If refmac left those residues alone I do not understand how planarity can
become distorted. And I would like to understand ...
As for the Wiki: I often find what I am looking for in a Wiki, but in this
email based BB I often find things which I was not looking for and am very
grateful for repetition of discussions.
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Tue, 16 Oct 2007, Anastassis Perrakis wrote:
On 16 Oct 2007, at 8:44, Tim Gruene wrote:
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Hi Iain,
I know there are (at least) two schools of thought and both have their
justification, and my suggestion does not explain you phenomenon.
However, instead of setting the occupancy to zero, I would rather delete
the affected atoms/ residues.
In my point of view this would make your submitted structure less error
prone, especially to non-crystallographers, because they usually just look
at the PDB file with a graphics viewer rather than the PDB file itself (and
most viewers, unlike coot, do not highlight atoms with zero occupancy).
Oh - its been a year since we did not have "Episode 17: The return of the
Positionally Challenged" !
Although I am confident Garib will clear the landscape soon (0 occ atoms are
ignored for for everything, including restraints; it is an old PROLSQ
'feature' that has been adopted by REFMACx as far as I know).
I personally btw like to leave the atoms there and let B's go high, with
similar arguments like Tim's, and with similar 'side-effects'. Better be
clear that a long side chains is there, rather than think its Alanine. But, I
am sure the archive has loads on that, including all the arguments that
counter the above.
Maybe I will set up a ballot in the (coming soon!) ARP/wARP blog ;-)
Tassos
Omitting these residues should help correct interpretation of you data by
others than you.
As a side effect, it would solve your problem of bonds becoming distorted.
Tim
- --
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Mon, 15 Oct 2007, Iain Kerr wrote:
Dear all,
I'm refining a structure (with TLS, Hs in riding positions) to 2.9A -
Rfree ~29.9%/Rfac 26.5% in Refmac5 v5.2.0019. Rmsd bonds 0.008A/1.1deg
angles.
In COOT (0.31) many of the residues whose side chains are (fully or
partially) set to 0.00 occupancy have really bad geometry...for want of a
better description, the side-chains literally look like they have
exploded...a few are intact but have distorted planarity. This occurs in
25 residues out of 480 in the ASU.
I have tried:
1. refining without TLS - no change
2. no hydrogens - no change
3. refining OVERall B-factors instead of ISOtropic - overall geometry much
worse (rmsd 0.088 bonds)
4. DAMP 0.5 0.5 - no change
5. BABINET scaling instead of SIMPLE - no change in geometry, Rfree and
Rfac increase ~3%
6. relaxing geometry (rmsd 0.019A bonds/1.8deg angles)
This occurs with two other structures at higher resolution (~2.5A),
although only a few violations..it seems to be much worse at low
resolution.
Any ideas ?
Thanks,
Iain
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.6 (GNU/Linux)
iD8DBQFHFF3uUxlJ7aRr7hoRAivQAKDcwJA3N7ogdVDkI/jgCaYYy7SoAQCg7GRX
zcKlycSzlE92bLXJlsrj+Iw=
=uxaZ
-----END PGP SIGNATURE-----
