There are 5 messages totaling 3613 lines in this issue.
Topics of the day:
1. How to address deposited structures poorly modeled? (5)
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
----------------------------------------------------------------------
Date: Sun, 1 Jun 2025 09:42:19 +0000
From: Julia Griese <julia.gri...@icm.uu.se>
Subject: Re: How to address deposited structures poorly modeled?
Dear Nikolas,
To answer your follow-up question, I believe it would indeed be a good idea to
give reviewers access to the model and map. This is already a fairly standard
procedure for manuscripts containing cryo-EM structures, so why not for crystal
structures? Maybe because the crystallography community is “older” and more set
in their ways, maybe because the validation report is more useful/more likely
to catch problems in the case of crystallographic data because validation of
cryo-EM data is still lagging behind (although we do have useful metrics by
now)? I don’t know.
What I would like to add is that the more I am asked to review manuscripts the
more I realise that it is not at all standard practice for journals to require
submission of the PDB validation report. I always request it in that case, but
that doesn’t necessarily result in me actually seeing it before the manuscript
is published.
Also, too many authors still hold back on releasing their PDB entries when
they’ve deposited a preprint (by not authorising the entry). I don’t see why
you wouldn’t when the preprint is out there.
Best,
Julia
Sent from Outlook for iOS<https://aka.ms/o0ukef>
________________________________
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Nikolas
<nikolas.ca...@gmail.com>
Sent: Saturday, May 31, 2025 7:44:59 PM
To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] How to address deposited structures poorly modeled?
Hi,
Thank you all for the incredibly instructive responses.
Being this my first time happening upon such a "situation" and I'm very glad it
brought to a fruitful conversation as well as a set of instructions on how to address
such things.
Indeed mistakes can be made and sometimes models cannot be improved beyond a
specific point for several reasons, just as sometimes things are rushed
-unfortunately- due to deadlines. Personally, I didn't think of it as
malevolence but more of it as a genuine oversight or mistake. I sincerely
thought that was a pity, considering the rest of the structure. But maybe
that's just me intertwining the joy of determining a structure with the pride
of making it the best I could with the means given (while also seeking second
opinions and help, if necessary).
I will try to re-refine, PDB-REDO and then, if any improvements are observed,
reach out to the depositors.
I will then try to give another prompt, since we are on topic: what would be
the best way to spot such mistakes early on, after the structures have left the
authors, aside from the Curators? Should we provide reviewers with the mtz and
the model instead of just the validation report? Should they ask for it, while
reviewing a manuscript?
Once again, thank you all; you've been wonderful.
My opinion about the depositors of such models is not suitable for this public
forum.
I've probably laughed too hard at this.
Cheers,
Nikolas
Il giorno sab 31 mag 2025 alle ore 07:40 Eleanor Dodson
<0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk<mailto:0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>>
ha scritto:
Don’t be too judgmental- Phil Evans once said - well, I have spent 95% of my
refinement time tweeking the 5% of the water molecules which no one will ever
ever look at!
Gross errors - bad; deliberate errors indefensible , but I don’t think I have
ever deposited a structure which couldn’t be “improved”.
On Sat, 31 May 2025 at 12:20, Robbie Joosten
<robbie_joos...@hotmail.com<mailto:robbie_joos...@hotmail.com>> wrote:
Hi Matthew,
are you willing to elaborate on the motives for “molecular crippleware”?
They seem to stem from the idea that you have a competitive advantage by not
fully disclosing your structure model. This is by now, fortunately, a very
old-fashioned way of thinking. But people have fought long and hard to get
fellow crystallographers to deposit their models and their experimental data.
Believe it or not, in the past there were several programs that could turn a
stereo image into 3D coordinates to deal with people not depositing their
coordinates.
Now that the extraordinary predictive potential of the PDB data has been
proven I would say that it's not justifiable to deposit anything where the
model is only complete to the extent that the primary research aims are met,
who knows what future patterns might be degraded?
This is what I teach, but having the time and resources to really optimise a
structure model before deposition is also a bit of a luxury in some settings.
I would hope that if I was ever responsible for something like this it would be
due to a mix-up with versions etc... but either way I would want to know!
If it is a clear mix-up I always try to get in touch with the depositors and I
hope that this discussion will encourage other to do the same.
Cheers,
Robbie
Best
Matthew.
Sent from Outlook for iOS <https://aka.ms/o0ukef>
________________________________
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>>
on behalf of Robbie
Joosten <robbie_joos...@hotmail.com<mailto:robbie_joos...@hotmail.com>>
Sent: Saturday, May 31, 2025 11:03:47 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
<CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] How to address deposited structures poorly modeled?
Hi Nikolas, There are many reasons for PDB entries to be worse then they
could be. The most obvious is just that when the models were made the
tools were not as easy to use as now and the depositors were less
experienced then they are now. This Hi Nikolas,
There are many reasons for PDB entries to be worse then they could be. The
most obvious is just that when the models were made the tools were not as
easy to use as now and the depositors were less experienced then they are
now. This is natural and, as Guillaume mentioned, to some extent PDB-REDO
can help here. Sometimes a lot, sometimes surprisingly little and on rare
occasions even making things worse (tell me if you find such a case). There
now is a related effort from Foldot where the community is encouraged to
treat a specific PDB entry as a model versus map puzzle. If the models from
that are clearly better than the PDB model (e.g. for the chain you mention)
then it will drip through to PDB-REDO.
Another reason for models appearing worse then expected is simple mix-ups.
I have seen cases where just an older version of the model, rather than the
final version, was deposited by accident. Also in series of structures there are
sometimes mix-ups where the wrong set of reflections were uploaded
making the map look terrible in relation to the model. These cases you can
sometimes tell from the cell dimensions and resolution of the reflection data.
