Hi Sajid,
You should first check whether your Se sites are correct or not. I
checked for my Se sites as follows:
1. Create predict_patterson map with se sites(obtained from shelx or solve) and
see if that matches with Ano-diff patterson map.
2. Create SAD phase using se sites. Use that to create Ano-diff Fourier map to
see if se sites are coming back. It should come as the map is biased by the
se sites. Now you can omit one by one se site and do the same thing as
described to see if the omitting se is coming back.
3. If your native and Se-der data are isomorphous, you can also create iso-diff
patterson map to see if the se sites are poping up.
So far with your situation I can suggest only these options to check your se
sites.
Wish you good luck...
Raja
----- Original Message ----
From: Tim Gruene <[EMAIL PROTECTED]>
To: CCP4BB@JISCMAIL.AC.UK
Sent: Friday, 9 May, 2008 4:05:38 PM
Subject: Re: [ccp4bb] phasing at low resolution
Hallo Sajid,
shelxe produces both .phs file. This can be displayed in coot as electron
density map. If you read in the .res file, it should show the 12 Se-sites.
They are good guiding points to start model building. They should also
help you judge whether your solution is at all usable and correct - near
the Se-sites there should be more features to represent the protein
backbone.
You may have done already: you should run shelxe twice, the second time
with all the options of the first run plus '-i'. This inverts the heavy
atom structure. The output files have '_i' appended to their file roots..
You should check both solutions!
Hope this helps, Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Fri, 9 May 2008, sajid akthar wrote:
> Hi All
> I have a data set of Se-Met crystal 3.65A resolution collected at Inflection
> and peak wavelength. Also I have a data set at same resolution in native
> form. The protein size is 28000 dalton. I dont have any model for this
> protein. So I started to find the heavy atom peak search to find out "Se"
> positions using Shelx programe. From ShelxD and E, I got refined 12 Se sites
> with two molecules per AU. This prediction is consistent with the expected
> number of Se incorporation per molecule.
> Since I dont have any model for my protein, I am not able to go beyond this.
> Though I'm trying to reproduce good diffracting crystals, they diffracts at
> this level only. Some native crystals diffaracting upto 3.29A. But they are
> twinned data set. So it is tough to process those data set.
> Can I do phasing for the model with the present 12 sites. Please give me your
> suggestions for this problem.
> Thank you
> Sajid
>
>
> From Chandigarh to Chennai - find friends all over India. Go to
> http://in.promos.yahoo.com/groups/citygroups/
Bollywood, fun, friendship, sports and more. You name it, we have it on
http://in.promos.yahoo.com/groups/bestofyahoo/
