Hi
As a frequent contributor to prior discussions on this same topic I
would like to broaden the discussion a bit. I'm sorry to say that most
of the comments on this threat are exactly the same positions that have
been expressed many times over the years. I don't want to spent time,
again, retyping my opinions on how I prefer to torment the parameters of
my models to express what I believe is going on inside my crystals.
The fundamental problem is that the parameters we are forced to use,
in our PDB depositions and in the refinement and model building programs
available to us, are wholly inadequate. We cannot accurately (or
precisely) describe what we are are envisioning for the surface side
chains, and sometimes entire stretches of main chain, in our proteins.
We can continue to argue with each other year after year, but there is
no solution to this problem other than changing the nature of PDB models
and allowing a reasonable description of multi-conformation models.
I believe it is fair to say that the consensus after a previous
round of this discussion was that, at the very least, we need a flag for
each atom which indicates whether that atom was placed based on electron
density or simply to make a chemically complete set of atoms for that
type of monomer. I haven't looked but I think that was about five or
ten years ago. Since then the PDB has made major changes to the
structure of PDB entries that will require most software for analysis of
macromolecular models be rewritten and right now that organization is
making a major push to get us to virtually attend a workshop to help us
make this transition. And yet I don't think there is anything in this
new data dictionary to help us with this important but intractable
problem.
Unless the PDB gives us the parameters we need to properly describe
a macromolecular model, and the refinement/model building developers
give us the tools to make use of them, we will be back here again, every
five years or so, rehashing this debate over exactly the same,
irreconcilably poor, solutions to this problem.
Dale E. Tronrud
On 3/10/2023 1:05 AM, Julia Griese wrote:
Hi all,
My impression has been that the most common approach these days is to
“let the B-factors take care of it”, but I might be wrong. Maybe it’s
time to run another poll?
Personally, I call any other approach R-factor cosmetics. The goal in
model building is not to achieve the lowest possible R-factors, it’s to
build the most physically meaningful, most likely to be correct, model.
So if you know that the side chain is part of the protein, you should
model it the best way you can. If it’s there, just disordered, then the
most correct way to model it is to let it have high B-factors. Most
molecular graphics programs don’t flag zero-occupancy atoms, so the user
might never notice. Truncation of a side chain, unless there is evidence
that it really physically isn’t there, is also misleading, in my
opinion. I don’t believe that it is more helpful to the non-expert user
than high B-factors either.
If people who are not structural biologists themselves don’t know how to
use a structure, then we need to educate them better. It is very
straightforward these days to look at electron density in the PDB
viewer. It used to be difficult, but nowadays there’s no excuse for not
checking the electron density. The PDB validation flags RSRZ outliers.
You can easily colour a structure by B-factors. It doesn’t take that
much effort to teach students how to validate structures. The main point
you need to get across is that it is necessary to do so. And this needs
to be done not only in courses aimed at prospective experimental
structural biologists, of course, but whenever students use structures
in any way.
This is just the opinion of someone who feels very strongly about
teaching structure validation and rejoices when students’ reply to the
question “What was the most important thing you learned today?” is:
“Don’t blindly trust anything.”
Cheers
/Julia
--
Dr. Julia Griese
Associate Professor (Docent)
Principal Investigator
Department of Cell and Molecular Biology
Uppsala University
BMC, Box 596
SE-75124 Uppsala
Sweden
email: julia.gri...@icm.uu.se
phone: +46-(0)18-471 4982
http://www.icm.uu.se/structural-biology/griese-lab/
<http://www.icm.uu.se/structural-biology/griese-lab/>
*From: *CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of
Bernhard Lechtenberg <0000968307750321-dmarc-requ...@jiscmail.ac.uk>
*Reply-To: *Bernhard Lechtenberg <lechtenber...@wehi.edu.au>
*Date: *Friday, March 10, 2023 at 05:07
*To: *"CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC.UK>
*Subject: *Re: [ccp4bb] To Trim or Not to To Trim
I found the poll I wrote about earlier. This actually is way older than
I had expected (2011). You can see the poll results (which was run by Ed
Pozharski) and discussion at the time here in the CCP4BB archive:
https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg20268.html
<https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg20268.html>
In brief, the results of 240 respondents were:
Delete the atoms 43%
Let refinement take care of it by inflating B-factors 41%
Set occupancy to zero 12%
Other 4%
Bernhard
*From: *CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Debanu
Das <debanu....@gmail.com>
*Date: *Friday, 10 March 2023 at 2:56 pm
*To: *CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
*Subject: *Re: [ccp4bb] To Trim or Not to To Trim
We dealt with this in-depth during structural genomics days when we
deposited over 1500 novel, high-quality, experimentally-phased
structures into the PDB. Think it’s prudent to trim/truncate side chains
without reliable density.
Non-structural biologists using PDB structures without expert help can
err in any of these scenarios: misinterpreting most common/random
rotamer, zero occupancy atoms, B-factors, etc.
What is the value of populating the PDB, which is a structural model
repository, with such information that is not there, i.e., reliable
structural model?
Any trained crystallographer/structural biologist can easily add in side
chain information if needed for modeling/computational chemistry reasons.
Best regards,
Debanu
On Thu, Mar 9, 2023 at 6:50 PM Jurgen Bosch <jxb...@case.edu
<mailto:jxb...@case.edu>> wrote:
I’d say no trimming to side chains for the following reason: There
are non-structural biologists using PDB files and if atoms are
missing they don’t know what to do. A better approach is where no
side chain density allows support of placement, pick the most common
rotamer and set the occupancy to zero for those atoms lacking
density support. More work for you but more accurate in my opinion.
Jürgen
_______________________________________________
Jürgen Bosch, PhD, MBA
Center for Global Health & Diseases
Case Western Reserve University
Cleveland, OH 44106
https://www.linkedin.com/in/jubosch/
<https://www.linkedin.com/in/jubosch/>
CEO & Co-Founder at InterRayBio, LLC
On Mar 9, 2023, at 9:45 PM, Bernhard Lechtenberg
<0000968307750321-dmarc-requ...@jiscmail.ac.uk
<mailto:0000968307750321-dmarc-requ...@jiscmail.ac.uk>> wrote:
Hi Rhys,
I am also all for leaving side chains and letting the B-factors
deal with the weak/absent density.
I don’t think there is a consensus, but I kind of remember that
somebody did a poll a few years ago and if I remember correctly
the main approaches were the one described above, or trimming
the side-chains.
Bernhard
*Bernhard C. Lechtenberg* PhD
NHMRC Emerging Leadership Fellow
Laboratory Head
Ubiquitin Signalling Division
E lechtenber...@wehi.edu.au <mailto:lechtenber...@wehi.edu.au>
T +61 3 9345 2217
*From: *CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Rhys Grinter
<000022087c81e8c6-dmarc-requ...@jiscmail.ac.uk
<mailto:000022087c81e8c6-dmarc-requ...@jiscmail.ac.uk>>
*Date: *Friday, 10 March 2023 at 12:26 pm
*To: *CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
<CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>>
*Subject: *[ccp4bb] To Trim or Not to To Trim
Hi All,
I'm trying to crowdsource an opinion on how people deal with
modelling side chains with poorly resolved electron or cryoEM
density.
My preference is to model the sidechain and allow the B-factors
to go high in refinement to represent that the side chain is
flexible. However, I'm aware that some people truncate
sidechains if density is not present to justify modelling. I've
also seen models where the sidechain is modelled but with zero
occupancy if density isn't present.
Is there a consensus and justifying arguments for why one
approach is better?
Cheers,
Rhys
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