I found a case of that last year, contacted the depositors and they updated
their PDB entry with te help of te PDB annotators. A friendly email can work
miracles is you have a good estimate of what is going on.
I'm sure there are many cases where people were just rushed into depositing
an unfinished model. We all know the pressures in our line of work. It is not
pretty, but understandable. Sometimes the models can be fixed by
automated means, sometimes it requires a bit more work. The depositors
may be quite well-willing to update their model if you take some of the
burden of fixing it out of their hands.
Then there are cases where there is genuine incompetence. That is, the
depositor really didn’t know they were doing things wrong or their
supervisor didn't supervise well (or at all). Sometimes reaching out to the
depositor can help (I have seen successful cases of that), but you may run
into significant resistance. Nobody likes to be told, however nicely, that they
were wrong. Here it also really matter whether the model is just suboptimal
or it really leads to wrong conclusions or, even worse, has lead to the wrong
conclusions. You risk putting yourself in a situation where you have to tell
someone that this part of their paper is wrong because the model is wrong.
You can reach out to the authors b hind the scenes, but it is also legitimate to
just in your scientific work on the topic mention the issue a set the record
straight without making it personal. You can also use such examples for
teaching to make sure the new generation is more competent. All in all these
are cases not just examples of individual failure but also of a failure of us
as a
community. In the long run, leading by example by making sure your
students are well trained and supervised is key. CCP4 organises a lot of
courses in crystallography where we help people improve their skill and
knowledge in the matter. I am of course completely biased, but I highly
recommend such courses.
Indifference is another reason for poor models in the PDB. The part of the
model in which the depositors were interested is perfectly fine but the rest
clearly lacks attention. Without knowing any of the details, the model you
mention may fall in this category. You may be able to get in touch with the
depositors to update the model, but don't hold your breath. If it is an older
model (pre 2008) just appreciate that they were bothered to deposit the
model and data at all. If the model answered the scientific question for which
the model was made correctly, then it is a sound model. It's just not that
useful for other applications. Devil's advocate: who are we to decide that
other researchers shut invest resources into improving a model beyond what
is needed for their primary research?
The final category is malevolence. Yes, there are cases in the PDB where
people purposely deposited worse models than what they describe in the
paper. I call that molecular crippleware. Most of the cases predate 2008
although there was one case after that about which I complained to the PDB.
Unfortunately there was very little they could do. There were also
documented cases of outright fraud, but these models actually appeared (in
some aspects at least) quite alright. My opinion about the depositors of such
models is not suitable for this public forum.
Anyway, good of you to reach out to the bulletin board and keep fighting the
good fight.
Cheers,
Robbie
-----Original Message-----
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>>
On Behalf Of
Nikolas
Sent: Friday, May 30, 2025 23:31
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] How to address deposited structures poorly modeled?
*enters the BB and kneels in reverence*
Dear BB,
Recently, delving among papers and structures for a current project, I
came across a deposited structure of interest that is terribly
modeled. In the PDB resolution is 2.00 Å (R/Rfree=0.19/0.22) and the
quality indicators are not terrible but upon opening it and checking
the maps there are some severe mistakes in the modeling.
For instance, a full chain that is in the negative Fo-Fc while
positive density is present, some density that is quite clear for SO4
molecules (buffer) modeled as water and density for water molecules
neglected. Some parts seem like “coot:runwater” has been used and not
checked. The catalytic site is well defined.
Now, I’ve started my journey in crystallography not too long ago and
I’ve got many years, structures to solve and things to learn, and I
know that sometimes the dataset “is what it is” but these seems quite big
mistakes.
Especially because I’ve worked with such proteins before and I know
the systems.
My question thus is: would it be right to contact the author of this
structure and point to these issues? What’s the best way to address
such things, possibly without coming off as obnoxious?
Thank you for your wisdom.
Cheers,
Nikolas
*bows and leaves the BB*
________________________________
To unsubscribe from the CCP4BB list, click the following link:
https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC
.exe?SUBED1=CCP4BB&A=1__;!!PDiH4ENfjr2_Jw!DIetizJCm94LYkFe6Jy4-
STeHd1x
qiTlYckYQhazL-JqrMkZQz1W00Onif_FtXKpKof041v7RfEwi3adRQ-
l0xMfnCZKvB5o24
BIUg$[jiscmail[.]ac[.]uk]
###############################################################
#########
To unsubscribe from the CCP4BB list, click the following link:
https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-
JISC.exe?SUBED1=CCP4BB&A=1__;!!PDiH4ENfjr2_Jw!DIetizJCm94LYkFe6Jy4-
STeHd1xqiTlYckYQhazL-JqrMkZQz1W00Onif_FtXKpKof041v7RfEwi3adRQ-
l0xMfnCZKvB5o24BIUg$[jiscmail[.]ac[.]uk]
This message was issued to members of
https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!PDiH4E
Nfjr2_Jw!DIetizJCm94LYkFe6Jy4-STeHd1xqiTlYckYQhazL-
JqrMkZQz1W00Onif_FtXKpKof041v7RfEwi3adRQ-
l0xMfnCZKvB4gf54SaA$[jiscmail[.]ac[.]uk], a mailing list hosted by
https://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!PDiH4ENfjr2_Jw!
DIetizJCm94LYkFe6Jy4-STeHd1xqiTlYckYQhazL-
JqrMkZQz1W00Onif_FtXKpKof041v7RfEwi3adRQ-
l0xMfnCZKvB4tB7WRHg$[jiscmail[.]ac[.]uk], terms & conditions are available
at
https://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/_
_;!!PDiH4ENfjr2_Jw!DIetizJCm94LYkFe6Jy4-STeHd1xqiTlYckYQhazL-
JqrMkZQz1W00Onif_FtXKpKof041v7RfEwi3adRQ-
l0xMfnCZKvB6BG0ZtyQ$[jiscmail[.]ac[.]uk]
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of
www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by
www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
________________________________
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
________________________________
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen
avsändaren och vet att innehållet är säkert.
CAUTION: Do not click on links or open attachments unless you recognise the
sender and know the content is safe.
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att
vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du
läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For
more information on how this is performed, please read here:
http://www.uu.se/en/about-uu/data-protection-policy
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
------------------------------
Date: Sun, 1 Jun 2025 10:22:40 +0000
From: Guillaume Gaullier <guillaume.gaull...@kemi.uu.se>
Subject: Re: How to address deposited structures poorly modeled?
Hi Nikolas,
I don’t know much about crystallography beyond the big picture from school. But
with cryoEM structures, the class of big problems you described in your first
email can be detected from the validation report only, especially from the
pictures of map and model overlayed, and from the per-residue Q-scores mapped
to the sequence and model. The atom inclusion plot at the recommended contour
level is also a quick way to detect if large parts of the model are out of
density (but less visual). Of course, direct inspection of the map and model is
best, especially for catching more subtle problems.
I agree with Julia that PDB entries should be released at the time a preprint is made
public. This is the official stance of the wwPDB since the 15th of October 2024 anyway:
they consider that a preprint constitutes publication and therefore triggers the release
of an entry marked "on hold until publication" (HPUB). See:
https://www.wwpdb.org/news/news?year=2024#670d48435697788818ca8c34
Cheers,
Guillaume
On 1 Jun 2025, at 11:42, Julia Griese
<julia.gri...@icm.uu.se<mailto:julia.gri...@icm.uu.se>> wrote:
Dear Nikolas,
To answer your follow-up question, I believe it would indeed be a good idea to
give reviewers access to the model and map. This is already a fairly standard
procedure for manuscripts containing cryo-EM structures, so why not for crystal
structures? Maybe because the crystallography community is “older” and more set
in their ways, maybe because the validation report is more useful/more likely
to catch problems in the case of crystallographic data because validation of
cryo-EM data is still lagging behind (although we do have useful metrics by
now)? I don’t know.
What I would like to add is that the more I am asked to review manuscripts the
more I realise that it is not at all standard practice for journals to require
submission of the PDB validation report. I always request it in that case, but
that doesn’t necessarily result in me actually seeing it before the manuscript
is published.
Also, too many authors still hold back on releasing their PDB entries when
they’ve deposited a preprint (by not authorising the entry). I don’t see why
you wouldn’t when the preprint is out there.
Best,
Julia
Sent from Outlook for iOS<https://aka.ms/o0ukef>
________________________________
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf
of Nikolas <nikolas.ca...@gmail.com<mailto:nikolas.ca...@gmail.com>>
Sent: Saturday, May 31, 2025 7:44:59 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
<CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] How to address deposited structures poorly modeled?
Hi,
Thank you all for the incredibly instructive responses.
Being this my first time happening upon such a "situation" and I'm very glad it
brought to a fruitful conversation as well as a set of instructions on how to address
such things.
Indeed mistakes can be made and sometimes models cannot be improved beyond a
specific point for several reasons, just as sometimes things are rushed
-unfortunately- due to deadlines. Personally, I didn't think of it as
malevolence but more of it as a genuine oversight or mistake. I sincerely
thought that was a pity, considering the rest of the structure. But maybe
that's just me intertwining the joy of determining a structure with the pride
of making it the best I could with the means given (while also seeking second
opinions and help, if necessary).
I will try to re-refine, PDB-REDO and then, if any improvements are observed,
reach out to the depositors.
I will then try to give another prompt, since we are on topic: what would be
the best way to spot such mistakes early on, after the structures have left the
authors, aside from the Curators? Should we provide reviewers with the mtz and
the model instead of just the validation report? Should they ask for it, while
reviewing a manuscript?
Once again, thank you all; you've been wonderful.
My opinion about the depositors of such models is not suitable for this public
forum.
I've probably laughed too hard at this.
Cheers,
Nikolas
Il giorno sab 31 mag 2025 alle ore 07:40 Eleanor Dodson
<0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk<mailto:0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>>
ha scritto:
Don’t be too judgmental- Phil Evans once said - well, I have spent 95% of my
refinement time tweeking the 5% of the water molecules which no one will ever
ever look at!
Gross errors - bad; deliberate errors indefensible , but I don’t think I have
ever deposited a structure which couldn’t be “improved”.
On Sat, 31 May 2025 at 12:20, Robbie Joosten
<robbie_joos...@hotmail.com<mailto:robbie_joos...@hotmail.com>> wrote:
Hi Matthew,
are you willing to elaborate on the motives for “molecular crippleware”?
They seem to stem from the idea that you have a competitive advantage by not
fully disclosing your structure model. This is by now, fortunately, a very
old-fashioned way of thinking. But people have fought long and hard to get
fellow crystallographers to deposit their models and their experimental data.
Believe it or not, in the past there were several programs that could turn a
stereo image into 3D coordinates to deal with people not depositing their
coordinates.
Now that the extraordinary predictive potential of the PDB data has been
proven I would say that it's not justifiable to deposit anything where the
model is only complete to the extent that the primary research aims are met,
who knows what future patterns might be degraded?
This is what I teach, but having the time and resources to really optimise a
structure model before deposition is also a bit of a luxury in some settings.
I would hope that if I was ever responsible for something like this it would be
due to a mix-up with versions etc... but either way I would want to know!
If it is a clear mix-up I always try to get in touch with the depositors and I
hope that this discussion will encourage other to do the same.
Cheers,
Robbie
Best
Matthew.
Sent from Outlook for iOS <https://aka.ms/o0ukef>
________________________________
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>>
on behalf of Robbie
Joosten <robbie_joos...@hotmail.com<mailto:robbie_joos...@hotmail.com>>
Sent: Saturday, May 31, 2025 11:03:47 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
<CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] How to address deposited structures poorly modeled?
Hi Nikolas, There are many reasons for PDB entries to be worse then they
could be. The most obvious is just that when the models were made the
tools were not as easy to use as now and the depositors were less
experienced then they are now. This Hi Nikolas,
There are many reasons for PDB entries to be worse then they could be. The
most obvious is just that when the models were made the tools were not as
easy to use as now and the depositors were less experienced then they are
now. This is natural and, as Guillaume mentioned, to some extent PDB-REDO
can help here. Sometimes a lot, sometimes surprisingly little and on rare
occasions even making things worse (tell me if you find such a case). There
now is a related effort from Foldot where the community is encouraged to
treat a specific PDB entry as a model versus map puzzle. If the models from
that are clearly better than the PDB model (e.g. for the chain you mention)
then it will drip through to PDB-REDO.
Another reason for models appearing worse then expected is simple mix-ups.
I have seen cases where just an older version of the model, rather than the
final version, was deposited by accident. Also in series of structures there are
sometimes mix-ups where the wrong set of reflections were uploaded
making the map look terrible in relation to the model. These cases you can
sometimes tell from the cell dimensions and resolution of the reflection data.
I found a case of that last year, contacted the depositors and they updated
their PDB entry with te help of te PDB annotators. A friendly email can work
miracles is you have a good estimate of what is going on.
I'm sure there are many cases where people were just rushed into depositing
an unfinished model. We all know the pressures in our line of work. It is not
pretty, but understandable. Sometimes the models can be fixed by
automated means, sometimes it requires a bit more work. The depositors
may be quite well-willing to update their model if you take some of the
burden of fixing it out of their hands.
Then there are cases where there is genuine incompetence. That is, the
depositor really didn’t know they were doing things wrong or their
supervisor didn't supervise well (or at all). Sometimes reaching out to the
depositor can help (I have seen successful cases of that), but you may run
into significant resistance. Nobody likes to be told, however nicely, that they
were wrong. Here it also really matter whether the model is just suboptimal
or it really leads to wrong conclusions or, even worse, has lead to the wrong
conclusions. You risk putting yourself in a situation where you have to tell
someone that this part of their paper is wrong because the model is wrong.
You can reach out to the authors b hind the scenes, but it is also legitimate to
just in your scientific work on the topic mention the issue a set the record
straight without making it personal. You can also use such examples for
teaching to make sure the new generation is more competent. All in all these
are cases not just examples of individual failure but also of a failure of us
as a
community. In the long run, leading by example by making sure your
students are well trained and supervised is key. CCP4 organises a lot of
courses in crystallography where we help people improve their skill and
knowledge in the matter. I am of course completely biased, but I highly
recommend such courses.
Indifference is another reason for poor models in the PDB. The part of the
model in which the depositors were interested is perfectly fine but the rest
clearly lacks attention. Without knowing any of the details, the model you
mention may fall in this category. You may be able to get in touch with the
depositors to update the model, but don't hold your breath. If it is an older
model (pre 2008) just appreciate that they were bothered to deposit the
model and data at all. If the model answered the scientific question for which
the model was made correctly, then it is a sound model. It's just not that
useful for other applications. Devil's advocate: who are we to decide that
other researchers shut invest resources into improving a model beyond what
is needed for their primary research?
The final category is malevolence. Yes, there are cases in the PDB where
people purposely deposited worse models than what they describe in the
paper. I call that molecular crippleware. Most of the cases predate 2008
although there was one case after that about which I complained to the PDB.
Unfortunately there was very little they could do. There were also
documented cases of outright fraud, but these models actually appeared (in
some aspects at least) quite alright. My opinion about the depositors of such
models is not suitable for this public forum.
Anyway, good of you to reach out to the bulletin board and keep fighting the
good fight.
Cheers,
Robbie
-----Original Message-----
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>>
On Behalf Of
Nikolas
Sent: Friday, May 30, 2025 23:31
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] How to address deposited structures poorly modeled?
*enters the BB and kneels in reverence*
Dear BB,
Recently, delving among papers and structures for a current project, I
came across a deposited structure of interest that is terribly
modeled. In the PDB resolution is 2.00 Å (R/Rfree=0.19/0.22) and the
quality indicators are not terrible but upon opening it and checking
the maps there are some severe mistakes in the modeling.
For instance, a full chain that is in the negative Fo-Fc while
positive density is present, some density that is quite clear for SO4
molecules (buffer) modeled as water and density for water molecules
neglected. Some parts seem like “coot:runwater” has been used and not
checked. The catalytic site is well defined.
Now, I’ve started my journey in crystallography not too long ago and
I’ve got many years, structures to solve and things to learn, and I
know that sometimes the dataset “is what it is” but these seems quite big
mistakes.
Especially because I’ve worked with such proteins before and I know
the systems.
My question thus is: would it be right to contact the author of this
structure and point to these issues? What’s the best way to address
such things, possibly without coming off as obnoxious?
Thank you for your wisdom.
Cheers,
Nikolas
*bows and leaves the BB*
________________________________
To unsubscribe from the CCP4BB list, click the following link:
https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC
.exe?SUBED1=CCP4BB&A=1__;!!PDiH4ENfjr2_Jw!DIetizJCm94LYkFe6Jy4-
STeHd1x
qiTlYckYQhazL-JqrMkZQz1W00Onif_FtXKpKof041v7RfEwi3adRQ-
l0xMfnCZKvB5o24
BIUg$[jiscmail[.]ac[.]uk]
###############################################################
#########
To unsubscribe from the CCP4BB list, click the following link:
https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-
JISC.exe?SUBED1=CCP4BB&A=1__;!!PDiH4ENfjr2_Jw!DIetizJCm94LYkFe6Jy4-
STeHd1xqiTlYckYQhazL-JqrMkZQz1W00Onif_FtXKpKof041v7RfEwi3adRQ-
l0xMfnCZKvB5o24BIUg$[jiscmail[.]ac[.]uk]
This message was issued to members of
https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!PDiH4E
Nfjr2_Jw!DIetizJCm94LYkFe6Jy4-STeHd1xqiTlYckYQhazL-
JqrMkZQz1W00Onif_FtXKpKof041v7RfEwi3adRQ-
l0xMfnCZKvB4gf54SaA$[jiscmail[.]ac[.]uk], a mailing list hosted by
https://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!PDiH4ENfjr2_Jw!
DIetizJCm94LYkFe6Jy4-STeHd1xqiTlYckYQhazL-
JqrMkZQz1W00Onif_FtXKpKof041v7RfEwi3adRQ-
l0xMfnCZKvB4tB7WRHg$[jiscmail[.]ac[.]uk], terms & conditions are available
at
https://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/_
_;!!PDiH4ENfjr2_Jw!DIetizJCm94LYkFe6Jy4-STeHd1xqiTlYckYQhazL-
JqrMkZQz1W00Onif_FtXKpKof041v7RfEwi3adRQ-
l0xMfnCZKvB6BG0ZtyQ$[jiscmail[.]ac[.]uk]
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of
www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by
www.jiscmail.ac.uk<http://www.jiscmail.ac.uk/>, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
________________________________
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
________________________________
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen
avsändaren och vet att innehållet är säkert.
CAUTION: Do not click on links or open attachments unless you recognise the
sender and know the content is safe.
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att
vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du
läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For
more information on how this is performed, please read here:
http://www.uu.se/en/about-uu/data-protection-policy
________________________________
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen
avsändaren och vet att innehållet är säkert.
CAUTION: Do not click on links or open attachments unless you recognise the
sender and know the content is safe.
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/p
------------------------------
Date: Sun, 1 Jun 2025 14:44:35 +0200
From: "Mark J. van Raaij" <mjvanra...@cnb.csic.es>
Subject: Re: How to address deposited structures poorly modeled?
Hi Nikolas,
I think that in crystallography it is becoming more common that reviewers ask
for the structure factors and coordiates before reviewing a manuscript, I
always do.
And also more common that journals ask for these during submission, IUCr
journals (https://journals.iucr.org/) and other journals do this, hopefully to
be followed by all.
Mark van Raaij
Dpto de Estructura de Macromoleculas, lab B5B
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. +34 91 585 4616 (internal 432092)
On 31 May 2025, at 19:44, Nikolas <nikolas.ca...@gmail.com> wrote:
Hi,
Thank you all for the incredibly instructive responses.
Being this my first time happening upon such a "situation" and I'm very glad it
brought to a fruitful conversation as well as a set of instructions on how to address
such things.
Indeed mistakes can be made and sometimes models cannot be improved beyond a
specific point for several reasons, just as sometimes things are rushed
-unfortunately- due to deadlines. Personally, I didn't think of it as
malevolence but more of it as a genuine oversight or mistake. I sincerely
thought that was a pity, considering the rest of the structure. But maybe
that's just me intertwining the joy of determining a structure with the pride
of making it the best I could with the means given (while also seeking second
opinions and help, if necessary).
I will try to re-refine, PDB-REDO and then, if any improvements are observed,
reach out to the depositors.
I will then try to give another prompt, since we are on topic: what would be
the best way to spot such mistakes early on, after the structures have left the
authors, aside from the Curators? Should we provide reviewers with the mtz and
the model instead of just the validation report? Should they ask for it, while
reviewing a manuscript?
Once again, thank you all; you've been wonderful.
My opinion about the depositors of such models is not suitable for this public
forum.
I've probably laughed too hard at this.
Cheers,
Nikolas
Il giorno sab 31 mag 2025 alle ore 07:40 Eleanor Dodson
<0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk
<mailto:0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>> ha scritto:
Don’t be too judgmental- Phil Evans once said - well, I have spent 95% of my
refinement time tweeking the 5% of the water molecules which no one will ever
ever look at!
Gross errors - bad; deliberate errors indefensible , but I don’t think I have
ever deposited a structure which couldn’t be “improved”.
On Sat, 31 May 2025 at 12:20, Robbie Joosten <robbie_joos...@hotmail.com
<mailto:robbie_joos...@hotmail.com>> wrote:
Hi Matthew,
are you willing to elaborate on the motives for “molecular crippleware”?
They seem to stem from the idea that you have a competitive advantage by not
fully disclosing your structure model. This is by now, fortunately, a very
old-fashioned way of thinking. But people have fought long and hard to get
fellow crystallographers to deposit their models and their experimental data.
Believe it or not, in the past there were several programs that could turn a
stereo image into 3D coordinates to deal with people not depositing their
coordinates.
