation flags<span style="mso-spacerun: yes">
</span><o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 0<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">MSMSLIB 1.3 started on Local PC<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 6pt; mso-bidi-font-size: 11.0pt"><font face="Calibri">Copyright M.F. Sanner (March 2000)<o:p></o:p></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><span style="COLOR: red"><font face="Calibri"><font size="3">Compilation flags<span style="mso-spacerun: yes"> [End of Reply Log]</span></font></font></span></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><font face="Calibri"><font size="3">So I’m not able to get back the calculations I want.<o:p></o:p></font></font></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><font size="3"><font face="Calibri">Also, when I attempt to use the Surface Analysis
</font><span style="FONT-FAMILY: Wingdings; mso-ascii-font-family: Calibri; mso-ascii-theme-font: minor-latin; mso-hansi-font-family: Calibri; mso-hansi-theme-font: minor-latin; mso-char-type: symbol; mso-symbol-font-family: Wingdings"><span style="mso-char-type: symbol; mso-symbol-font-family: Wingdings">à</span></span><font face="Calibri">
Attributes Calculator to run the following function : sum(atom.buriedSASArea) and check the “Restrict formula domain to current selection, if any”<span style="mso-spacerun: yes">
</span>and “Save calculation results to file,” after selecting the “C” atoms I get the reply:<o:p></o:p></font></font></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><font face="Calibri"><i style="mso-bidi-font-style: normal"><span style="mso-spacerun: yes"><font size="3"> </font></span></i><i style="mso-bidi-font-style: normal"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 9pt; mso-bidi-font-size: 11.0pt">Formula
evaluation error: expecting vector argument in function</span><o:p></o:p></i></font></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><font size="3"><font face="Calibri">Is there something I need to do before I attempt these actions?
<o:p></o:p></font></font></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><font size="3"><font face="Calibri">Also, I have very little experience with programs in general (I’m a chemistry major/upcoming experimental chemist working with theortical physicist…a little out of my element).</font></font></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><font size="3"><font face="Calibri">Thanks in advance,</font></font></p>
<p style="MARGIN: 0in 0in 10pt" class="MsoNormal"><font size="3"><font face="Calibri">-Yen Bui<o:p></o:p></font></font></p>
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