AMBER Archive (2006)

Subject: Re: AMBER: RMS & PCA

From: Zu Thur Yew (yewzt_at_intern.bii-sg.org)
Date: Tue Jul 18 2006 - 00:12:35 CDT

Hi,

Thanks for the replies and script!

ZT

Guanglei Cui wrote:
> Hi,
>
>> 1. Is it possible to rms fit structures with respect to backbone
>> atoms, but get a residue by residue rmsd, like residue 1 compared to
>> residue 1 of the reference structure?
> You can certainly calculate residue RMSD for a single structure or a
> trajectory. If you am familiar with VMD, below is a python script that
> calculate the average residue RMSD for a trajectory.
>
> import molecule
> from AtomSel import AtomSel
>
> molid = molecule.new("trajectory")
> molecule.read(molid, "parm7", "CK_TSAC.cym276.top", waitfor=-1)
> molecule.read(molid, "crd", "cym.nowat.x", waitfor=-1)
>
> refid = molecule.new("reference")
> molecule.read(refid, "parm7", "CK_TSAC.cym276.top", waitfor=-1)
> molecule.read(refid, "rst7", "CK_TSAC.cym276.crd", waitfor=-1)
>
> nframe = molecule.numframes(molid)
> ref = AtomSel("backbone", refid)
>
> fout = open("rmsd.byres.cym.bk.dat", "w")
> for j in range(0, 374):
> sum = 0.0
> for i in range(nframe-5000, nframe):
> sel = AtomSel("backbone", molid, frame=i)
> sel.align(ref, frame=i)
> res_ref = AtomSel('backbone and residue %i' % j, refid)
> res_fra = AtomSel('backbone and residue %i' % j, molid, frame=i)
> sum = sum + res_fra.rmsd(res_ref)
> fout.writelines("%6i%8.3f\n" % (j+1, sum/5000.0))
> fout.close()
>
>>
>> 2. Is it correct to say that "image" is not needed, but a rms fit is
>> required for PCA?
>
> I think you only need to superimpose for PCA analysis. This is for
> removing translation and rotation.
>
>>
>> Thanks, any help/advice is much appreciated!
>>
>> ZT
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