Now that the extraordinary predictive potential of the PDB data has been
proven I would say that it's not justifiable to deposit anything where the
model is only complete to the extent that the primary research aims are met,
who knows what future patterns might be degraded?
This is what I teach, but having the time and resources to really optimise a
structure model before deposition is also a bit of a luxury in some settings.
I would hope that if I was ever responsible for something like this it would be
due to a mix-up with versions etc... but either way I would want to know!
If it is a clear mix-up I always try to get in touch with the depositors and I
hope that this discussion will encourage other to do the same.
Cheers,
Robbie
Best
Matthew.
Sent from Outlook for iOS <https://aka.ms/o0ukef>
________________________________
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Robbie
Joosten <robbie_joos...@hotmail.com <mailto:robbie_joos...@hotmail.com>>
Sent: Saturday, May 31, 2025 11:03:47 AM
To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> <CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] How to address deposited structures poorly modeled?
Hi Nikolas, There are many reasons for PDB entries to be worse then they
could be. The most obvious is just that when the models were made the
tools were not as easy to use as now and the depositors were less
experienced then they are now. This Hi Nikolas,
There are many reasons for PDB entries to be worse then they could be. The
most obvious is just that when the models were made the tools were not as
easy to use as now and the depositors were less experienced then they are
now. This is natural and, as Guillaume mentioned, to some extent PDB-REDO
can help here. Sometimes a lot, sometimes surprisingly little and on rare
occasions even making things worse (tell me if you find such a case). There
now is a related effort from Foldot where the community is encouraged to
treat a specific PDB entry as a model versus map puzzle. If the models from
that are clearly better than the PDB model (e.g. for the chain you mention)
then it will drip through to PDB-REDO.
Another reason for models appearing worse then expected is simple mix-ups.
I have seen cases where just an older version of the model, rather than the
final version, was deposited by accident. Also in series of structures there are
sometimes mix-ups where the wrong set of reflections were uploaded
making the map look terrible in relation to the model. These cases you can
sometimes tell from the cell dimensions and resolution of the reflection data.
I found a case of that last year, contacted the depositors and they updated
their PDB entry with te help of te PDB annotators. A friendly email can work
miracles is you have a good estimate of what is going on.
I'm sure there are many cases where people were just rushed into depositing
an unfinished model. We all know the pressures in our line of work. It is not
pretty, but understandable. Sometimes the models can be fixed by
automated means, sometimes it requires a bit more work. The depositors
may be quite well-willing to update their model if you take some of the
burden of fixing it out of their hands.
Then there are cases where there is genuine incompetence. That is, the
depositor really didn’t know they were doing things wrong or their
supervisor didn't supervise well (or at all). Sometimes reaching out to the
depositor can help (I have seen successful cases of that), but you may run
into significant resistance. Nobody likes to be told, however nicely, that they
were wrong. Here it also really matter whether the model is just suboptimal
or it really leads to wrong conclusions or, even worse, has lead to the wrong
conclusions. You risk putting yourself in a situation where you have to tell
someone that this part of their paper is wrong because the model is wrong.
You can reach out to the authors b hind the scenes, but it is also legitimate to
just in your scientific work on the topic mention the issue a set the record
straight without making it personal. You can also use such examples for
teaching to make sure the new generation is more competent. All in all these
are cases not just examples of individual failure but also of a failure of us
as a
community. In the long run, leading by example by making sure your
students are well trained and supervised is key. CCP4 organises a lot of
courses in crystallography where we help people improve their skill and
knowledge in the matter. I am of course completely biased, but I highly
recommend such courses.
Indifference is another reason for poor models in the PDB. The part of the
model in which the depositors were interested is perfectly fine but the rest
clearly lacks attention. Without knowing any of the details, the model you
mention may fall in this category. You may be able to get in touch with the
depositors to update the model, but don't hold your breath. If it is an older
model (pre 2008) just appreciate that they were bothered to deposit the
model and data at all. If the model answered the scientific question for which
the model was made correctly, then it is a sound model. It's just not that
useful for other applications. Devil's advocate: who are we to decide that
other researchers shut invest resources into improving a model beyond what
is needed for their primary research?
The final category is malevolence. Yes, there are cases in the PDB where
people purposely deposited worse models than what they describe in the
paper. I call that molecular crippleware. Most of the cases predate 2008
although there was one case after that about which I complained to the PDB.
Unfortunately there was very little they could do. There were also
documented cases of outright fraud, but these models actually appeared (in
some aspects at least) quite alright. My opinion about the depositors of such
models is not suitable for this public forum.
Anyway, good of you to reach out to the bulletin board and keep fighting the
good fight.
Cheers,
Robbie
-----Original Message-----
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of
Nikolas
Sent: Friday, May 30, 2025 23:31
To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] How to address deposited structures poorly modeled?
*enters the BB and kneels in reverence*
Dear BB,
Recently, delving among papers and structures for a current project, I
came across a deposited structure of interest that is terribly
modeled. In the PDB resolution is 2.00 Å (R/Rfree=0.19/0.22) and the
quality indicators are not terrible but upon opening it and checking
the maps there are some severe mistakes in the modeling.
For instance, a full chain that is in the negative Fo-Fc while
positive density is present, some density that is quite clear for SO4
molecules (buffer) modeled as water and density for water molecules
neglected. Some parts seem like “coot:runwater” has been used and not
checked. The catalytic site is well defined.
Now, I’ve started my journey in crystallography not too long ago and
I’ve got many years, structures to solve and things to learn, and I
know that sometimes the dataset “is what it is” but these seems quite big
mistakes.
Especially because I’ve worked with such proteins before and I know
the systems.
