Re: [ccp4bb] Analysis of NMR ensembles

[Pearce, N.M. (Nick)]

If you want something comparable to B-factors don’t forget to put the MSF in 
the B-factor column, not the RMSF. Will change the scaling of the tube radius 
considerably!

Nick

On 27 May 2021, at 11:16, Harry Powell - CCP4BB 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Cool…

Purely for visualisation this does look like the approved CCP4 way -



Harry

On 27 May 2021, at 10:01, Stuart McNicholas 
<19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Drawing style (right menu in display table) -> Worm scaled by -> Worm
scaled by NMR variability

in ccp4mg?

This changes the size of the worm but not the colour.

On Thu, 27 May 2021 at 09:56, Harry Powell - CCP4BB
<193323b1e616-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Anyway, thanks to all those who answered my original question - especially

   Tristan: Chimerax (+ his attached script)
   Michal, Scott: Theseus (https://theobald.brandeis.edu/theseus/)
   Bernhard: Molmol (https://pubmed.ncbi.nlm.nih.gov/8744573/ )
   Rasmus CYRANGE (http://www.bpc.uni-frankfurt.de/cyrange.html) and 
https://www.ccpn.ac.uk/ (of course…)
   Andrew (uwmn - not sure if this is buildable on a modern box)
   Smita: PyMol (not sure if I’m allowed to say that on ccp4bb…)

or I could script it and use Gesamt or Superpose for the superposition if I 
wanted to stay in the ccp4 universe and had the time to spare ;-)

Harry



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Re: [ccp4bb] Unmodeled density

[Pearce, N.M. (Nick)]

Is it on a symmetry axis? If so it could be the superposition of two molecules 
(a molecule and a copy of itself).

On 26 May 2021, at 15:08, leo john 
mailto:ljohn16012...@gmail.com>> wrote:

Hi Group
Can you please suggest what this unmodeled blob can be (see appended picture)?
I have Malonate, Boric Acid and Peg in my condition, and crystals were soaked 
in GOL.

I have tried fitting PO4 and SO4 so far.

Thank You
John






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[ccp4bb] Deadline today -- IUCr SARS-CoV-2 special symposia.

[Pearce, N.M. (Nick)]

Dear BB,

As you might be aware, there are a few microsymposia that have been added to 
this year’s IUCr conference on developments around SARS-CoV-2.

Given the wide interests of this board, I wanted to advertise all four of the 
sessions, for which the (official) deadline is TODAY:

- Structural biology of coronaviruses
This session covers new structural and functional insights about the life cycle 
and virus-host interaction of SARS-CoV-2 and other coronaviruses with a 
particular view to integrative uses of crystallography in connection with other 
methods.

- New methods to fight the pandemic
This session covers new methods in crystallography and structural biology to 
better understand SARS-CoV-2 and the COVID-19 pandemic, including advances in 
computational methods, beamline instrumentation and integrative structural 
biology.

- Crystallography against Corona
This session covers the efforts of the crystallographic community to find drug 
candidates for COVID-19 both in-silico and in the lab by using structural 
models of viral proteins.

- Using crystallography for education during the pandemic
Using crystallography for education during the pandemic

*** Please submit your abstracts today! If this isn’t possible, email us to let 
us know you intend to submit an abstract in the coming days! ***

For each session, 4 relevant abstracts will be selected for 20-minute 
presentations.

You can submit your abstracts through the conference website: 
https://iucr25.org/scientific/

Looking forward to reading the abstracts,
Session co-chairs



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[ccp4bb] Abstracts for IUCr SARS-CoV-2 methods session

[Pearce, N.M. (Nick)]

Dear BB,

Sorry for any cross-posting with the phenixBB.

Jane Richardson & I are co-chairing a late-breaking session added to the lineup 
of microsymposia at the IUCr congress in August.

Its title is "New Methods in Structural Biology to help with the COVID-19 
Pandemic” and it will take place remotely/hybrid on August 16 at 8:45-11:10am 
EDT.

We’d love to have a variety of speakers speaking on a variety of methodologies 
that have either been developed specifically during the pandemic, or else 
applied like never before.

