Dear All, I am kind of in agreement with Manfred, but I also have concerns.
The RCSB and the databases are public databases used by non-structural biology experts a lot. They take the model as if it is an experimental result - rather than it being a model. Example: I just got a paper with reviewers' comments. The reviewer insists that there is a crystal structure that clearly shows the conformation is XXX in the pdb and our interpretation of the biochemical data is wrong. The B-factors of the atoms that he says contradict our results are over 100, and there is no density for them in the ED map. I am writing with a justification, explaining all these - but I will see if it is accepted. But the fact remains that this person who is an expert in a different field - still uses it and makes poor interpretations. Are we doing a dis-service to the large group of non-experts, who think the positions are experimental results and interpret data? They are often the audience for who we generate and deposit the data. Thanks, and cheers! Rams [email protected] On Mar 17, 2023, at 4:57 AM, Manfred S. Weiss <[email protected]> wrote: ---- External Email: Use caution with attachments, links, or sharing data ---- Dear all, many views have been expressed in this thread, which I have been following with great interest. Unfortunately, I have to say that many of the views are more based on personal preferences, than on the scientific evidence behind. Here are some facts, that one may want to consider: 1. When you have crystallized your protein, and collected data from it, the obvious assumption is that it is still intact. Unless you have additional information, e.g. from mass spec, that some side chains are cleaved off, they are there. 2. Absence of evidence (meaning missing electron density) is NOT evidence of absence !!!! 3. If you trim, you give the impression that the respective atoms are not there. This means that the solvent model will be incorrect, because the area will be defined as solvent. In my view, the best approach is to build the side chains in their most plausible conformation, or maybe in 2 or 3 or 5 different conformations, and let the ADPs refine freely. All the best Manfred <http://www.icm.uu.se/structural-biology/griese-lab/> ________________________________ -- Dr. Manfred S. Weiss Macromolecular Crystallography Helmholtz-Zentrum Berlin Albert-Einstein-Str. 15 D-12489 Berlin ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta Koch-Unterseher Geschäftsführung: Prof. Dr. Bernd Rech, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 14109 Berlin Deutschland Diese E-Mail kann vertrauliche und/oder rechtlich geschützte Informationen enthalten. Wenn Sie diese E-Mail irrtümlich erhalten haben, informieren Sie bitte sofort den*die Absender*in und vernichten Sie diese Mail. Das unerlaubte Kopieren, die Veröffentlichung sowie die unbefugte Weitergabe dieser Mail ist nicht gestattet. This email may contain confidential and/or proprietary information. If you have received this e-mail in error, please inform the sender immediately and destroy this e-mail. Unauthorized copying, publishing or distribution of this e-mail is not permitted. ________________________________ 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/
