<!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">
Thanks for the suggestions, everyone.<br>
<br>
I am pretty sure I have the spacegroup and the protein-per-unit-cell
correct. The mathews coefficient is at the maximum for P3 with 3
molecules but near the minimum for the other spacegroups. <br>
<br>
It was also suggested to me that i may have one of two problems: <br>
<br>
1)that my protein may sit on the axis of symmetry.<br>
2)that I many have a high degree of NCS which would falsely generate a
high z-score.<br>
<br>
i will follow up on these suggestions.<br>
<br>
thanks again for your time<br>
zach cp<br>
<br>
<br>
<br>
On 04/17/2009 10:32 AM, <a class="moz-txt-link-abbreviated" href="mailto:sbiswas2@ncsu.edu">sbiswas2@ncsu.edu</a> wrote:
<blockquote
cite="mid:2117.152.1.132.71.1239978739.squirrel@webmail.ncsu.edu"
type="cite">
<pre wrap="">Hi,
It could be a problem of space group as rightly pointed out by one of us.
Try re running and ask phaser to find the space group for you this helps
sometimes. I dont think its a good idea to increase the clashes, at least
thats what the phaser manual says. Also I noticed that your RFZ is higher
than TFZ does anyone else think this is a problem?
Shya
Department of Structural Biochemistry,
NCstate University,
Raleigh,
NC27695
</pre>
<blockquote type="cite">
<pre wrap="">Hi,
I have a problem and i wonder if someone has had a similar experience. I
have been using phenix.automr program to find an MR solution for a
protein. When I ask Phaser to use copies=2 I find a number of solutions
with poor z-scores (3-4). When I ask it to use copies=3, I get great
Z-scores (see below) but no solution due to the high number of clashes
(>100!).
As an x-ray newbie I am a bit perplexed of what to make of this: the
solution is not good because there is not enough space in the unit cell
to comfortably accommodate all three molecules yet the Z-score indicates
the structure is good.
My structure does have several loops and these may be contributing to
the clashing residues. As a newbie I have a newbie question - what does
this mean (great z-score but no solutions)? Is this non-solution a
possible solution if I play with it, or is the packing simply too tight
and the Z-scores are not valid?
In the meantime I am chopping my protein into sub-domains as recommended
in the Phaser documentation, but if anyone has seen something like this
before, any suggestions are welcome.
thanks
zach charlop-powers
Packing Table: Space Group P 3
------------------------------
Solutions accepted if number of clashes = 135 (lowest number of
clashes in list)
provided this number of clashes <= 10 (maximum number of allowed
clashes)
# #Clashes # Accepted Annotation
1 188 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5
TFZ=10.4
2 156 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5
TFZ=10.2
3 151 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5
TFZ=9.8
4 146 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5
TFZ=9.7
5 187 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3
TFZ=10.5
6 202 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5
TFZ=9.2
7 170 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5
TFZ=9.1
8 144 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3
TFZ=10.2
9 177 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5
TFZ=9.1
10 153 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5
TFZ=8.9
11 150 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5
TFZ=8.8
12 217 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5
TFZ=8.6
13 182 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5
TFZ=8.6
14 135 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5
TFZ=8.5
15 175 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5
TFZ=8.3
16 159 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5
TFZ=8.3
17 192 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5
TFZ=8.3
18 165 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3
TFZ=9.2
19 169 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3
TFZ=9.1
20 158 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5
TFZ=8.0
21 173 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5
TFZ=8.0
22 154 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3
TFZ=8.9
23 206 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5
TFZ=7.8
0 accepted of 23 solutions
_______________________________________________
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://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.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://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<br>
</body>
</html>