Adding to what Tom said: if you want to visually verify the Xe sites,
create an anomalous difference map using the autobuilt model for
phasing (phenix.maps can do this, also in the GUI). The Xe atoms
should be located in anomalous peaks; I would be very surprised if
Phaser got this wrong. You can also use the experimental phasing
module of Phaser to output the log-likelihood gradient map that it
uses for substructure completion.
-Nat
On Thu, Feb 2, 2012 at 8:53 AM, Terwilliger, Thomas C
Hi Brennan,
The number of sites that you ask for affects the HYSS heavy-atom search procedure, but not too much else. Once some sites are found by HYSS, then autosol uses phaser to identify additional sites (that's why you got 22 sites, not 2). I am a little surprised that changing the number of sites from 2 to 4 makes the difference between finding correct sites and not finding them at all, but it does seem possible.
For your experiment, one thing you could do: once you figure out where the "standard" Xe sites are, just feed them in to autosol with a sites_file=xxx.pdb for all your datasets. Then they are all starting out with pretty much the same information.
All the best, Tom T
________________________________________ From: CCP4 bulletin board [[email protected]] on behalf of Brennan Bonnet [[email protected]] Sent: Thursday, February 02, 2012 9:43 AM To: [email protected] Subject: [ccp4bb] Lysozyme/Xenon derivatives & Phenix.
Hi all,
I have a strange result using Phenix's AutoSol to look for xenon sites in lysozyme.
For a few months now I have been trying to produce xenon derivatives of lysozyme using pressures in the range of 50-350psi and time ranges between 5-60min trying to find the "sweet spot" so that this technique can be applied to other proteins.
For each dataset, I AutoSol using phenix and have it look for 2, 3, and 4 xenon sites. I haven't had much success though and typical values when asked to look for 2 sites have been Rwork/Rfree = 0.5585/0.5892, CC=0.14, Bayes-CC=6.5 and with xenon sites:
(a, b, c, alpha, beta, gamma, space group) CRYST1 78.870 78.870 36.940 90.00 90.00 90.00 P 41 21 2
(columns after numbering are a, b, c, occ, B factor) HETATM 1 XE XE Z 1 48.601 67.475 1.088 0.06 6.58 XE HETATM 2 XE XE Z 2 54.986 76.636 2.746 0.11 7.49 XE
which, to me, says that there is no binding (or at least nothing obvious).
I finally got a good result though with 350psi and 5 minutes pressurization. After AutoSol, FOM=0.436, Bayes-CC=33.57, Model CC=0.83, Rwork/Rfree=0.2843/0.3023, 117/125 residues build and placed. And even though I told it to only look for 2 sites, Phenix went ahead and found 22 sites:
(a, b, c, alpha, beta, gamma, space group) CRYST1 79.130 79.130 36.920 90.00 90.00 90.00 P 43 21 2
(colums after numbering are a, b, c, occ, B factor) HETATM 1 XE XE Z 1 -36.117 -56.764 -1.825 0.18 9.43 XE HETATM 2 XE XE Z 2 -54.805 -54.805 0.000 0.14 6.44 XE HETATM 3 XE XE Z 3 -8.337 -31.695 -16.766 0.08 8.26 XE HETATM 4 XE XE Z 4 -5.702 -64.959 -35.134 0.05 5.21 XE HETATM 5 XE XE Z 5 -9.535 -22.397 -31.839 0.06 14.33 XE HETATM 6 XE XE Z 6 -7.319 -66.343 -35.123 0.05 6.02 XE HETATM 7 XE XE Z 7 -8.580 -21.153 -30.274 0.05 7.43 XE HETATM 8 XE XE Z 8 -1.494 -29.583 -2.339 0.06 7.36 XE HETATM 9 XE XE Z 9 -0.518 -16.483 -16.776 0.05 6.56 XE HETATM 10 XE XE Z 10 -0.464 -29.847 -4.386 0.06 6.04 XE HETATM 11 XE XE Z 11 -1.222 -16.234 -18.952 0.04 6.51 XE HETATM 12 XE XE Z 12 -6.001 -20.380 -4.532 0.05 7.22 XE HETATM 13 XE XE Z 13 -5.169 -27.522 -10.128 0.05 3.54 XE HETATM 14 XE XE Z 14 -11.931 -67.039 -4.699 0.05 7.96 XE HETATM 15 XE XE Z 15 -6.538 -10.408 -3.761 0.04 10.22 XE HETATM 16 XE XE Z 16 -0.458 -23.897 -31.221 0.05 6.85 XE HETATM 17 XE XE Z 17 -3.308 -65.181 -8.754 0.03 8.08 XE HETATM 18 XE XE Z 18 -11.080 -29.129 -2.144 0.04 5.61 XE HETATM 19 XE XE Z 19 -5.720 -73.029 -2.035 0.04 11.24 XE HETATM 20 XE XE Z 20 10.236 60.097 33.822 0.03 5.38 XE HETATM 21 XE XE Z 21 5.980 68.581 3.532 0.03 7.49 XE HETATM 22 XE XE Z 22 11.107 13.277 27.334 0.03 7.10 XE
I'm pretty sure there aren't 22 sites for xenon to bind in lysozyme but it looks to me like the top 2 (maybe top 3) are actual sites which is great. The strange part is that when I use the same data and have Phenix look for 3 or 4 sites it then only finds 3 or 4 very low occupancy sites and the CC's/R's are again all very poor. Has anyone had this problem or does anyone know what's going on? This is the first success that I'm having with xenon derivatization and it seems to me that if Phenix can find 22 sites when asked to find 2 it should have no problem when asked to find 3 or 4.
Thanks in advance, ~Brennan~ _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb