Dear Dr Peligro,
I imagine this evaluation review of protonation prediction that we published
will be of interest:-
https://www.tandfonline.com/doi/abs/10.1080/08893110903213700
If you don’t have access to this article (ie it is behind a paywall) perhaps we
can dialogue offline…
Best wishes,
On 11 Nov 2022, 19:46, Murpholino Peligro wrote:
Can hydrogens be added in a pH/pka-dependent manner? Something like this
(https://server.poissonboltzmann.org/) but get a pdb file ready for
phenix.refine/buster/refmac?
You might want to try http://newbiophysics.cs.vt.edu/H++/. It outputs an
I used to use the riding hydrogens from shelx when I was doing a neutron
refinement a few years ago, now. It might be worth looking at some recent
neutron papers to see how the H/D atoms are handled. I think it is mainly done
with phenix these days ;-0
If you have electrostatic calculations or
Hi
What is the best way to add hydrogens to a pdb file for a, probably, last
round of refinement?
Can hydrogens be added in a pH/pka-dependent manner? Something like this (
https://server.poissonboltzmann.org/) but get a pdb file ready for
phenix.refine/buster/refmac?
Thanks
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
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
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
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
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 Dale,
your last sentence is of great importance:
"leaving the (hopefully) manually inspected and curated Hydrogen atoms in
the deposited PDB"
I believe this hope is unrealistic. Most people do probably not think or
understand what refinement programs do about hydrogen atoms. In Refmac5 it
Hi Dale,
You make very valid points and there are good reasons to keep the refined
hydrogen positions (methyl twists an protonation of HIS are good examples).
There is a way of distinguishing refined a modelled hydrogens in mmCIF and we
should start using that.
About protonation of hustidines:
Matthew:
I think your nice summary leaves out an important point that has not been
explicitly mentioned. That is the question of whether depositing hydrogens
actually adds information to the model. I submit that for a typical protein
refinement it does not. The model is adequately described by
because the Depositor refinement
statistics would differ from that calculated from the submitted structure
missing the hydrogens.
Regards,
Alex
From: Diana Tomchick
Date: Friday, February 28, 2020 at 12:34 PM
To: Alexander Aleshin
Cc: CCP4
Subject: Re: [ccp4bb] Hydrogens in PDB File
[EXTERNAL
@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>"
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Hydrogens in PDB File
[EXTERNAL EMAIL]
Here is just one of many examples that illustrates what I was trying to say
about deposition of the final mmCIF file from the final output of
On Friday, 28 February 2020 11:19:37 PST Diana Tomchick wrote:
> If you deposit an mmCIF file that contains both the observed and calculated
> structure factors from your final round of refinement, then the PDB
> auto-validation reports the same (or so close to the same as to be
> negligible) R
If you deposit an mmCIF file that contains both the observed and calculated
structure factors from your final round of refinement, then the PDB
auto-validation reports the same (or so close to the same as to be negligible)
R factors.
Phenix outputs all of this automatically for you if you
On Thursday, 27 February 2020 16:34:50 PST Alexander Aleshin wrote:
> Ethan wrote:
> - If you are not making claims about hydrogens but just want to
> describe what you did during refinement, I'd go with taking them out
>
> I've noticed that REFMAC and Phenix use riding hydrogens to calculate
Matthew
---
Matthew J. Whitley, Ph.D.
Research Instructor
Department of Pharmacology & Chemical Biology
University of Pittsburgh School of Medicine
From: Ethan A Merritt
Sent: Thursday, February 27, 2020 6:57 PM
To: Whitley, Matthew J
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Hydroge
ical Biology
University of Pittsburgh School of Medicine
From: Ethan A Merritt<mailto:merr...@uw.edu>
Sent: Thursday, February 27, 2020 6:57 PM
To: Whitley, Matthew J<mailto:mjw...@pitt.edu>
Cc: CCP4BB@jiscmail.ac.uk<mailto:CCP4BB@jiscmail.ac.uk>
Subject: Re: [ccp4bb] Hydrogens in PDB
On Thursday, 27 February 2020 15:35:05 PST Whitley, Matthew J wrote:
> Hello all,
>
> I am nearly finished refining the structures of two mutant proteins from
> crystals that diffracted to very high resolution, 1 Å and 1.2 Å,
> respectively. Refinement was conducted in the presence of explicit
>
Hello all,
I am nearly finished refining the structures of two mutant proteins from
crystals that diffracted to very high resolution, 1 Å and 1.2 Å, respectively.
Refinement was conducted in the presence of explicit hydrogens on the models.
I am preparing to deposit these models into the PDB
Dear All,
I have been working on a high resolution protein structure using Shelx
for refinement.
In the PDB output by Shelxl the hydrogen atom names are in duplicate
which is causing difficulty in PDB deposition.
I am aware of the use of shelxpro's B option to prepare for pdb
deposition, it
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Dear Swastik,
unless this is a structure from neutron data I recommend not to
deposit hydrogen atoms at all, because their positions are calculated
rather than refined.
Best,
Tim
On 06/20/2013 11:40 AM, Swastik Phulera wrote:
Dear All, I have been
Hi,
I've generally used PRODRG to create paramater files for any ligands I
add during refinement with CCP4 and/or PHENIX. I've been trying READYSET
from PHENIX as it greatly helps refining some metal ion positions. But
when I use READYSET, any ligand I add (in this case EDO or ethylene
glycol)
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Hi Chris,
If the absence/ presence of hydrogens in the coordinate file made a
difference in the refinement, I guess some parameter setting for the
refinement program is awkward. Did you refine with riding hydrogens in
both cases? Hydrogens can and
Hi Tim,
Yeah, riding hydrogens have always been on. I guess I need some more
investigation.
Chris
On Mon, 2012-05-07 at 15:36 +0200, Tim Gruene wrote:
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Hi Chris,
If the absence/ presence of hydrogens in the coordinate file made a
Hi Chris,
- there is Phenix mailing list for Phenix-related questions. Please check
http://www.phenix-online.org/
- the data resolution of 2.5A does not mean hydrogen atoms are not present
in the crystal. There are methods to account for them. For details see (and
references therein):
On
Dear CCP4bb-ers,
I have come across a problem with Refmac when I do a few cycles of rigid
body refinement. Somewhere in the process I lose all the hydrogen atoms
from the input pdb file even though I'm using the 'hout YES' option.
Refmac version (from log file):
CCP4 6.0: Refmac_5.2.0019
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