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It seems to me that the best solution here would be to model what is actually going on: disorder. For the example of a lysine where there is limited or poor electron density beyond the C-beta, the best representation of the physical model would be an ensemble of all possible rotamers of what is physically present in the crystal. Having "N" sidechains (alternate conformers) with occupancies of 1/N would be extremely clear to all users (novice and expert alike) as well as most if not all software. -Tom -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Anastassis Perrakis Sent: Wednesday, January 10, 2007 7:47 AM To: CCP4 Board Subject: Re: [ccp4bb]: Modelling disordered side-chains *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** My two cents and a summary: 1. omitting the atoms on a clearly indicated LYS residue is a choice. It creates a striking phenotype and does not mislead. It might however cause trouble in 'user' analysis software that will not like LYS without its atoms. Plus, we know for sure that these atoms are there, so we omit them ... 2. modeling the lys in a common rotamer is also a legitimate choice, since B's will inflate. But, indeed thats not obvious when you look at the structure. Also, most unfortunately most analysis software and users will ignore B's. 3. putting occupancy to 0.0 does not look like a good choice to me. the atoms still show on display and no user or software uses occupancies any more than B factors, so to me it combines all the trouble together. on top, some refinement programs when occ is 0, they might switch off geometric restraints including VdW repulsion and then its a real mess. i still hesitate between 1 and 2, but my current choice is to use 2 (let B's inflate) and i admit i have limited sympathy for PDB users that ignore B values and also cant be bothered to use the EDS (i.e. i ignore the problem, which is not very nice, but ...) Tassos This email (including any attachments) may contain material that is confidential and privileged and is for the sole use of the intended recipient. Any review, reliance or distribution by others or forwarding without express permission is strictly prohibited. If you are not the intended recipient, please contact the sender and delete all copies. Exelixis, Inc. reserves the right, to the extent and under circumstances permitted by applicable law, to retain, monitor and intercept e-mail messages to and from its systems.
