Clearly, it is a good idea to keep hydrogens:
http://phenix-online.org/presentations/hydrogens.pdf
Not sure why this keeps coming up as a topic given how much it was said
about it in the past, all the MolProbity arguments, etc..
Issue of missing side chains and loops is tricker indeed.
Pavel
O
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On 3/2/2020 10:12 AM, Alexander Aleshin wrote:
> Dear Dale,
> You raised a very important issue that has been overly ignored by the
> crystallographic community. The riding hydrogens are just a tip of an
> iceberg. It is absolutely unclear even to an experienced crystallographer how
> to treat p
Dear Thomas,
Thank you for the explanation. I use an old version 1.7.2.3, and I believe that
the problem is fixed in a newer one. What about residues with missing side
chains? How are they treated when a surface is calculated? I began placing the
"riding side chains" into my models to avoid prob
Dear Alex,
PyMOL by default shows cartoon (secondary structure) only for the first alt
conformation. Do you have an example PDB code were you do not get the expected
representation?
See also:
https://pymolwiki.org/index.php/Cartoon_all_alt
Thomas
> On Mar 2, 2020, at 7:12 PM, Alexander Aleshi
ON BEHALF OF DIAMOND LIGHT SOURCE– LIFE SCIENCES :
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Dear Dale,
You raised a very important issue that has been overly ignored by the
crystallographic community. The riding hydrogens are just a tip of an iceberg.
It is absolutely unclear even to an experienced crystallographer how to treat
poorly ordered side chains or even whole residues. As a ma
--
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--
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While we're at it, it would also be a great improvement if the PDB would list
nominal resolution in all 3 directions for structures with significantly
anisotropic data. I'm never 100% sure what to do in those cases.
Thanks,
Phoebe
~~~
Phoebe A. Rice
Dept. of Bioch
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Dear Tim,
I am in agreement with Ethan and you that a complete description of
the restraints and constraints applied to the model should be included
in the deposition. This is currently a major failing of the wwPDB. For
hydrogen atoms we, at least, have the "Riding hydrogen atoms were added"
Dear Guenter,
No, unless you intend to start with MR (option -M0) -- in such case
pointless is not run.
I could add such option, although it may take a while before it's done
and before it goes as an update to CCP4 7.1.
Do you want to skip pointless to save time, or you get wrong result?
Best re
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