Hi Jianghai, Yes, looks bad. For a cluster, run at low resolution. Try 4 A, then 5, then 6... -Tom T At 10:51 AM 1/17/2007, you wrote:
Hi Tom,
Thanks for the response. It doesn't look like hyss has found anything. So far what I got is as following.
p=016 f=000 cc=0.050 r=010 cc=0.094 [ best cc: 0.107 0.106 ] p=016 f=001 cc=0.056 r=010 cc=0.090 [ best cc: 0.107 0.106 ] ...
I didn't get any good CC.
How to get hyss to find a heavy atom cluster, i.e. tantalum bromide clusters?
Jianghai
On Jan 17, 2007, at 11:33 AM, Tom Terwilliger wrote:
Hi Jianghai, Maybe Ralf will reply to you too, but this sounds way too long. Have a look at the output of hyss...and compare with the one below:
A good output:
f = peaklist index in two-site translation function cc = correlation coefficient after extrapolation scan r = number of dual-space recycling cycles cc = final correlation coefficient ... p=001 f=001 cc=0.088 r=010 cc=0.127 [ best cc: 0.144 ] p=001 f=002 cc=0.079 r=010 cc=0.138 [ best cc: 0.144 0.138 ] Number of matching sites of top 2 structures: 2 p=002 f=000 cc=0.074 r=010 cc=0.141 [ best cc: 0.144 0.141 ] Number of matching sites of top 2 structures: 2 ... p=010 f=001 cc=0.085 r=010 cc=0.119 [ best cc: 0.333 ] p=010 f=002 cc=0.110 r=010 cc=0.339 [ best cc: 0.339 0.333 ] Number of matching sites of top 2 structures: 45
A bad one would look just like this good one except there would be a long list of correlations, and none would be very high. An ok correlation is 0.3, good is 0.4 or more bad is 0.2 or less.
The run above with 50 sites took 11 minutes... -Tom T
At 08:48 AM 1/17/2007, you wrote:
Hi,
I am trying to use phenix.hyss to find 50 Se sites from my MAD data. Phenix.hyss has been running for more than 24 hrs now and is still going. I have 4 GB memories on my workstation. Phenix.hyss used more 95% of it and makes the machine basically unusable now. Is it normal for phenix.hyss to use so much memories? I am using Phenix 1.24.1b.
Jianghai
+++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++
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Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB