Dear Ccp4 user,
on behalf of Dr. Muthiah Kumaraswami I would like to inform you that
there is a postdoc position available in the Department of Pathology and Genomic Medicine
at the Houston Methodist Hospital Research Institute.
The group employs a multidisciplinary approach to dissect the mechanisms of bacterial signaling
pathways and to understand the implications of such signaling pathways in bacterial pathogenisis.
Key areas the group is currently investigating include bacterial communication systems and the bacterial
sensory systems for metal and carbohydrate acquisiton.
To this end, we are using a wide range of techniques including X-ray crystallography, SAXS, bacterial genetics,
biochemical and transcriptome analyses, and animal infection studies.
Qualifications and Experience:
Qualified candidates will have or are about to obtain a PhD degree. Candidates are expected to have experience
in protein biochemistry and crystallography. Experience in MAD phasing and model building as well as biochemical/
analytical techniques are a plus. The ability to work in a team, good organizational and communication skills in
English as well as initiative, flexibility and good learing ability are also desired.
Applicants should send a CV with description of current and future research interests, pdfs of representative publications,
and the names, addresses, phone number and e-mail addresses of 2-3 references to
mkumarasw...@houstonmethodist.org
Best wishes,
Nicola
Gesendet: Montag, 02. März 2015 um 05:49 Uhr
Von: "Avisek Mondal" <avisekmonda...@gmail.com>
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] substructure solution.
Von: "Avisek Mondal" <avisekmonda...@gmail.com>
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] substructure solution.
Thank you all for the guidance.
Avisek
On Mon, Mar 2, 2015 at 4:24 PM, Tim Gruene <t...@shelx.uni-ac.gwdg.de> wrote:
Dear Avisek,
did you try shelxd for substructure solution? I think that it tries to
avoid the Uranium solution. There are a couple of caveats with soaks,
e.g. you are not sure about the number of sites and their occupancies.
Occupancies are refined by shelxd, and you can test a few number of
search sites - shelxd has a certain tolerance with respect to the number
of sites. Do you have a native data set, too? Maybe you could try SIRAS
instead of SAD for better phases?
If you feel unfamiliar with shelxc / shelxd shelxe , you can use the GUI
through ccp4i, or also hkl2map which guide you through the process.
Note that autotracing may not work well at 3A resolution.
Best regards,
Tim--
On 02/23/2015 02:29 PM, Avisek Mondal wrote:
> Dear all,
> I am trying to phase a large novel structure of 150 kDa with P21 space
> group. So far I have collected 3.0A datasets from iodinated derivatives in
> Cu-K alpha. In SAD phasing I got 0.745 figure of merit (FOM) and LLG about
> 476208.27 (sites in inverse hand gave the same FOM and LLG),by Phenix
> Phaser-EP. But i am seeing monstrous peak from the substructure solution,
> it seems that all phases merge into huge fourier peak (like Urenium-atom
> solution and Fourier truncation ripples; Ref.Bernerd and Rupp) .But it is
> clear that the iodine has incorporated into the proteins lysine residues
> where the large electron density has been seen (from partial molecular
> replacement solution). Would anyone be able to advise me on how it'd be
> best to improve my phases/density given the limitations of the data? it
> will be very helpful for me as a learner.
>
> Avisek
>
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
