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 21 October 2014 07:39, Appu kumar <appu.kum...@gmail.com> 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. > 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 >> > >
