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.
########################################################################
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/
