Dear Manfred, In addition to personal preference I think there are some philosophical differences in what the model actually means. I would argue that what we see in the density is stronger evidence of the chemical identity than what we believe we have used as a starting material. After all we don’t know what reactions can happen during crystallisation or even data collection. I would also argue that the model should not primarily represent the chemical composition as such, but rather those atoms that are actually ordered. So if there is no electron density, it is not evidence of that particular atom being absent, but it that doesn’t mean we should model it. If one would apply the same logic to hydrogen atoms we should include them in the model since there is no evidence of their absence. Similarly we could explicitly model water molecules in the disordered solvent and just let them refine to high ADPs, since we have no evidence of the absence of water molecules. Or any disordered region of the protein such as termini. By not modelling these termini, hydrogens or water molecules we could also give the impression that they are not there, but I think the users of the models can and should be expected to understand the limitations of the model. I would find it more misleading to model things that we don’t see but assume to be there versus not modelling them. I think if the “end users" of the model are educated enough that they notice unphysically high ADPs they will also understand a truncated lysine side chain.
Just my 2c, Esko On 17 Mar 2023, at 09:57, Manfred S. Weiss <manfred.we...@helmholtz-berlin.de<mailto:manfred.we...@helmholtz-berlin.de>> wrote: 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/
