Hi Martin, You’ll find that you’ll get some very opinionated, but different, answers to this question! (myself included)
Here’s a link to a discussion on this topic from a few years ago: https://www.mail-archive.com/[email protected]&q=subject:%22%5C%5Bccp4bb%5C%5D+To+Trim+or+Not+to+To+Trim%22&o=newest Hope that helps see a few different sides of the coin. Best regards, Rob On 2 Jul 2026, at 15:47, 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/