My question thus is: would it be right to contact the author of this
structure and point to these issues? What’s the best way to address
such things, possibly without coming off as obnoxious?
Thank you for your wisdom.
Cheers,
Nikolas
*bows and leaves the BB*
________________________________
To unsubscribe from the CCP4BB list, click the following link:
https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC
.exe?SUBED1=CCP4BB&A=1__;!!PDiH4ENfjr2_Jw!DIetizJCm94LYkFe6Jy4-
STeHd1x
qiTlYckYQhazL-JqrMkZQz1W00Onif_FtXKpKof041v7RfEwi3adRQ-
l0xMfnCZKvB5o24
BIUg$[jiscmail[.]ac[.]uk]
###############################################################
#########
To unsubscribe from the CCP4BB list, click the following link:
https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-
JISC.exe?SUBED1=CCP4BB&A=1__;!!PDiH4ENfjr2_Jw!DIetizJCm94LYkFe6Jy4-
STeHd1xqiTlYckYQhazL-JqrMkZQz1W00Onif_FtXKpKof041v7RfEwi3adRQ-
l0xMfnCZKvB5o24BIUg$[jiscmail[.]ac[.]uk]
This message was issued to members of
https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!PDiH4E
Nfjr2_Jw!DIetizJCm94LYkFe6Jy4-STeHd1xqiTlYckYQhazL-
JqrMkZQz1W00Onif_FtXKpKof041v7RfEwi3adRQ-
l0xMfnCZKvB4gf54SaA$[jiscmail[.]ac[.]uk], a mailing list hosted by
https://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!PDiH4ENfjr2_Jw!
DIetizJCm94LYkFe6Jy4-STeHd1xqiTlYckYQhazL-
JqrMkZQz1W00Onif_FtXKpKof041v7RfEwi3adRQ-
l0xMfnCZKvB4tB7WRHg$[jiscmail[.]ac[.]uk], terms & conditions are available
at
https://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/_
_;!!PDiH4ENfjr2_Jw!DIetizJCm94LYkFe6Jy4-STeHd1xqiTlYckYQhazL-
JqrMkZQz1W00Onif_FtXKpKof041v7RfEwi3adRQ-
l0xMfnCZKvB6BG0ZtyQ$[jiscmail[.]ac[.]uk]
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB
<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk
<http://www.jiscmail.ac.uk/>, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
------------------------------
Date: Sun, 1 Jun 2025 17:24:50 +0100
From: srikannathasan velupillai <srikannatha...@googlemail.com>
Subject: Re: How to address deposited structures poorly modeled?
Hi Nick,
Thanks for raising the issue. You mentioned that you're relatively new to
the field—if so, that's absolutely fine, and we all appreciate your
engagement. If you've worked on this structure yourself and believe there
may be issues, have you considered depositing your version for comparison?
Even if there’s already a PDB entry, reviewing different interpretations
can still be valuable.
You mentioned that the existing model may be incorrectly built. Would you
be able to share a few more details—such as the PDB ID (if available),
electron density maps, or screenshots of the specific problem areas?
Several people have already offered advice, but having a bit more context
would really help the community provide more constructive feedback. Sharing
this via the CCP4 forum or directly here could allow others with relevant
experience to assist further.
Looking forward to hearing more about your observations.
Thank you
kannan
On Sat, 31 May 2025 at 09:09, Guillaume Gaullier <
guillaume.gaull...@kemi.uu.se> wrote:
Hi Nikolas,
Contacting the original authors/depositors of this entry is indeed a good
thing to do. Try putting yourself in their shoes: if you were to receive an
email essentially saying that your model is very poor, how would you like
it phrased? Then phrase your request as nicely as you can to get these
people on your side (i.e. willing to revise their model).
If they don’t follow up, or worse get angry at you, well at least you
tried. And then you are free to propose your own revised model: this is
what publicly available data is for.
In this situation, I would get in touch first and maybe offer to help
revise the model (if this is something I am willing to spend time on)
depending on how the initial contact goes. If this went nowhere and I still
needed a correct model, I would revise it myself for my own use.
I don’t know what the PDB’s policy is in cases where one wants to
independently deposit a revised model for an existing entry they did not
deposit themselves. But if the original authors/depositors are willing to
cooperate, then it’s relatively easy: all PDB entries are versioned, so
depositing a revised atomic model is only a matter of issuing a new version
(the accession code will remain the same). It is even possible to amend the
depositor list, so the original authors can give you credit this way if you
did more work than only pointing out a poor model.
Different people will receive this kind of request differently, and you
don’t know until you try.
Alternatively, if you don’t want to initiate such a discussion and only
want a revised model quickly, check if it has been re-refined by PDB-REDO:
https://pdb-redo.eu
It won’t do miracles for very large errors though, and in such cases
manual rebuilding may be best. But could be useful to check.
I hope this helps!
Cheers,
Guillaume
On 30 May 2025, at 23:30, Nikolas <nikolas.ca...@gmail.com> wrote:
*enters the BB and kneels in reverence*
Dear BB,
Recently, delving among papers and structures for a current project, I
came across a deposited structure of interest that is terribly modeled. In
the PDB resolution is 2.00 Å (R/Rfree=0.19/0.22) and the quality indicators
are not terrible but upon opening it and checking the maps there are some
severe mistakes in the modeling.
For instance, a full chain that is in the negative Fo-Fc while positive
density is present, some density that is quite clear for SO4 molecules
(buffer) modeled as water and density for water molecules neglected. Some
parts seem like “coot:runwater” has been used and not checked. The
catalytic site is well defined.
Now, I’ve started my journey in crystallography not too long ago and I’ve
got many years, structures to solve and things to learn, and I know that
sometimes the dataset “is what it is” but these seems quite big mistakes.
