Agreed, ANIS is the command to try.
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On 3 Jun 2021, 20:18, Philip D. Jeffrey wrote:
> R1 of 17% is bad for small molecule.
> 0.8 Å is in the eye of the beholder - if you're using macromolecular cutoffs
> then these might be too aggre
*Postdoctoral Fellow position at UT Health School of Medicine, San Antonio,
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The laboratory of Dr. Yogesh Gupta (http://ccri.uthscsa.edu/YGupta.html) at
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Hi Jacob,
>>The systematic absences in the hkl file pointed to P212121 being the
space group, which is what it was processed in.
If the data were processed in this space group (Laue class), the analysis
of the systematic absence won't tell anything else. Probably, it would be
more useful to proces
Quick reminder about the CCN deadline in about one week. Rough drafts are
an acceptable submission with the realisation that it can be worked into
reasonable standard.
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National L
The systematic absences in the hkl file pointed to P212121 being the space
group, which is what it was processed in. As for the peaks, the highest peaks
are 3.92 at 2.72 A from an oxygen (Q1), 3.67 at 2.74 A from an oxygen (Q2), and
2.68 at 2.75 A from an oxygen (Q3). Q1 and Q3 seem to be about
Dear Gerlind,
I'm glad that we were of help! I should point out that the "Make link (click 2
atoms)" is dangerous as it only generates a LINK record but not a full link
dictionary - it should only be used for common known links that are present in
the monomer library. This issue is discussed in
R1 of 17% is bad for small molecule.
0.8 Å is in the eye of the beholder - if you're using macromolecular cutoffs
then these might be too aggressive for small molecule-type refinement stats -
try a more conservative cutoff lie 0.9 and see how that changes R1. However I
suspect it's more to do w
Dear David and Rob,
thanks a lot for your help and your suggestions.
Following your suggestions I found in Coot the very neat solution "Make
link (click 2 atoms ...): Much better than my previous dinosaur approach.
Thanks again and all the best,
Gerlind
On 03/06/2021 20:17, David Briggs wrote
Dear Jacob,
An R-value of 17% is indeed suspiciously high for a small molecule structure.
Some thoughts:
Are you sure the space group is correct?
There might be twinning involved,. Have you checked the ’signs of twinning’ for
small molecules?
There might be disordered solvent molecules, which
Greetings!
I am currently trying to reduce the R factor of a cyclic small molecule peptoid
in ShelXle. The max resolution of the molecule is 0.8 angstroms. The molecule
itself fits the density very well, but there are a few unexplained densities
around the molecule which do not seem to be anyth
Dear Gerlind,
Where did you get your mad_monlib.cif file? It shouldn't be neccesary for you
to be manually modifying such restraint dictionaries (any more). You can
generate these using AceDRG, either via CCP4i2 or Coot.
Shameless plug:
https://journals.iucr.org/d/issues/2021/06/00/ir5021/index
Hi Gerlind,
Rob Nicholls gave a talk on how to deal with covalent linkages using AceDrg at
CCP4 study weekend in 2020.
https://youtu.be/p4oTJ0bjD3M
And Paul Emsley has written up a guide about it...
https://pemsley.github.io/coot/blog/2020/06/30/make-a-link.html
Hopefully these will be useful
Dear all,
I am going litteraly mad (or just old).
I would like to make a covalent link between a carbohydrate moiety and
and ASP of my well-cheered protein.
The identifier for the carbohydrate moiety is MAD, chain C, res number 1.
The link is established between C5 of MAD and OD2 of ASP 518,
Dear Nick,
I like your idea and your comments on this substance. 1,2-hexandiol
supposed to be chiral but probably it is used as a racemic mixture in
cosmetics. There is even a crystal structure in the PDB (4EUS) and an
associated 3 letter code. I´ll give it a try because it seems to fit
nicel
Hi Peer,
Reminds me of a lipocalin structure I solved which co-purified fatty acid with
it. I could model fatty acids and we along with our collaborators used several
complementary biophysical methods followed by functional assays to identify the
ligand.
https://www.sciencedirect.com/science/art
Dear Peer,
This reminds me of my colleague Michael Rossmann's discovery of a Pocket
Factor which is a fatty acid-like molecule residing in a hydrophobic pocket
underneath the "canyon" in enteroviruses. See
https://link.springer.com/article/10.1007/s13238-014-0092-6. You likely
have an endogenous
Hi Peer,
this density reminds me of something I saw in one of my own structures as well
and which also was not a component that should have been in there (PDB ID
6SMT). I never truly found out what it was, but I modeled it as 2-ethylhexanol,
which is known to be a precursor for the synthesis a
Hi Peer,
If I understand you correctly you are saying that you do not know what
substance may be in the density; then perhaps you only need to extend by
an extra atom to create a new kind of symmetrical molecule that will fit
the density?
BW,
D
On 03/06/2021 11:55, SHEPARD William wrote:
Hi Peer,
Have you tried to model the hydroxyl O1 disordered at the carbonyl
position? Check the H-bonding pattern to the end groups, this might give
some clues.
Cheers,
Bill
Le 03/06/21 12:50, « Peer Mittl » a écrit :
>I'm struggling with the electron density shown in the attachment. The
>
Hi
This is more or less what I do in PyMOL, but I was looking for some
quicker and more user-friendly tool.
A (less cumbersome ?) procedure is the following (thanks to Arwen
Pearson for the hint). It requires external manipulation of the PDB
files and some matrix calculations (I have not tes
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