<br><br><div class="gmail_quote">On Sat, Mar 26, 2011 at 11:57 AM, Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov">nechols@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im">On Sat, Mar 26, 2011 at 9:45 AM, Jason <<a href="mailto:phenix.upitt@gmail.com">phenix.upitt@gmail.com</a>> wrote:<br>
> I was hoping to identify the ligand binding position by resolving the<br>
> anomalous map first. Shouldn't this be the procedure to locate ligand?<br>
<br>
</div>It depends on the ligand, I guess. �If it's large enough and actually<br>
bound, it should be detectable in the Fo-Fc map - this would be a good<br>
sanity check to make sure that the anomalous map generation is working<br>
properly.<br></blockquote><div>�</div><div>Unfortunately my ligand is fairly small, about 12 atoms.The Fo-Fc map won't be that helpful.<br>�</div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im">
> I know CCP4 can also generate anomalous difference map. But I myself have<br>
> never done it (I googled online and found it not that straight forward). Can<br>
> anybody go through it for me please, or there are other handy programs that<br>
> can make anomalous difference map?<br>
<br>
</div>You don't need to use CCP4 to make the map, just to process the data -<br>
i.e. use MOSFLM/SCALA (xia2 will automate this), or you could also try<br>
HKL2000, then use that as input for Phenix. �But I doubt this is going<br>
to give you a different answer.<br></blockquote><div><br>XDS is the only program that is able to process my data (small oscillation angle and huge data file). On the other hand I am pretty sure xds is doing what it's supposed to do. I was more thinking of another program to generate anomalous map. Since it's phenixbb, probably it's not the right place :)<br>
�<br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
Also: run Xtriage and look at the plot of anomalous signal vs. resolution.<br>
<br>
-Nat<br>
</blockquote></div><br><br><div>======================</div>Jason<div>Structural Biology Department</div><div>University of Pittsburgh</div><div>======================</div><br>