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Dear Zach,<br>
<br>
are you sure about your spacegroup? And what about the matthews
parameter (<a class="moz-txt-link-freetext" href="http://www.ruppweb.org/Mattprob/">http://www.ruppweb.org/Mattprob/</a>)?<br>
<br>
Best Regards,<br>
Georg<br>
<br>
<br>
<br>
Andreas Förster schrieb:
<blockquote cite="mid:49E88D82.8070900@gmail.com" type="cite">
<pre wrap="">Hey Zach,
remove the loops from your search model and rerun the MR.
Alternatively, increase the maximum number of clashes allowed until you
get a solution written out. See where your solutions clash. Again, if
it's in a loop region, cut the loop and rerun. Your z-scores look
great. (Notice that you have zed-scores when you run phaser through
ccp4i and zee-scores when you run phaser through phenix.)
Andreas
zach powers wrote:
</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
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</pre>
</blockquote>
<pre wrap=""><!---->
</pre>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
Universität Tübingen
Interfakultäres Institut für Biochemie
Dr. Georg Zocher
Hoppe-Seyler-Str. 4
72076 Tuebingen
Germany
Fon: +49(0)-7071-2973374
Mail: <a class="moz-txt-link-abbreviated" href="mailto:georg.zocher@uni-tuebingen.de">georg.zocher@uni-tuebingen.de</a>
<a class="moz-txt-link-freetext" href="http://www.ifib.uni-tuebingen.de">http://www.ifib.uni-tuebingen.de</a></pre>
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