Iain, did you try to set occupancies to 0.01 to have them regularized by refmac? If that makes these residues well-behaved, you could still do a final cycle with occ=0, to get R-factors for the paper which are undistorted by that 1% unwanted occ.
Kay Anastassis Perrakis schrieb:
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 ;-) TassosOmitting 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 change3. refining OVERall B-factors instead of ISOtropic - overall geometry much worse (rmsd 0.088 bonds)4. DAMP 0.5 0.5 - no change5. 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-----
-- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
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