have a look in the ccp4bb archives, this has been discussed multiple times without a clear conclusion
my approach would be to keep them and let the B-factors refine to high values, the reason is that you know the side-chains are there and with full occupancy (the validation statistics may be worse but that is normal for low-res structures) Mark van Raaij Dpto de Estructura de Macromoleculas, lab B5B Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. +34 91 585 4616 (internal 432092) > On 2 Jul 2026, at 16:47, Martin Hu > <[email protected]> wrote: > > Dear all, > > I would like to ask for some advice on the best way to handle poorly defined > side chains for deposition of a low-resolution (~3.6 Å) X-ray structure. > > For a number of residues in my structure, there is little or no side-chain > density, so I do not feel confident modelling the full side chains. At the > moment, I have deleted the residues that are not supported by the electron > density, which also gives better geometry and refinement statistics. > > I asked the PDBe deposition team whether they had any preference between > deleting the unsupported side-chain atoms or keeping them with zero > occupancy. They replied that they do not have any specific requirements, as > long as the deposited model is appropriate. > > I was therefore wondering how people here would normally deal with this > situation for PDB deposition. Would you generally: > > * delete the unsupported side-chain atoms, > * keep the full side chains but set the unsupported atoms to zero occupancy, > * or use another approach? > > I’d be interested to hear what people usually do for structures around this > resolution. > > Many thanks in advance. > > Best regards, > > Martin Hu > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
