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Hi Pavel,
maybe I should have explained in better detail to avoid confusion. The
importance of the contribution to the X-ray term from hydrogens has
been well-known (and used in refinement programs) for - I guess - more
than 40 years, but I am sure yo
Hi, Tim,
When we were working on our paper in 2011, refmac had a bug that always
indicated in depostions that riding hydrogens were used, whether they were or
not. Published methods did not always clarify this issue. Since we could not be
definitive, we refrained from saying too much about it.
Hi Tim,
just to spice your words up with some numbers
You may also want to note that constrained hydrogen positions are a
> crude approximation and only work with X-ray data where hydrogen atoms
> have little impact on the data.
This contribution can be as large as 1.5% difference in R-fact
Dear Jeff,
I would assume that clashing hydrogen atoms beome less and less an issue
with current refinement programs, since those I am familiar with
(refmac5 and phenix) both genereate constrained hydrogen atoms by
default now, and it has been like this for quite some time - so the
situation shoul
Hi, all,
I am glad to see these matters being discussed. I think we all believe that
protein crystallographers should be concerned with producing models that
modelers and chemists can respect and use.
Schrödinger spends a lot of time thinking about ligands; its refinement
program, PrimeX, ha
On Friday, 13 June 2014 10:12:50 AM Tim Gruene wrote:
> Hi Ethan,
>
> Maybe I miss something, but whenever an error in one of the cif-files
> has been reported, be it directly to Garib, or publicly on the ccp4bb,
> Garib (I assume) fixed very quickly - I don't quite understand why we
> need a new
Do those fixes also make it to the phenix version of the library? Yes,
this is the CCP4bb, but the monomer library is also used by Phenix, and
a good number of structures (almost half of those deposited this year?)
in the PDB now come from phenix.refine. Or in other words, is there a
central, h
Hi Ethan,
Maybe I miss something, but whenever an error in one of the cif-files
has been reported, be it directly to Garib, or publicly on the ccp4bb,
Garib (I assume) fixed very quickly - I don't quite understand why we
need a new term for this process?
Best,
Tim
On 06/12/2014 10:45 PM, Ethan A
-
*From:* CCP4 bulletin board on behalf of Tom
Peat
*Sent:* 13 June 2014 09:08
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Hosed-Up X-Ray Structures: A Big Problem
I’ll wade into this quagmire before the weekend starts.
There are wit
From: CCP4 bulletin board on behalf of Tom Peat
Sent: 13 June 2014 09:08
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Hosed-Up X-Ray Structures: A Big Problem
I’ll wade into this quagmire before the weekend starts.
There are without question some dodgy structures and
: Re: [ccp4bb] Hosed-Up X-Ray Structures: A Big Problem
On Thursday, 12 June, 2014 20:24:43 Joel Tyndall wrote:
> Hi,
>
> I saw Jeffs post with interest and have held off until now. It is relatively
> easy to find structures with bad geometry for small molecules but it does not
&
Behalf Of Tim
> Gruene
> Sent: Friday, 13 June 2014 5:54 a.m.
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Hosed-Up X-Ray Structures: A Big Problem
>
> Hi Jeff,
>
> there are quite a few implications in your brief email that each might open a
> long thread of disc
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Hosed-Up X-Ray Structures: A Big Problem
Hi Jeff,
there are quite a few implications in your brief email that each might open a
long thread of discussion. As brief as possible I think one has to be a good
scientist and a good crystallographie
Hi Jeff,
there are quite a few implications in your brief email that each might
open a long thread of discussion. As brief as possible I think one has
to be a good scientist and a good crystallographier to fully understand
the meaning of a crystal structure, and I think many people believe a
cryst
Hi, Tim,
Thanks for your comment. Do you agree with the editorial's claim that some 25%
of the deposited protein-ligand complexes might be dodgy in significant
details?
This editorial comment represents something that I often hear from drug
discovery professionals. Is it a matter of PR betwe
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I hope that the contents of this section is obvious to most readers of
the ccp4 bulletin board.
Cheer,
Tim
On 06/10/2014 03:40 PM, Jeffrey Bell wrote:
> An editorial comment about protein crystallography appeared under
> that title. It's short and wo
An editorial comment about protein crystallography appeared under that title.
It's short and worth considering.
http://pipeline.corante.com/
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