Dear All,

Thank you very much for valuable suggestions and educating me on the normal mode refinement. Actually, I am trying to refine a protein (cytosolic domain and trans-membrane domain). I found a solution through PHASER and density looks really good in both domain but as i proceeds with refinement density remain great in both domain till Rfree around 38%. Interestingly, with further refinement cycle, Rfree reduced to 30% but the density in the trans-membrane domain becomes very weak. That is why i am wondering whether it is possible to improve the density in the trans-membrane domain by using Normal mode refinement. Conservatively speaking, it could be possible that trans-membrane is highly flexible or disordered and after much cerebration, i am thinking to incorporate the normal mode refinement to monitor if there is any improvement in electron density trans-membrane domain.

I would follow suggestions of Dr, Mande and Dr. Ethan. Also, would give a try to what Arpita has suggested. I further, warmly welcome any suggestion on refinement procedure to improve electron density in flexible or disordered trans-membrane domain.

Appu

On 20 October 2014 23:41, Arpita Goswami <[log in to unmask]> wrote:

Hello,

You can also contact elNemo or NOMAD-Ref server developers about getting covariance/correlation matrices from normal mode analysis outputs to know the correctly coordinated mobile atoms. In this way you can compare with biological data also. In Shekhar's said paper K. Suhre (one of the developer of el-Nemo server) has done the same very correctly.

best wishes,
Arpita

On Tue, Oct 21, 2014 at 5:40 AM, Appu kumar <[log in to unmask]> wrote:
Dear CCP4 Users,
I seek your valuable advice and suggestion in carrying out the normal mode structure refinement which manifest the dynamics of protein as linear combination of harmonic modes, used to describe the motion of protein structure in collective fashion. Studies suggest that it is highly useful in refining the protein structure which harbors a considerable magnitude of flexibility in atomic position owing to high thermal factors.
Therefor I want to know is there any software/script available to execute the normal mode of refinement. Thanks a lot in advance for your imperative suggestions

Appu

--
Arpita

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Arpita Goswami
Senior Research Fellow
Structural Biology Laboratory
Centre for DNA Fingerprinting and Diagnostics (CDFD)
Tuljaguda (Opp MJ Market),
Nampally, Hyderabad 500 001
INDIA
Phone: +91- 40- 24749401/404
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