Re: [ccp4bb] To Trim or Not to To Trim

Sun, 19 Mar 2023 02:28:45 -0700 

Dear all,
well at least ChatGPT is still way off the heart of the matter and several steps behind some of the best views in the community. 
I asked it:
Please write a paragraph on the subject: "10 things I hate about structural biology data deposition policy" 

It gave me this:
"As an AI language model, I do not have personal opinions or feelings. However, I can provide a general response to the topic you have given me. Structural biology data deposition policies are critical to ensure that research data is accessible and reproducible, facilitating scientific progress. However, some researchers may find these policies frustrating, especially when they encounter obstacles during the process. Ten things that researchers may dislike about structural biology data deposition policies could include complicated data formats, unclear data preparation instructions, data release delays, data sharing restrictions, lack of feedback from data repositories, non-standardized metadata requirements, confidentiality concerns, data loss risks, high submission fees, and legal obligations. Despite these challenges, data deposition policies remain necessary to promote transparency, collaboration, and scientific integrity in the field of structural biology." 

Ciao

Pietro




On 18-03-2023 10:28, Dale Tronrud wrote:

I'm going to dive back in here again to expand this discussion.
Whether this diversion clarifies or obscures issues surrounding the
"crystallographers' dilemma" I'll leave for others to decide.

   There is currently considerable discussion, among people who care
about cell phone cameras, over the behavior of the cameras in some
Samsung cell phones when photos are taken that include the Moon.

https://www.reddit.com/r/Android/comments/11nzrb0/samsung_space_zoom_moon_shots_are_fake_and_here/

   In this post, evidence is presented that photos taken with one of
these phone cameras, and includes the Earth's largest satellite, the
image shows a properly exposed and detailed image of the orb.  This
despite the fact that the test photograph described in the post is of
a tableau containing a deliberately blurred photo of the cratered
globe. The claim is made that the Samsung app is adding information
from sources other than the camera's light sensor and therefore the
image is "fake".

   I expect that Samsung would reply that, once the app is confident
that the silver disk in the image is the nighttime traditional symbol
of romance, it is perfectly reasonable to make that, now identified
aerial, phenomenon appear in the image as expected by every sighted
human in the history of our species.  There have been billions of high
quality photos of the silicate sphere taken. (This is both literally
true and a gross underestimate.)  How can the photo be fake if it
better reflects what the photographer saw than what can be deduced
from only the raw pixels of the sensor?

   Of course, this example differs only in degree from common practice
going back to the beginning of photography.  Photos have always been
modified, sometimes in order to deceive the viewer, but most often to
make the photos more like what the photographer believed the scene
actually looked like.  For example, in nearly every photo I take I
"correct" the color balance.

   Is the photo with a detailed Moon fake?  Are my photos taken at the
forest floor, but without everything being some shade of green, fake?
I think most people would be satisfied if there was a way for them to
know what sources of information were used in creating the image.

   We, as scientists, are much more demanding of our PDB models.  We
build better models when we use all the knowledge at our disposal.  If
we are interpreting a 9A resolution map of hemoglobin and see a
disk-shaped piece of density where we know the heme goes, we are
perfectly justified to build an atomic model of heme.  We are also
obliged to make clear that the exact atomic positions, bond lengths
and angles, were not derived from that map, just as a journalist needs
to make clear to the reader that their photo has been processed to
include detail which was not present when the image was "taken".

   I have deposited models that contained features which were only
"consistent" with the electron density but supported by enough other
forms of evidence to make me confident in their existence.  I have
done my best to make the justification of these models clear in the
reports I have written but continue to be frustrated by the lack of
tools to represent the precise interplay of data sources that support
my model WITHIN the deposition.  I am not so naive to believe that
everyone who has cited my papers have actually read them.

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: [email protected]

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 <[email protected]> on behalf of Bernhard Lechtenberg <[email protected]> 
*Reply-To: *Bernhard Lechtenberg <[email protected]>
*Date: *Friday, March 10, 2023 at 05:07
*To: *"[email protected]" <[email protected]>
*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/[email protected]/msg20268.html <https://www.mail-archive.com/[email protected]/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 <[email protected]> on behalf of Debanu Das <[email protected]> 
*Date: *Friday, 10 March 2023 at 2:56 pm
*To: *[email protected] <[email protected]>
*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 <[email protected] <mailto:[email protected]>> 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
        <[email protected]
        <mailto:[email protected]>> 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 [email protected] <mailto:[email protected]>
        T +61 3 9345 2217

        *From: *CCP4 bulletin board <[email protected]
        <mailto:[email protected]>> on behalf of Rhys Grinter
        <[email protected]
        <mailto:[email protected]>>
        *Date: *Friday, 10 March 2023 at 12:26 pm
        *To: *[email protected] <mailto:[email protected]>
        <[email protected] <mailto:[email protected]>>
        *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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