Hi<br>
<br>
Okay I have calculated the DOPE scores and I will use these. Just out
of interest, is there are way of utilising the Z scores or compactness
scores from GA341? From the example below I am assuming that the lower
the Z score the better, would this be correct? Also when it comes to
the compactness value is a higher or lower score better?<br>
<br>
Many thanks<br>
Jo<br>
<br>model1<br>
% sequence identity &nbsp; &nbsp; &nbsp;: &nbsp; &nbsp;30.174000<br>
Sequence length &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;: &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;531<br>
Compactness &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;: &nbsp; &nbsp; 0.270804<br>
Native energy (pair) &nbsp; &nbsp; : &nbsp;-225.273799<br>
Native energy (surface) &nbsp;: &nbsp; -13.946407<br>
Native energy (combined) : &nbsp; &nbsp;-6.357012<br>
Z score (pair) &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; : &nbsp; &nbsp;-9.813731<br>
Z score (surface) &nbsp; &nbsp; &nbsp; &nbsp;: &nbsp; &nbsp;-7.147611<br>
Z score (combined) &nbsp; &nbsp; &nbsp; : &nbsp; -11.464915<br>
GA341 score &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;: &nbsp; &nbsp; 1.000000<br>
<br>
model2<br>
% sequence identity &nbsp; &nbsp; &nbsp;: &nbsp; &nbsp;30.174000<br>
Sequence length &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;: &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;531<br>
Compactness &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;: &nbsp; &nbsp; 0.256617<br>
Native energy (pair) &nbsp; &nbsp; : &nbsp;-268.422282<br>
Native energy (surface) &nbsp;: &nbsp; -16.727187<br>
Native energy (combined) : &nbsp; &nbsp;-7.618686<br>
Z score (pair) &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; : &nbsp; &nbsp;-9.969647<br>
Z score (surface) &nbsp; &nbsp; &nbsp; &nbsp;: &nbsp; &nbsp;-7.755271<br>
Z score (combined) &nbsp; &nbsp; &nbsp; : &nbsp; -12.156111<br>
GA341 score &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;: &nbsp; &nbsp; 1.000000<br><div><span class="gmail_quote">On 2/21/06, <b class="gmail_sendername">Modeller Caretaker</b> &lt;<a href="mailto:modeller-care@salilab.org">modeller-care@salilab.org</a>&gt; wrote:
</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">jo hanna wrote:<br>&gt; After having built my models, i have decided to assess them using the
<br>&gt; ga341 score.<br><br>&gt; the ouput of this script for two different models is:<br>&gt;<br>&gt; model1<br>&gt;
GA341
score&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;:&nbsp;&nbsp;&nbsp;&nbsp;
1.000000<br>&gt;<br>&gt; model2<br>&gt; GA341
score&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;:&nbsp;&nbsp;&nbsp;&nbsp;
1.000000<br>&gt;<br>&gt; how do i interpret these outputs? should both scores be 1?<br><br>GA341 is not sufficiently sensitive to distinguish between two 'very<br>good' models. Any good model will give a score very close to 1 (
e.g.<br>running GA341 on most PDB structures will give a 1.0 score). You should<br>use it only to discard 'bad' models (e.g. those with score less than<br>0.6). DOPE may be more sensitive in your case.<br><br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Ben Webb, Modeller Caretaker
<br>--<br><a href="mailto:modeller-care@salilab.org">modeller-care@salilab.org</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href="http://www.salilab.org/modeller/">http://www.salilab.org/modeller/</a><br>Modeller mail list: <a href="http://salilab.org/mailman/listinfo/modeller_usage">
http://salilab.org/mailman/listinfo/modeller_usage</a><br></blockquote></div><br>