[phenixbb] depositing phenix-refined coordinates
emalito at uchicago.edu
Wed Jul 4 19:23:37 PDT 2007
I have just completed the refinement of 2 structures by phenix, and
I'm really really impressed.
Particularly impressed by elbow and LigandFit, just wonderful.
However, I would be very grateful if someone could point me to the topic
already posted in the message below by Dr. Scott few days ago,
"a quick description for depositing phenix-refined coordinates?",
though the full message contained very interesting points I would
love to hear about
(I also performed refinement by refmac/phenix, and observed kind of a
for those numbers).
Thanks in advance.
Ben-May Department for Cancer Research
Center for Integrative Science, W423J
The University of Chicago,
929 E. 57th Street,
Chicago, IL, 60637
On Jun 30, 2007, at 1:16 PM, William Scott wrote:
> Hi folks:
> With the helpful advice of the phenix crew, I've re-refined 2goz, an
> entry in the pdb in which I used refmac5 the first time around.
> There was a small error in the pdb: One nucleotide (C8 in chain A)
> was rotated 180 degrees about the glycosylic bond from where it
> should have been. The net result is one oxygen atom was in the wrong
> place in the structure, and this was apparent within the difference
> Fourier. After I rotated the base and re-refined in refmac, the
> Rfactor and other stats remained essentially unchanged (so this fix
> has nothing to do with the following):
> My refinement results in Refmac:
> REMARK 3 R VALUE (WORKING SET) : 0.191
> REMARK 3 FREE R VALUE : 0.241
> REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS
> REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1503 ;
> 0.009 ; 0.021
> REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2331 ; 1.676 ;
> Then I refined in phenix.
> I get
> REMARK Final: r_work = 0.1737 r_free = 0.2224 bonds = 0.003 angles =
> So the working and free R factor are both lower, and the geometry is
> substantially tighter.
> If I relax the weights in phenix, even to get rms bonds of around
> 0.006, the free-R goes up, which tells me this is not something I am
> justified in doing.
> Phil Evans once told me that anything tighter than about 0.01
> (conservatively) was science-fiction, in that this is within the
> error of the idealized libraries for bond lengths.
> Other people have asked me about this too, and I didn't know how to
> Is bonds = 0.003 angles = 0.745 realistic, or have I done something
> wrong? Even if I do structure idealization in Refmac, I can't get
> the rms bonds below about 0.005 (and my understanding is that it uses
> the same monomer library).
> Why is the weight multiplied by 0.5 by default? Since changing that
> to 1.0 slightly increases freeR, I assume it is the default for some
> All the best,
> PS: Could someone point me to a quick description for depositing
> phenix-refined coordinates? (The latest phenix installer seems to
> have omitted the docs.)
> William G. Scott
> contact info: http://chemistry.ucsc.edu/~wgscott
> phenixbb mailing list
> phenixbb at phenix-online.org
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