Especially because I’ve worked with such proteins before and I know the
systems.
My question thus is: would it be right to contact the author of this
structure and point to these issues? What’s the best way to address such
things, possibly without coming off as obnoxious?
Thank you for your wisdom.
Cheers,
Nikolas
*bows and leaves the BB*
------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner
igen avsändaren och vet att innehållet är säkert.
CAUTION: Do not click on links or open attachments unless you recognise
the sender and know the content is safe.
När du har kontakt med oss på Uppsala universitet med e-post så innebär
det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör
det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal
data. For more information on how this is performed, please read here:
http://www.uu.se/en/about-uu/data-protection-policy
------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
------------------------------
Date: Sun, 1 Jun 2025 23:05:31 +0200
From: "Mark J. van Raaij" <mjvanra...@cnb.csic.es>
Subject: Re: How to address deposited structures poorly modeled?
before making the PBD id public I would give the authors some time to respond
(as others and Nikolas himself have suggested).
Then it is more likely to be solved in a friendly, efficient and thorough way.
While it’s possible to resolve problems with the current structure factors and
model, having the authors themselves look into it first is better, they might
realise some other problem, such as the wrong structure factors having been
uploaded for example.
Mark J van Raaij
Dpto de Estructura de Macromoleculas, lab B5
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. +34 91 585 4616 (internal 432092)
On 1 Jun 2025, at 18:24, srikannathasan velupillai
<0000b52eb5457384-dmarc-requ...@jiscmail.ac.uk> wrote:
Hi Nick,
Thanks for raising the issue. You mentioned that you're relatively new to the
field—if so, that's absolutely fine, and we all appreciate your engagement. If
you've worked on this structure yourself and believe there may be issues, have
you considered depositing your version for comparison? Even if there’s already
a PDB entry, reviewing different interpretations can still be valuable.
You mentioned that the existing model may be incorrectly built. Would you be
able to share a few more details—such as the PDB ID (if available), electron
density maps, or screenshots of the specific problem areas?
Several people have already offered advice, but having a bit more context would
really help the community provide more constructive feedback. Sharing this via
the CCP4 forum or directly here could allow others with relevant experience to
assist further.
Looking forward to hearing more about your observations.
Thank you
kannan
On Sat, 31 May 2025 at 09:09, Guillaume Gaullier <guillaume.gaull...@kemi.uu.se
<mailto:guillaume.gaull...@kemi.uu.se>> wrote:
Hi Nikolas,
Contacting the original authors/depositors of this entry is indeed a good thing
to do. Try putting yourself in their shoes: if you were to receive an email
essentially saying that your model is very poor, how would you like it phrased?
Then phrase your request as nicely as you can to get these people on your side
(i.e. willing to revise their model).
If they don’t follow up, or worse get angry at you, well at least you tried.
And then you are free to propose your own revised model: this is what publicly
available data is for.
In this situation, I would get in touch first and maybe offer to help revise
the model (if this is something I am willing to spend time on) depending on how
the initial contact goes. If this went nowhere and I still needed a correct
model, I would revise it myself for my own use.
I don’t know what the PDB’s policy is in cases where one wants to independently
deposit a revised model for an existing entry they did not deposit themselves.
But if the original authors/depositors are willing to cooperate, then it’s
relatively easy: all PDB entries are versioned, so depositing a revised atomic
model is only a matter of issuing a new version (the accession code will remain
the same). It is even possible to amend the depositor list, so the original
authors can give you credit this way if you did more work than only pointing
out a poor model.
Different people will receive this kind of request differently, and you don’t
know until you try.
Alternatively, if you don’t want to initiate such a discussion and only want a
revised model quickly, check if it has been re-refined by PDB-REDO:
https://pdb-redo.eu <https://pdb-redo.eu/>
It won’t do miracles for very large errors though, and in such cases manual
rebuilding may be best. But could be useful to check.
I hope this helps!
Cheers,
Guillaume
On 30 May 2025, at 23:30, Nikolas <nikolas.ca...@gmail.com
<mailto:nikolas.ca...@gmail.com>> wrote:
*enters the BB and kneels in reverence*
Dear BB,
Recently, delving among papers and structures for a current project, I came
across a deposited structure of interest that is terribly modeled. In the PDB
resolution is 2.00 Å (R/Rfree=0.19/0.22) and the quality indicators are not
terrible but upon opening it and checking the maps there are some severe
mistakes in the modeling.
For instance, a full chain that is in the negative Fo-Fc while positive density
is present, some density that is quite clear for SO4 molecules (buffer) modeled
as water and density for water molecules neglected. Some parts seem like
“coot:runwater” has been used and not checked. The catalytic site is well
defined.
Now, I’ve started my journey in crystallography not too long ago and I’ve got
many years, structures to solve and things to learn, and I know that sometimes
the dataset “is what it is” but these seems quite big mistakes. Especially
because I’ve worked with such proteins before and I know the systems.
My question thus is: would it be right to contact the author of this structure
and point to these issues? What’s the best way to address such things, possibly
without coming off as obnoxious?
Thank you for your wisdom.
Cheers,
Nikolas
*bows and leaves the BB*
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen
avsändaren och vet att innehållet är säkert.
CAUTION: Do not click on links or open attachments unless you recognise the
sender and know the content is safe.
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att
vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du
läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For
more information on how this is performed, please read here:
http://www.uu.se/en/about-uu/data-protection-policy
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
------------------------------
End of CCP4BB Digest - 31 May 2025 to 1 Jun 2025 (#2025-145)
************************************************************