The abstract deadline has been extended to May 15 for this session, and 4 
relevant abstracts will be selected for 20-minute presentations.

You can submit your abstracts through the conference website: 
https://iucr25.org/scientific/

Looking forward to reading the abstracts,
Nick & Jane





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Re: [ccp4bb] unknown density

[Pearce, N.M. (Nick)]

This doesn’t surprise me in the slightest, given what how the two maps are 
calculated.

The polder map is essentially the same as your "simple omit map” without the 
bulk solvent contribution that is present in the omit-refine map. Since this is 
an approximately constant contribution, if you recontour the Polder map to a 
higher contour you should be able to get the two maps to look basically the 
same.

Nick

On 23 Mar 2021, at 09:36, Sam Tang 
mailto:samtys0...@gmail.com>> wrote:

Dear colleagues

Thanks a lot for the comments. I echo that this pentagon-like density may 
likely be water molecules. What had puzzled us a bit was that the output of 
Polder map which gave some interlinked density.

I should also mention that this site is close to a predicted peptide binding 
site and that is what we are actually looking for. (To me the strong positive 
density in Polder map is not indicative of an amino acid residue as well.)

My Polder map looks like this:
https://drive.google.com/file/d/10dGpdcDhrp_ld6wPH3Er7iZ3KVgU2RCN/view?usp=sharing

BRS

Sam

On Tue, 23 Mar 2021 at 04:43, Bernhard Rupp 
mailto:hofkristall...@gmail.com>> wrote:
Textbook knowledge 
http://www.ruppweb.org/Garland/gallery/Ch12/pages/Biomolecular_Crystallography_Fig_12-28.htm

--
Bernhard Rupp
http://www.hofkristallamt.org/
b...@hofkristallamt.org
+1 925 209 7429
+43 676 571 0536
-
Doors and corners – that’s where they get you
-





From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Sharan Karade
Sent: Monday, March 22, 2021 13:10
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] unknown density

Hi

Please look at the pic attached. found similar pentagon water network.



On Mon, Mar 22, 2021 at 12:40 PM Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Definitely water pentamer, no doubt at all ;-0
Cheers, Jon.C.

Sent from ProtonMail mobile



 Original Message 
On 22 Mar 2021, 14:16, Mark J. van Raaij < 
mjvanra...@cnb.csic.es> wrote:

The ring looks too big to be imidazole or a nucleotide or a carbohydrate, so 
it’s probably mainly water molecules.
Perhaps partially replaced by PEG to explain the density between them (i.e. 
water molecules in most copies of the protein and PEG in some other copies). 
I’ve seen horse-shoe shaped PEG in a high-res structure before, PEGs in several 
confirmations might explain a circle.
Practically speaking, I’d first model five waters and see if they refine well.

Mark


On 22 Mar 2021, at 14:58, Sam Tang 
mailto:samtys0...@gmail.com>> wrote:

Hello fellow colleagues

Hope you are all well while the pandemics persists. I just wonder if anyone may 
have an idea what this density (looking like a pentagon) might be. The data was 
collected to 1.8 A and crystal was grown in Bis-tris + PEG3350. Imidazole 
residual? Nucleotide (the protein itself is nucleotide-binding, but shouldn't 
be at this particular site)?

https://drive.google.com/file/d/1L9UBFmW72P214itM2HJR_DVy3FaA6FEZ/view?usp=sharing

Thanks!

BRS

Sam



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--
Sharan Karade
Postdoc-fellow
IBBR-UMD, 9600 Gudelsky Dr,
Rockville
Maryland 20850




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Re: [ccp4bb] Open position - data management in biophysics

[Pearce, N.M. (Nick)]

"If you do your work well, you will get more ..” Is a nice ideal, but I don’t 
think it factors in the real-life factors such as administrative burden (i.e. 
wasted time), mental-health effects and frankly, random chance. Does anyone 
enjoy applying for grants/jobs? Does it improve their lives/productivity? Does 
it improve the science? I suspect (more accurately, I’m damned sure that) I 
would have been much more productive over the last couple of years if I hadn’t 
been constantly worried about missing the next hurdle (ironically making it all 
the more likely that I _would_ miss the hurdle!). On top of that, I could have 
enjoyed such lofty ambitions as “thinking about buying a house and starting a 
family” which is difficult when you don’t have career stability over longer 
than 1-2 years.

