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<div class=Section1><pre><span lang=EN-US>Hi, Justin<o:p></o:p></span></pre><pre><span
lang=EN-US><o:p> </o:p></span></pre><pre><span lang=EN-US>Thank you for your patience.<o:p></o:p></span></pre><pre><span
lang=EN-US>According your reply, I used trjconv to write only protein group into another file.<o:p></o:p></span></pre><pre><span
lang=EN-US>I execute do_dssp again in group “protein”and “mainchain” respectively but still get coils more than total residues.<o:p></o:p></span></pre><pre><span
lang=EN-US>Why?<o:p></o:p></span></pre><pre><span lang=EN-US><o:p> </o:p></span></pre><pre><span
lang=EN-US>Hsin-Lin<o:p></o:p></span></pre><pre><span lang=EN-US><o:p> </o:p></span></pre><pre><span
lang=EN-US><o:p> </o:p></span></pre><pre><span lang=EN-US>Hsin-Lin wrote:<o:p></o:p></span></pre><pre><span
lang=EN-US>><i> Hi, Justin:<o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> <o:p></o:p></i></span></pre><pre><span lang=EN-US>><i> Thank you for your reply.<o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> I try to select the group, 'mainchain', when prompted, and get the quantity<o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> of coil still larger than the number of residues of my protein.<o:p></o:p></i></span></pre><pre><span
lang=EN-US><o:p> </o:p></span></pre><pre><span lang=EN-US>Then some other elements of your system are being detected as containing <o:p></o:p></span></pre><pre><span
lang=EN-US>relevant atoms. What happens if you run do_dssp on a single structure <o:p></o:p></span></pre><pre><span
lang=EN-US>containing only your protein?<o:p></o:p></span></pre><pre><span
lang=EN-US><o:p> </o:p></span></pre><pre><span lang=EN-US>><i> The data is the same as the output that generated by the selection, "1.<o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> Protein".<o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> If I select backbone, I get the fatal error: <o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> Failed to execute command: /Prousr/statphys/hsinlin/dssp/dsspcmbi -na<o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> ddhIPvCe ddJ6Yv7a > /dev/null 2> /dev/null <o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> <o:p></o:p></i></span></pre><pre><span lang=EN-US>><i> And I don't understand even if I can run the selection, "backbone",<o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> successfully.<o:p></o:p></i></span></pre><pre><span
lang=EN-US><o:p> </o:p></span></pre><pre><span lang=EN-US>No, you can't.<o:p></o:p></span></pre><pre><span
lang=EN-US><o:p> </o:p></span></pre><pre><span lang=EN-US>><i> According the dssp web of wiki:<o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> <a href="http://en.wikipedia.org/wiki/DSSP_%28protein%29">http://en.wikipedia.org/wiki/DSSP_%28protein%29</a><o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> the hydrogen bonds are dicided by O, C, H, and N four atoms.<o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> How can we get dssp analysis by backbone that includes only NCCNCCNCC.....?<o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> <o:p></o:p></i></span></pre><pre><span lang=EN-US><o:p> </o:p></span></pre><pre><span
lang=EN-US>You can't - DSSP requires the presence of the carbonyl O in order to determine <o:p></o:p></span></pre><pre><span
lang=EN-US>hydrogen bonding geometry. If you don't have a full carbonyl, the analysis fails.<o:p></o:p></span></pre><pre><span
lang=EN-US><o:p> </o:p></span></pre><pre><span lang=EN-US>-Justin<o:p></o:p></span></pre><pre><span
lang=EN-US><o:p> </o:p></span></pre><pre><span lang=EN-US>><i> Sincerely yours,<o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> Hsin-Lin<o:p></o:p></i></span></pre><pre><span lang=EN-US>>><i> Hsin-Lin wrote:<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>>><i> Hi,<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>>><i><o:p> </o:p></i></span></pre><pre><span
lang=EN-US>>>><i> I use do_dssp to generate xvg file collect the last line to make a plot.<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>>><i> There are something written in this way:<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>>><i> ------------------<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>>><i> @ s0 legend "Structure"<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>>><i> @ s1 legend "Coil"<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>>><i> @ s2 legend "Bend"<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>>><i> 0 5 14 1<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>>><i> -------------------<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>>><i> My system is dimer and each peptide has 6 residue.<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>><i> Then you have a problem. Your output indicates 14 residues are in a<o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> random<o:p></o:p></i></span></pre><pre><span lang=EN-US>>><i> coil, so either you have more than 12 total residues, or something went<o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> wrong<o:p></o:p></i></span></pre><pre><span lang=EN-US>>><i> in<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>><i> the dssp calculation.<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>><i><o:p> </o:p></i></span></pre><pre><span lang=EN-US>>>><i> And the number I choose to analyze is "1. Protein".<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>>><i><o:p> </o:p></i></span></pre><pre><span
lang=EN-US>>><i> Perhaps this is why you had a problem. Normally, choosing "Protein" would<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>><i> cause<o:p></o:p></i></span></pre><pre><span lang=EN-US>>><i> the calculation to hang, but maybe that is not the case any more. See<o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> here<o:p></o:p></i></span></pre><pre><span lang=EN-US>>><i> for<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>><i> the proper group to choose and the rationale:<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>><i><o:p> </o:p></i></span></pre><pre><span lang=EN-US>>><i> <a
href="http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp">http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp</a><o:p></o:p></i></span></pre><pre><span
lang=EN-US>>><i><o:p> </o:p></i></span></pre><pre><span lang=EN-US>>>><i> Now I have a question, if I want to calculate the percentage of<o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> secondary<o:p></o:p></i></span></pre><pre><span lang=EN-US>>>><i> structure.<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>>><i> In the example above, is it calculated in this way 5/12=42%?<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>>><i><o:p> </o:p></i></span></pre><pre><span
lang=EN-US>>><i> I'd question your results first...you don't have 12 residues in your<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>><i> calculation, otherwise your protein is 14/12 = 117% random coil! Also<o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> realize<o:p></o:p></i></span></pre><pre><span lang=EN-US>>><i> that (by default) the "Structure" term only includes alpha helix, beta<o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> strand,<o:p></o:p></i></span></pre><pre><span lang=EN-US>>><i> bend, and turn. Other structural elements are not included. That may or<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>><i> may<o:p></o:p></i></span></pre><pre><span lang=EN-US>>><i> not be what you want, depending on the structural elements of your<o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> protein.<o:p></o:p></i></span></pre><pre><span lang=EN-US>>><i> -Justin<o:p></o:p></i></span></pre><pre><span
lang=EN-US>>><i><o:p> </o:p></i></span></pre><pre><span lang=EN-US>>>><i> Hsin-Lin<o:p></o:p></i></span></pre><pre><span
lang=EN-US>><i> <o:p></o:p></i></span></pre><pre><span lang=EN-US>><i> <o:p></o:p></i></span></pre>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
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