Hello Paul, thank you for the kind reply.
Btw. wouldn't AI-assisted coding help you? Americans are already pretty near this milestone - you get like the most of it written and than just go through it and make it perfect... I think it is like with the progressive Italians making their marble sculptures using 400 000 USD robots - they make 99 %, but the final human touch makes them perfect... OK, I may drop a line to Sjors. May be I will add, besides stressing how important is the cross-eye stereo, some other suggestions, like a hot key for moving by 10 residues (thanks for space forward and shift+space backward, that is awesome) (ctrl+space 10 forward and ctrl+shift+space 10 backward?). Michal --- Michal Navrátil, PhD čt 22. 1. 2026 v 18:39 odesílatel Paul Emsley <[email protected]> napsal: > Hello Michal, > > On 21/01/2026 01:58, Michal Navratil wrote: > > > Dear Prof. Emsley, > > > Max Perutz once came to York to give a presentation to the PhD students > where he was introduced as "Professor Perutz" - he gently corrected the > host saying "I work at the LMB, I am not a professor - but my son is!" > The audience chuckled. (Likewise I am not a professor either.) > > > > > thank you for estimating how much of your precious time would be needed. > > > > I really appreciated the cross-eye stereo feature, because I could > > refine my structures just everywhere using my notebook. And in our > > lab, I was not bound to the few computers with 3D goggles , which were > > btw. crappy and constantly failing. > > Likewise ours. Pre-covid I routinely saw people using stereo. Post-covid > I have seen no-one. > > > > > On the other hand, there were some other, perhaps more important > > issues in Coot. For example, grabbing a certain part of peptide chains > > for the quick fitting feature (into el. dens. map) in a large protein > > was pretty laborious and slow, and at least I often grabbed some > > completely different parts of the protein. > If your molten zone is more than about 200 residues that can be an issue > on older hardware, but still, it sounds disappointing. For large > regions, using the GM restraints is a good idea, I have a YouTube video > on it I think, and I did one for SBGrid several years ago now (and > things have become smoother and faster since then). > > > > Also, selecting multiple amino acids on a large protein was quite > > difficult - one had to constantly scroll back and forth in a small > > single line window... That was quite unpractical. > > Sound painful. Typically, one extracts (copies) a working fragment > (using Copy Fragment), does the modelling operations on that, the slots > that fragment back into the main molecule using Replace Fragment. > > Or you can make the residue selection using Python, for example > > coot.refine_residues_py(0, [["A", r, ""] for r in range(10,21)]) > > > > > I wish someone had the patience to teach me programming things like > > this... > > Funny you should mention that. I have been working on a way to have > Claude communicate with Coot (i.e. "program" Coot using prose). I am > enthusiastic about it and will write it up soon - in a blog article at > least. > > > > I wish there wasn't so much sheer disregard like this for > > scientists... I wish I could fund you for the one extra week of your > > work, or write a letter to the King Charles III about how such work is > > worth funding... > > Made me laugh. A letter to the king probably won't do much good. > However, if you or anyone else would like to send a letter of support > for my work to my boss (who doesn't see the value of Coot and/or my work > in the way that I do (he isn't a crystallographer)) that would be more > valuable. > > His name is Sjors Scheres, scheres@(same-place-as-me) > > Regards, > > Paul. > > > <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Virenfrei.www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#m_-7688741256874285788_m_-3557549483419750674_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> ######################################################################## 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/
