Thanks Mark and <span class="HOEnZb"><font color="#000000">Clemens for your suggestions. By both the ways i.e. by cutting the data to lower resolution as well as by providing a list of heavy atom sites in a separate file worked fine. <br>
<br><br><br>Regards,<br>Abhi<br></font></span><br><div class="gmail_quote">On Tue, Oct 30, 2012 at 7:54 PM, Clemens Vonrhein <span dir="ltr"><<a href="mailto:vonrhein@globalphasing.com" target="_blank">vonrhein@globalphasing.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Abhimanyu,<br>
<div class="im"><br>
On Tue, Oct 30, 2012 at 05:06:28PM +0100, abhimanyu singh wrote:<br>
> Recently I have collected a Se-SAD data set diffracting at around 1.7A in<br>
> I23 space group and am trying to process it through Autosharp.<br>
<br>
</div>Sounds good.<br>
<div class="im"><br>
> While running when the program tries to find heavy atom sites using<br>
> ShelxD it terminates reporting "ARRAYS TOO SMALL TO STORE REFLECTION<br>
> DATA - TRY -L1" error.<br>
<br>
</div>That seems to point to an error in SHELXD? Which version are you<br>
running? The latest or the latest beta version of SHELXD?<br>
<div class="im"><br>
> Have any one ever encountered such an error and could suggest me any<br>
> possible reason behind it?<br>
<br>
</div>You simply seem to have too many reflections (very large cell?). Two<br>
possibilities I could think of:<br>
<br>
1. run autoSHARP with lower-resolution data (eg. cut at 2.5A): that<br>
should be enough for finding your Se sites (if it is possible at<br>
all).<br>
<br>
If you run this autoSHARP job only to the heavy-atom detection<br>
stage, you will get a set of initial sites (in a *.hatom file -<br>
basically fractional coordinates). Put this *.hatom file into<br>
your sharpfiles/datafiles directory.<br>
<br>
Then re-run the same autoSHARP job again, but:<br>
<br>
* use all data up to 1.7A<br>
<br>
* pick the *.hatom file you just copied over.<br>
<br>
Now autoSHRP will skip the HA detection with SHELXD (avoiding<br>
that error) and start with the sites found in the previous 2.5A<br>
run. But since you have all data now, it should give you phases,<br>
maps and (hopefully) model to 1.7A.<br>
<br>
2. you could write a shelxd wrapper to supply this -L1 flag (never<br>
came across that before though) and point<br>
$SHARP_home/machines/*/shelx.setup to the location with that<br>
rapper (and a link to the true shelxc binary)?<br>
<br>
I would go for option 1: it also shows you how one can run autoSHARP<br>
with a starting set of known HA positions (which could come from all<br>
kind of external programs or calculations you did). This is very<br>
sueful if the default way of running SHELXC/D inside autoSHARP doesn't<br>
give you a good enough answer ... or stops with a warning message like<br>
you just hit upon.<br>
<br>
Kind regards<br>
<span class="HOEnZb"><font color="#888888"><br>
Clemens Vonrhein<br>
<br>
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<br>
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</font></span></blockquote></div><br><br clear="all"><br>-- <br><b>Abhimanyu Kumar Singh<br></b>Ph.D. Student<br>Department of Macromolecular Structures<br>National Center for Biotechnology (CNB-CSIC)<br>C/ Darwin 3, Campus de Cantoblanco,<br>
28049 Madrid, Spain.<br>E-Mail: <a href="mailto:abhimanyu.singh@cnb.csic.es" target="_blank">abhimanyu.singh@cnb.csic.es</a><br><br><br>