Dear list members, the validation of TLS parameters used and refined for a particular model of a crystal structure was, at one point, the subject of thorough research, for example: >From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation https://journals.iucr.org/d/issues/2018/07/00/rr5149/index.html
>From deep TLS validation to ensembles of atomic models built from elemental motions https://journals.iucr.org/d/issues/2015/08/00/rr5096/index.html Validation of crystallographic models containing TLS or other descriptions of anisotropy https://pmc.ncbi.nlm.nih.gov/articles/PMC2917275/ Optimal description of a protein structure in terms of multiple groups undergoing TLS motion https://pubmed.ncbi.nlm.nih.gov/16552146/ Corresponding tools are available to the community, as cited in the papers above. Unfortunately, neither database curators nor major atomic model validation bodies have adopted these tools and methods as standard for validating refined TLS parameters. For this conversation to be constructive, one would need to take the TLS parameters in question, decompose them into descriptors of elemental motions, and assess whether these motions make physical sense in the context of the given TLS partitioning. These methods are all detailed in the works above, and the tools to do this are available to you! All the best, Pavel On Tue, Oct 29, 2024 at 8:38 AM Italo Carugo Oliviero < olivieroitalo.car...@unipv.it> wrote: > In a few months, I will retire, because my brain thinks it is still young > but the rest of the body disagrees and thinks the brain is slightly senile. > Of course, I will miss the protein structures very much, so unpredictable > in their insolent beauty. > > > I have devoted several years of my life to the B-factors of their atoms. > > > Initially, almost 30 years ago, some colleagues mocked me, telling me that > the B-side of proteins was nothing but dust hidden under the carpet, > nothing but background noise. Some later changed their minds, and it is now > generally agreed that the B-side of proteins deserves to be visited and > admired. > > > However, I am concerned about more recent developments that are turning > B-factors into real junk. TLS refinements as audacious as they are > ridiculously unprofessional are producing disasters. For example, the 8q66 > structure is very strange. It has been split into individual TLS > mini-blocks, which clearly demonstrates that the authors are unaware of the > TLS procedure and its proper application. A protein containing two > structural domains was divided into six small TLS blocks, one of which > belongs to both domains. Where are physics and chemistry? > > > > How can this happen? Here is the answer from a friend and colleague: > “unfortunately, the crystallographic programs became so automatic and easy > to use nowadays, that even complete ignorant people can get something from > them, and do not think if what they got makes sense or not.” > > > Are computational models preferable in the end? > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## 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/
