Hi
I have a ligand with phosphate that works well in coot and pymol but when I
open it in QTMG it shows phosphate as a separate moiety than the rest of
the ligand. There are two methyl groups attached to the phosphate but those
bonds are not visible too. so the whole compound looks like there are t
Hi Eike,
one of the points is that, only because you got used to a certain
operation (over many years after someone showed it to you), does not
mean it is intuitive. This could be judged by e.g. showing an ignorant
user both methods and let the person judge which one is easier to use...
Cheers,
T
Hi Tim,
I don't think that metaphor is quite correct. To me it seems that no matter
what button you pushed you got coffee. In my opinion intuitive software is a
blessing and should not easily be disregarded.
But as I said before, I am happy to read into new stuff.
Also there seem to be mixe
Dear Herman,
Am 09.09.2020 um 17:46 schrieb Schreuder, Herman /DE:
The old real-space refinement was intuitive and easy to use and did exactly
what the user expected, without having to consult the manual!😊 The result might
not have been perfect, but was good enough for subsequent Refmac, Buste
Dear Tim,
I really like your example.
Has anyone of the disappointed users asked how to do it properly? Maybe
it is just as easy.
I think it's also up to me to do it properly and put more effort in it.
Often we are restrained in time and improving your toolboox in an
unexpected manner is ha
Dear all,
after the plethora of complaints about v. 0.9 when compared to v. 0.8, I
would like to argue in favour of the new version.
I find RSR is now much more robust, with a larger radius of convergence,
with very useful tools like tandem refinement, etc. which are
particularly useful with cry
Dear Georg and others,
if I followed the thread correctly, the coffee story should really go
like this:
for years you have been pushing the button of a machine
showing a cup with a black liquid inside. After ten years, the
manufacturer of the machine tells you:
"Sorry guy, it is not coffee what
Dear Paul,
I fully agree with Georg and the others. As I said in my first reaction, with
the new coot, the inhibitor or side chain often does not end up a little wrong,
but goes off completely in the wrong direction, which makes me wonder whether I
had somehow selected the wrong map. It might a
Dear Paul,
people are complaining that they have issues fitting their model in real
space using coot 0.9.x. Personally, I very briefly used coot other the
last months but also have problems using RSR properly because I'm used
to do it the way it was over the last 10 years. This might be due to
Surely an opportunity for machine learning to make a real difference?Â
There's enough data in the PDB by now, that you can conceive of a
classifier generating the most likely set of restraints appropriate
given an OMIT map.
On 09/09/2020 11:37, Eleanor Dodson wrote:
I know how difficult it i
You are invited to join a Thermo Fisher Scientific webinar on Sep 29.
_Cryo-EM and MicroED in drug discovery_ (incl. routine structure
determination)
Lectures:
* Dr. Christopher Phillips, Astra Zeneca
* Prof. Paul Midgley, University of Cambridge
* Prof. Patrick Sexto
I know how difficult it is to get the chemistry right, and that really has
to be up to the researcher..
a database of high resolution structures with metals would be useful as a
sanity check. Robbie mentioned
MetalPDB (http://metalweb.cerm.unifi.it/).
E
On Wed, 9 Sep 2020 at 11:18, Garib Murshu
Hi Eleanor,
Obviously I agree that people should use restraints for metals. It will make
metal refinement easy and coordination consistent with chemistry
For distance and angle restraints there is an external distance restraint
mechanism. PDB-REDO can generate for some of the metals. Unfortuna
Dear Paul,
sorry for the delay.
I did not answer your previous questions in detail, because going back to coot
0.8 did solve the problem for me, which kept me busy. But of course, to do sth.
about the situation you need to understand a lot better what is going on.
What I have is a “phenotyp
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