<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Hi Jianghai,<br>
<br>
I have no quick answer. I will have a look within next few days and let
you know. It may be a side effect of runtime optimization - I'm trying
to save some refinement runs by looking at the available accumulated
statistics and extrapolating from that. Anyway, I guess it's time to
review that code (given the amount of usage). May be it is safer to
give up some runtime over the robustness and predictability... will see.<br>
<br>
Have a great week-end!<br>
Pavel.<br>
<br>
<br>
On 5/28/10 9:41 PM, Jianghai Zhu wrote:
<blockquote
cite="mid:D2FCB301-9A39-43EC-B647-23F6A918A28C@idi.harvard.edu"
type="cite">
<pre wrap="">After a few trials, looks like the angles_rmsd_max cannot be set to a value lower than 1.0. Everytime I did that, the values for bonds_rmsd_max and angles_rmsd_max reverted to the default numbers in the refinement and the limits I set in the input file are not effective. How do I fix that? Thanks.
-- Jianghai
On May 26, 2010, at 11:30 AM, Pavel Afonine wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Jianghai,
</pre>
<blockquote type="cite">
<pre wrap="">Yes, these limits fixed the problem.
</pre>
</blockquote>
<pre wrap="">thanks for letting know, I'm glad it worked for you!
</pre>
<blockquote type="cite">
<pre wrap="">But the default values should be 0.02 and 2, respectively, I believe.
</pre>
</blockquote>
<pre wrap="">Well, I guess better to have it resolution dependent, and best to have it local per bond or so. I have no intention to open another can of worms, but where those 0.02 and 2 come from? Can you really see that level of details at say 2.5A resolution and lower? I guess at that resolutions they should be both zero. In contrast, at higher resolution larger deviations are justified just by the data and so larger margins in restraints should be allowed. I know there is a heap of good papers on this matter, including the recent ones, and there are long threads on bb, but to me this question is still somewhat open. May be someone on the board can thoroughly/convincingly comment on this, summarizing all previous discussions?
Anyway, I agree, 0.05 and 3.5 is probably too generous.
All the best!
Pavel.
_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<pre wrap=""><!---->
_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
</body>
</html>