I would also consider amending the statement to "If you do your work well, you 
_might_ get more ..”.

It seems to me a lot of time and energy could be saved by skipping the 
biennial/triennial re-employment ritual/lottery, and if I am lucky enough to 
ever make it to the point where I am able to employ people, I hope I remember 
how thoroughly miserable the experience of this purgatory has made me, and make 
the effort to employ my staff on reasonable contract lengths (i.e. for as long 
as possible), and petition to funding bodies to change their policies. For 
instance, if the Wellcome Trust now leaves it up to the project leader to 
decide such things, as Eleanor has stated, they should absolutely be applauded 
for that.

After all, as Frank said, we do this for the science, and it shouldn’t need to 
include personal sacrifice.

Nick

On 22 Jan 2021, at 11:18, Pearce, N.M. (Nick) 
mailto:n.m.pea...@uu.nl>> wrote:

Meant to write “perpetual impending unemployment”.

Thanks,
Nick

On 22 Jan 2021, at 11:02, Jan Dohnalek 
mailto:dohnalek...@gmail.com>> wrote:


On Fri, Jan 22, 2021 at 10:54 AM Pearce, N.M. (Nick) 
mailto:n.m.pea...@uu.nl>> wrote:
Academia, one of the only careers where _success_ is rewarded with perpetual 
impending employment every two+ years.

Which translates "If you do your work well, you will get more .."

Jan





Nick

On 22 Jan 2021, at 08:25, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk<mailto:176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>>
 wrote:

It is a long time since I had any practical concerns with this issue, but some 
funding bodies are more flexible than others. Welcome gives project grants then 
leaves it up to the recipient to hire and plan. And I guess the big research 
institutes like the crick and lmb have similar systems. It is obvious that this 
approach is much more productive than the shorter term grants - is there any 
mileage in someone doing a survey of “outcomes”(horrible word) and pointing out 
that productivity increases with more security?
And as for the national scandal of milking money fir visas from those who come 
here from abroad - already saving us from the cost of their education - I don’t 
know what to say!
Eleanor

On Fri, 22 Jan 2021 at 07:11, Frank von Delft 
mailto:frank.vonde...@cmd.ox.ac.uk>> wrote:
For me as hiring PI, what's repeatedly dismaying is that it's our funders and 
universities that set the terms, and only with extreme creativity can one shift 
the dial, and only on indidual recruitments, certainly not the high politics of 
the system as a whole.

No, I don't know what will break this - it exploits our fundamental weakness, 
that we go into science because we want to do it, and are already investiging 
all our energy at convincing a system that something else is worth doing 
(getting our mad science funded at all) -- so things like collective striking 
or unionising don't really come naturally.

I do hope the next wave of scientists (am I that old already?) have some 
aggressively constructive thoughts, because mine and the one before mine sure 
don't.


Frank



On 20/01/2021 23:38, Navdeep Sidhu wrote:

Dear Gerlind, Markus, All:

Well, sometimes the (written) promise of a 2-year contract also ends up
boiling down systematically (for some PIs) to only a 6-month contract
after all.--And that after you've spent half a year or more and multiple
trips to the country concerned trying to get a work visa and housing,
all at your own expense--particularly tough for migrants and their families:

"Many come here with a promise of a two-year contract, which later turns
out to be a six month scholarship, which is renewed six months at a
time. Many feel that they have been fooled."
 - From Palle Liljebaeck. "Postdoctoral fellows at KI must be given
better terms." Naturvetarna (Sweden), Nov. 7, 2013
<https://www.naturvetarna.se/vi-erbjuder/tidning-och-nyheter/2013/nr-4-2013/Postdoctoral-fellows-at-KI-must-be-given-better-terms/><https://www.naturvetarna.se/vi-erbjuder/tidning-och-nyheter/2013/nr-4-2013/Postdoctoral-fellows-at-KI-must-be-give

Re: [ccp4bb] Open position - data management in biophysics

[Pearce, N.M. (Nick)]

Meant to write “perpetual impending unemployment”.

