Dear Klaus depends how many missing residue you want advertised in the header of your deposited file. The pdb will put in a special Remark 610 and Remark 615 to indicate any missing residues from your heterogen list. However the policy is not to list every missing (or zero occupancy) atom. I have fitted fragments of pegs into density - so I know there are defined hetero residues for several sizes of small fragments. But if you name a PEG as a larger fragment than you can see then, as each PEG would be only one residue, effectively you get only one line in a remark 610 for each PEG with missing bits. Zero occupancy is generally a deprecated way of dealing with missing density as it is confusing for less experienced user of the coordinates. I think zero occupancy can be useful during refinement as the atoms help fill space (or for example satisfy NCS restraint format requirement) but then these atoms can be stripped out before deposition. They should in any case never be included in B-factor refinement as they will skew the statistics and possibly the B-factor restraint model. It seems that large numbers of missing heterogen atoms were anticipated when the format was drawn up - hence the absence of a requirement to list all heterogen atoms that are missing. Hope that helps. Martyn
EBI, Cambridge --- On Thu, 12/8/10, Klaus Sengstack <sengstack-kl...@yahoo.de> wrote: From: Klaus Sengstack <sengstack-kl...@yahoo.de> Subject: [ccp4bb] PEG in the pdb? To: CCP4BB@JISCMAIL.AC.UK Date: Thursday, 12 August, 2010, 9:16 Hi everybody, I just solved the structures of an enzyme an some variants. In the active site cavity of each variant I found one or two fragments of PEG1000 bound. I used PEG1000 in the crystallization condition. Among the enzyme variants the number of non-hydrogen atoms of these PEG fragments varies between 7 and 19 atoms. Now I want to deposit the structures in the pdb and my question is, if I have to define each fragment as a single ligand (what would be a lot of work) or can I define them as PEG1000 molecules? Thanks. K.S.
