Dear all, trying to be more constructive in this particular discussion concerning TLS, I remind you an article especially devoted to a question if the applied TLS model and its results are physically meaningful and, if not (indeed, in very many cases), how to make them such (if possible) or to avoid such errors :
Afonine et al., 2018, Acta Cryst, D74, 621-631 Look especially its part 3. " PDB analysis and improvement of the TLS decomposition" This is not a definite remedy but helps to avoid some errors in this kind of modeling. Talking more generally, I fully agree with Tassos, and I teach this to my students for decades, that programs always give you SOME numbers (if not fail), and it is up to the researcher, and only to them, to see if these numbers are meaningful before showing them. Have a nice day, and sorry for reacting late, Sacha Urzhumtsev ----- Le 29 Oct 24, à 18:52, a perrakis <[email protected]> a écrit : > Dear all, > As I somehow identify with the mention of "some ayatollahs” who perhaps > underwent several rounds of meticulous refinement of demeanor, I fail to see > any wrong to what Oliviero wrote. Oliviero, explains that a third party > proclaimed that "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.”. > He > is not offending anyone in particular or in general as ignorant. He is simply > stating, that “ignorant people” unfortunately exist, and are responsible for > atrocities in the PDB. I would venture to further proclaim that ignorant > people > exist in all walks of life and are responsible for worse atrocities than the > occasionally unreasonable assignment of TLS groups. I am not claiming these > people are ignorant by choice, and I am not claiming they are here reading > this > BB - if they were reading, they would not be as ignorant, or at least they > would be actively trying to limit their ignorance. > Having previously limited my ignorance in X-ray crystallography largely due to > reading this BB, and having my ignorance exposed to this BB, I fail to see > anything wrong with good old-fashioned ignorance. And this BB has a large > willingness to cure ignorance. But, lets face a fact: 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. There are such people out there, sorry to > say > that. Ignorance exists. The ignorant is not the same as the non-expert. Anyone > who writes here asking any question, is by definition not ignorant: by > communicating here we all make a first crucial step, acknowledging the limit > of > our knowledge (which is the extend of our ignorance). And we ask to learn. > These are in my view the non-experts that Gerlind is referring to, and are > here > to learn, and many try to help (I admit I am not helping much the last decade, > mostly as I am hands-off lately). But, the non-expert crowd, is not the same > as > the ignorant crowd. They are different. > My best regards to all and specifically to my good and thoughtful and very > gentle and kind friends Oliviero and Gerlind. > Apologies for my long and largely irrelevant rant - > Tassos >> On 29 Oct 2024, at 17:08, Gerlind Sulzenbacher >> <[email protected]> wrote: >> LET OP: Deze e-mail is afkomstig van buiten de organisatie. Open alleen >> links of >> bijlagen als je de afzender kent en weet dat de inhoud veilig is. >> CAUTION: This email originated from outside of the organization. Do not click >> links or open attachments unless you recognize the sender and know the >> content >> is safe. >> Dear Italo, >> It seems to me that the ccp4bb has always been a very gentle and empathic >> platform of exchange of ideas and offering a great deal of help to >> non-experts, >> "ignorants" as your friend calls them. >> I remember that in the late 90thies there were some ayatollahs, which have >> become gentle civils by now, that used accusatory citations to underpin their >> claims. This period is over, or at least I hope so. >> If ignorance exists, it's our fault of not being able to teach properly the >> young generation. >> I understand your frustation and may be it deserves a letter in an Acta >> Journal, >> but please, please, refrain of citing the "ignorants" in this bb. >> Wishing you a happy retirement and nice and fruitfuil projects, other than >> B-factors, for your future. >> Gerlind >> On 29/10/2024 16:38, Italo Carugo Oliviero wrote: >>> Ce mail provient de l'extérieur, restons vigilants >>> 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 | >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ] >> -- >> Gerlind Sulzenbacher >> Architecture et Fonction des Macromolécules Biologiques >> UMR7257 CNRS, Aix-Marseille Université >> Case 932 >> 163 Avenue de Luminy >> 13288 Marseille cedex 9 >> France >> Tel +33 413 94 95 27 >> E-mail: [ mailto:[email protected] | >> [email protected] ] >> To unsubscribe from the CCP4BB list, click the following link: >> [ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 | >> 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 | > 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/
