Dear Pietro, 1. Obvious. 2. This is not the case in the structure I mentioned.
Oliviero Il giorno mer 30 ott 2024 alle ore 08:27 PIETRO ROVERSI < [email protected]> ha scritto: > My twopenny worth: > > > 1. TLS reduces the number of degrees of freedom in the parametrisation > of thermal motion (when compared to individual B factors) when more than > 6+6+8=20 atoms are grouped together; > 2. I do not object in principle to a TLS body spanning an interdomain > or an intermolecular interface - if the interactions are strong it may well > be that the motions are correlated across the interface. > > > Pietro > > Sent from Outlook for iOS <https://aka.ms/o0ukef> > ------------------------------ > *From:* CCP4 bulletin board <[email protected]> on behalf of Italo > Carugo Oliviero <[email protected]> > *Sent:* Wednesday, October 30, 2024 7:00:41 AM > *To:* [email protected] <[email protected]> > *Subject:* Re: [ccp4bb] Structures refined ad mentula canis (this is > Latin) > > > Dear Pavel, > > > thanks for this information. > > > Nevertheless, I believe that the vast majority of people employed in > macromolecular crystallography laboratories (group leaders, post-docs, > PhDs, and master students) are unable to read and comprehend these articles > due to their extremely superficial knowledge of crystallography and their > lack of the requisite mathematical tools to address these issues. > > > Best > > > Oliviero > > Il giorno mer 30 ott 2024 alle ore 03:51 Pavel Afonine <[email protected]> > ha scritto: > > 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 < > [email protected]> 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 > ######################################################################## 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/
