Hello, Recently, I deposited a structure in PDB with a ligand, and they changed how the ligand is described to match PDB guidelines, which slightly altered the validation parameters (primarily for Clashscore, but also others) of the structure compared to what I submitted initially.
In my submission, the ligand was defined in the .cif file as a small molecule covalently attached to a nucleotide in RNA. However, PDB described the small molecule as the ligand, and the nt was merged into the RNA backbone. While there was no positional change of either the small molecule or the nt from what was modeled, my validation parameters (determined by MolProbity) are slightly different (for example, clashscore increases from 8 to 9). Given the whole molecule has a low MW (60 kDa), I have noticed that differences in one or two residues can affect the MolProbity scores. I would greatly appreciate any suggestions to circumvent the issue. While the difference is not huge, I would still like to know the reason behind this observation. Thank you! Best, Suparno Nandi, Ph.D. Postdoctoral Fellow Department of Biochemistry Emory University Atlanta, GA, USA ######################################################################## 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/
