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<P DIR=LTR><SPAN LANG="en-ca"><FONT FACE="Calibri">You have been very helpful in explaining different items that</FONT></SPAN><SPAN LANG="en-ca"> <FONT FACE="Calibri">use the command line.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"><FONT FACE="Calibri">I have a PDB file that was determined by NMR. Thus there are a large number of chains</FONT></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri"> number as</FONT></SPAN><SPAN LANG="en-ca"><B> <FONT COLOR="#FF0000" FACE="Calibri">pdb (#</FONT></B></SPAN><SPAN LANG="en-ca"><B><FONT COLOR="#FF0000" FACE="Calibri">0.1) Chain A</FONT></B></SPAN><SPAN LANG="en-ca"><B><FONT COLOR="#FF0000" FACE="Calibri"> </FONT></B></SPAN><SPAN LANG="en-ca"> <FONT FACE="Calibri">etc.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"><FONT FACE="Calibri">So I know that I can select a single chain, and build up an image with Chains</FONT></SPAN><SPAN LANG="en-ca"> <FONT FACE="Calibri">A, B, etc using the #0.1 chain number.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"><FONT FACE="Calibri">I want to visualize three Gly residues</FONT></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri"> in one chain. So I learned that I can use the command</FONT></SPAN><SPAN LANG="en-ca"><B> <FONT COLOR="#FF0000" FACE="Calibri">ribbackbone</FONT></B></SPAN><SPAN LANG="en-ca"><B><FONT COLOR="#FF0000" FACE="Calibri"> </FONT></B></SPAN><SPAN LANG="en-ca"> <FONT FACE="Calibri">to visualize the backbone atoms of the amino acids that I want to show. S</FONT></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri">o when I use that command all</FONT></SPAN><SPAN LANG="en-ca"> <FONT FACE="Calibri">the backbone</FONT></SPAN><SPAN LANG="en-ca"> <FONT FACE="Calibri">atoms of the residues selec</FONT></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri">ted</FONT></SPAN><SPAN LANG="en-ca"> <FONT FACE="Calibri">are visualized including the side chains. I also know that if I use the command</FONT></SPAN><SPAN LANG="en-ca"><B> <FONT COLOR="#FF0000" FACE="Calibri">~ribbackbone</FONT></B></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri"> </FONT></SPAN><SPAN LANG="en-ca"> <FONT FACE="Calibri">all the backbone atoms are suppressed leaving only the atoms of the side chains. I know that without any residues or atoms</FONT></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri"> specified the command applies to the whole model.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"><FONT FACE="Calibri">Now as I said that I want to visualize three Gly residue</FONT></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri">s in one of the chains. The Gly residue numbers are 33, 37, 38. T</FONT></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri">hey are on Chain #0.1 K.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"><B></B></SPAN><B><SPAN LANG="en-ca"></SPAN></B><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"><FONT FACE="Cambria">The information on the</FONT></SPAN><B><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"> <FONT COLOR="#FF0000" FACE="Cambria">ribbackbone</FONT></SPAN><SPAN LANG="en-ca"></SPAN></B><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"><FONT FACE="Cambria"></FONT></SPAN><B><SPAN LANG="en-ca"></SPAN></B><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"> <FONT FACE="Cambria"> in the Chimera users guide, indicates that I should be able to do this by using parameter</FONT></SPAN><B><SPAN LANG="en-ca"></SPAN></B><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"><FONT FACE="Cambria">s termed</FONT></SPAN><B><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"><FONT COLOR="#4F81BD" FACE="Cambria"></FONT></SPAN><SPAN LANG="en-ca"></SPAN></B><SPAN LANG="en-ca"><I></I></SPAN><SPAN LANG="en-ca"><I> <FONT COLOR="#00B0F0" FACE="Cambria">atom-spec.</FONT></I></SPAN><B><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"><FONT COLOR="#4F81BD" FACE="Cambria"> i.e.</FONT></SPAN><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"> <FONT COLOR="#000000" SIZE=4 FACE="Times New Roman">ribbackbone </FONT></SPAN><SPAN LANG="en-ca"></SPAN></B><A HREF="file://frameatom_spec.html"><B><SPAN LANG="en-ca"><I></I></SPAN><SPAN LANG="en-ca"><I><U></U></I></SPAN><SPAN LANG="en-ca"><I><U></U></I></SPAN><I><U><SPAN LANG="en-ca"><FONT COLOR="#0000FF" SIZE=4 FACE="Times New Roman">atom-spec</FONT></SPAN></U></I><SPAN LANG="en-ca"></SPAN></B></A><B><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"></SPAN></B></P>
<P DIR=LTR><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"><FONT FACE="Calibri">I looked elsewhere for how to designate the parameters for</FONT></SPAN><SPAN LANG="en-ca"><B><I></I></B></SPAN><B><I><SPAN LANG="en-ca"> <FONT COLOR="#00B0F0" FACE="Calibri">atom-spec</FONT></SPAN></I></B><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri"> and tried a few things,</FONT></SPAN><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri"> but I was not able to achieve the specificity of showing the backbone atoms of</FONT></SPAN><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri"> only</FONT></SPAN><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri"> the Gly residues. I don’t think that I have to indicate that I want only the Gly residues in Chain K</FONT></SPAN><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"><FONT FACE="Calibri"> #0.1 because I can select the Gly residues from the sequence of Chain K #0.1.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"><FONT FACE="Calibri">So after this</FONT></SPAN><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"> <FONT FACE="Calibri">long description of what I want to do, would you kindly inform me of how I can visualize the backbone atoms of only Gly.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"><FONT FACE="Calibri">Thank you</FONT></SPAN><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"><FONT FACE="Calibri">Arthur G. Szabo</FONT></SPAN><SPAN LANG="en-ca"></SPAN><SPAN LANG="en-ca"></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"><B></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"></SPAN></P>
<P DIR=LTR><SPAN LANG="en-ca"></SPAN></P>
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