On Tuesday, 21 October 2014 07:39:53 AM Appu kumar wrote:
> 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.
Please keep in mind that if the density is poor because the protein really
is disordered, a perfect description of those disordered cell contents will
perfectly reproduce that poor density. So "improved description" does not
necessarily imply "improved map quality".
This is quite different from the case of a poor model for a well-ordered
structure. Here also you will see a low quality map, but in this case it
will improve as your description of the cell contents improves.
Ethan
> 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 <bt.arp...@gmail.com> 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 <appu.kum...@gmail.com> 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
> >
> > --
> > 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
> > Mobile: 9390923667, 9502389184
> > Email: arp...@cdfd.org.in
> >
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