[gmx-users] B-FACTOR

[Ramon Crehuet]

The B-factor is indeed RMSF, precisely 8*pi**2*RMSF. At least formally. In practice it is the result of the refinement procedure that is used in crystallography. If you would like to calculate it, you should simulate a crystal. This is almost never done, but Bojan Zagrovich did it and compared RMSF with B-factors obtained from the refinement process. The results are explained in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3926004/ and I recommend this work whenever you want to compare X-ray and MD B-factors. 




The usual procedure is to overlap or superimpose all structures and calculate RMSF. This again can be done in different ways. The conventional method is performing a least-squares superposition, and then calculating the SD of each atom. But one can also superimpose based on Maximum Likelihood. An approach that Douglas Theobald has pioneered. Here you can find the publications and the software to do it: http://www.theseus3d.org/ It will automatically report RMSF which can be converted in B-factors. 




Hope this helps. 




Ramon 




Thanks for the answer !
I tired that too , but the problem is when we tired viewing the pdb
structure in pymol and MOE software , both show different structural
changes ...

Can you please help me how to over come this problem. How to analyse the
output file of  B-FACTOR  in pymol...?

On 9 May 2017 9:31 p.m., "RAHUL SURESH" < drrahulsuresh at gmail.com > wrote:

I am not sure but I think u can calculate t along with rmsf calculation
where you have to generate additional output as pdb file.
On Tue, 9 May 2017 at 6:58 PM, Kingsley Theras Primus Dass . < 105726107 at gms.tcu.edu.tw > wrote:

> Hi everyone ! > I want to calculate b-factor , but I don't kno how to calculate. Can > anyone please tell me how to calculate b-factor for a protein and how to > analyse it ... > > > Thanks in advance > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > --
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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