Dear Ed, In the end it boils down to personal preferences. With the number of crystal structures I refine each year, I am not going to go over every flexible surface residue to decide whether to truncate the side chain or whether there may be some low level density justifying to keep the side chain, so I opt for the biochemical evidence. For me the added advantage is that I only have a single pdb file to take care of. And again, I see no problem in having a model with some atoms with a larger error bar.
You are right that terminii are often truncated. In contrast to a missing side chain, here we really have no reasonable hypothesis where the missing residues are. They may even have been removed by a protease. Cheers, Herman -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Ed Pozharski Sent: Monday, March 26, 2012 4:50 PM To: [email protected] Subject: Re: [ccp4bb] REFMAC5 residues with bad geometry On Mon, 2012-03-26 at 16:30 +0200, [email protected] wrote: > It is like with Heisenbergs uncertainty principle. Either one has a > complete model with a number of atoms having a coordinate uncertainty > of 4-6 Å, or one has a model where the uncertainty of all atoms is > below say 0.5 Å, but with a lot of truncated side chains with clearly > contradict available biochemical evidence. Excellent analogy. I am not sure why truncated arginine (as long as it is not renamed to alanine) contradicts biochemical evidence though. Termini are routinely truncated, no problem there. I have plenty of biochemical evidence that there are more waters in the crystal than I model. If the truncated model contradicts biochemical evidence, the projected model contradicts crystallographic evidence. I agree that a truncated model may lead to interpretation problems, and thus the option of depositing a projected model resolves that. Cheers, Ed. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
