[phenixbb] what about heavy atom as model for MR

Terwilliger, Thomas C terwilliger at lanl.gov
Sat Jun 22 19:31:04 PDT 2013

I'm not sure if there is a tool that will create the file you want for this.  You could however just write a little script that reads in a .sca file and calculates F from I, subtract F+ - F- to get Dano, square that, write out Dano**2 and sigma(Dano**2) as another .sca file.  Then you could use this as input to molecular replacement with your sites from the P4322 dataset.

There is an important caveat to this approach however:  your sites from the P4322 have to be all part of the same molecule, and this might or might not happen automatically.  If some sites are from one molecule and others from another molecule, then in the other crystal form their relationship won't be correct.  If there is only one molecule in the au then this might or might not be a big problem. If there are more than one it is very likely to be a big problem.   This would apply to the density search that you carried out as well.  If your density is good enough to see where the molecule is, you might be able to figure out which of the symmetry-related sites to include in your MR search.

Nevertheless as this is easy it seems like a fine thing to do.  However I am wondering if it will work because your 2.6 A semet anomalous dataset did not yield a solution by itself, which is a little surprising...  Also of course if your P4322 solution is not actually right or even just not close enough it would not work.

-Tom T

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of 赵岩 [zhaoy at moon.ibp.ac.cn]
Sent: Sunday, June 23, 2013 7:52 AM
To: phenixbb at phenix-online.org
Subject: [phenixbb] what about heavy atom as model for MR

Hi everyone,

The heavy atoms(Se-Met) were located at P4322 space group(4A). But the initial density map is so bad that I can not build the initial model.

Meanwhile, I have another two datasets, native(2.6A) and  se-met anomalous dataset with space group P2221. But these two datasets have no solution. I have tried the initial map from sp P4322 as a model to do molecular  replacement. But no MR solution.

So, I want to know how can I use the heavy atom as model to do MR with isomorphous or anomalous differences?



Yan Zhao, M.Phil.
National Laboratory of Protein Sciences
Institute of Biophysics
Chinese Academy of Sciences
15 Datun Rd.
Beijing, 100101
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