Hello All,
I agree with Dale that we don't have a good way to model these things and it has been a discussion for a very long time with no proper answer.
Two more small points- we (or at least I do this all the time) don't model the N- or C-terminal residues that I don't see. They are most likely there somewhere (waving goodbye in the solvent mask) and that seems to be (relatively) standard practice, so I'm not sure how different this is to not putting in side chains that can't be seen? We don't replace with Ala, so people should know what the actual sequence is, but there is no evidence for a side chain. A multi-model is likely the better way to go, but isn't as feasible currently as the single model we normally deposit. As mentioned by others, we shouldn't try to put in ligands or co-factors that we don't see either...
One other point- although we should educate, the PDB has estimated that 99% of the users are not structural biologists (nor modellers or others with training), so no matter how much we try to educate people, the vast (vast, vast) majority of people will take the models as the 'truth'. So if we don't see something, the conservative approach is to probably avoid putting it in, otherwise it will get propagated forever.
My two cents. cheers, tom
From: CCP4 bulletin board <[log in to unmask]> on behalf of Dale Tronrud <[log in to unmask]>
Sent: Saturday, March 11, 2023 7:15 AM
To: [log in to unmask] <[log in to unmask]>
Subject: Re: [ccp4bb] To Trim or Not to To TrimHi
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: [log in to unmask]
>
> 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 <[log in to unmask]> on behalf of
> Bernhard Lechtenberg <[log in to unmask]>
> *Reply-To: *Bernhard Lechtenberg <[log in to unmask]>
> *Date: *Friday, March 10, 2023 at 05:07
> *To: *"[log in to unmask]" <[log in to unmask]>
> *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:
>
> [log in to unmask]" target="_blank">https:[log in to unmask]
> <[log in to unmask]" target="_blank">https:[log in to unmask]>
>
> 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 <[log in to unmask]> on behalf of Debanu
> Das <[log in to unmask]>
> *Date: *Friday, 10 March 2023 at 2:56 pm
> *To: *[log in to unmask] <[log in to unmask]>
> *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 <[log in to unmask]
> <mailto:[log in to unmask]>> 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
> <[log in to unmask]
> <mailto:[log in to unmask]>> 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 [log in to unmask] <mailto:[log in to unmask]>
> T +61 3 9345 2217
>
> *From: *CCP4 bulletin board <[log in to unmask]
> <mailto:[log in to unmask]>> on behalf of Rhys Grinter
> <[log in to unmask]
> <mailto:[log in to unmask]>>
> *Date: *Friday, 10 March 2023 at 12:26 pm
> *To: *[log in to unmask] <mailto:[log in to unmask]>
> <[log in to unmask] <mailto:[log in to unmask]>>
> *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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