Thank you both for the responses,
I'm a litter worried that my N and C terminal ends don't have higher
bfactors, however the rest of the bfactors follow suit (core ss low near
active site, greater on distal residues, distinctions between ss structure
and coil, etc.). Graph can be found here ->
http://research.parkerdewaal.com/furge/bfactor_byres.xlsx
Now that I have an bfactors generated is there a method to map them into
the average pdb? Or does this have to be done by hand?
Cheers,
Parker
On Mon, Jul 15, 2013 at 5:08 PM, Thomas Cheatham <tec3.utah.edu> wrote:
>
> > > Thank you for the response, I believe I understand the steps required
> > > however I do not know how to perform the the RMS fit to the average
> pdb.
> > >
> > > Here are my two tenative *.ptraj files
> > >
> > > step1.ptraj:
> > > trajin density_extend.nc # load density trajectory
> > > rms first :1-465.CA # rms first to the first
> frame
> > > for
> > > CA
> > > average step_1_average.pdb pdb # output the average pdbfile
> > >
> > > step2.ptraj
> > > ???? somehow load the average pdb?
> > >
> >
> > Look for the "reference" command. This will load a reference structure.
>
> An alternative trick is to simply load up the PDB first:
>
> trajin avg.pdb
> trajin density_extend.nc
> rms first mass out rms :1-465.CA
> ^
> need residue designator
>
> so step1
>
> trajin density_extend.nc
> trajout avg.pdb pdb
> rms first mass out rms :1-465.CA
>
> step2
>
>
> trajin avg.pdb
> trajin density_extend.nc
> rms first mass out rms :1-465.CA
> atomicfluct out bfactor.dat :1-465 bfactor
>
> (and you can look by atom or by residue with the fluctuations)
>
> --tec3
>
> p.s. if you look on Google for "bfactor ptraj" a number of hits come up
> from the reflector that already describe how to do this.
>
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Received on Mon Jul 15 2013 - 16:30:02 PDT