Thanks,
Nick

On 22 Jan 2021, at 11:02, Jan Dohnalek  wrote:


On Fri, Jan 22, 2021 at 10:54 AM Pearce, N.M. (Nick) 
mailto:n.m.pea...@uu.nl>> wrote:
Academia, one of the only careers where _success_ is rewarded with perpetual 
impending employment every two+ years.

Which translates "If you do your work well, you will get more .."

Jan





Nick

On 22 Jan 2021, at 08:25, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk<mailto:176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>>
 wrote:

It is a long time since I had any practical concerns with this issue, but some 
funding bodies are more flexible than others. Welcome gives project grants then 
leaves it up to the recipient to hire and plan. And I guess the big research 
institutes like the crick and lmb have similar systems. It is obvious that this 
approach is much more productive than the shorter term grants - is there any 
mileage in someone doing a survey of “outcomes”(horrible word) and pointing out 
that productivity increases with more security?
And as for the national scandal of milking money fir visas from those who come 
here from abroad - already saving us from the cost of their education - I don’t 
know what to say!
Eleanor

On Fri, 22 Jan 2021 at 07:11, Frank von Delft 
mailto:frank.vonde...@cmd.ox.ac.uk>> wrote:
For me as hiring PI, what's repeatedly dismaying is that it's our funders and 
universities that set the terms, and only with extreme creativity can one shift 
the dial, and only on indidual recruitments, certainly not the high politics of 
the system as a whole.

No, I don't know what will break this - it exploits our fundamental weakness, 
that we go into science because we want to do it, and are already investiging 
all our energy at convincing a system that something else is worth doing 
(getting our mad science funded at all) -- so things like collective striking 
or unionising don't really come naturally.

I do hope the next wave of scientists (am I that old already?) have some 
aggressively constructive thoughts, because mine and the one before mine sure 
don't.


Frank



On 20/01/2021 23:38, Navdeep Sidhu wrote:

Dear Gerlind, Markus, All:

Well, sometimes the (written) promise of a 2-year contract also ends up
boiling down systematically (for some PIs) to only a 6-month contract
after all.--And that after you've spent half a year or more and multiple
trips to the country concerned trying to get a work visa and housing,
all at your own expense--particularly tough for migrants and their families:

"Many come here with a promise of a two-year contract, which later turns
out to be a six month scholarship, which is renewed six months at a
time. Many feel that they have been fooled."
 - From Palle Liljebaeck. "Postdoctoral fellows at KI must be given
better terms." Naturvetarna (Sweden), Nov. 7, 2013
<https://www.naturvetarna.se/vi-erbjuder/tidning-och-nyheter/2013/nr-4-2013/Postdoctoral-fellows-at-KI-must-be-given-better-terms/><https://www.naturvetarna.se/vi-erbjuder/tidning-och-nyheter/2013/nr-4-2013/Postdoctoral-fellows-at-KI-must-be-given-better-terms/>.

(By the way, work contracts often entail health, pension and other
benefits which may be limited or unavailable on a scholarship.)

Fortunately, many PIs don't agree with such practices. But they do
occur, including unfortunately for jobs advertized on the CCP4 bulletin
board--and so perhaps the IUCr or other institutions can help set better
standards.

Cheers,
Navdeep


---
On 20.01.21 22:34, Gerlind Sulzenbacher wrote:


Dear Markus,

thank you for opening this discussion.

I'd like to add that in some countries, like France, where I work, this
goes often along with with 12 months contracts.
Imagine moving continent, eventually with family (yes, PostDocs happen
to have a family) just for a 12 months contract, under the conditions
you mentioned.
Sad, as you said, ... and I am quite sure that it has not always been
like that.
I wish all members of the BB a good mood,
Best,
gerlind


On 20/01/2021 21:48, Markus Heckmann wrote:


Dear PI s, and senior scientists' involved in recruitment,

Why do so many (especially postdoc) positions these days indicate:



Readiness for high workload
able to work independently but also effectively and collaboratively
with other lab member
Candidates should have a documented publication record in
peer-reviewed journals, able to work both independently and as an
effective team member.


Do the candidates need to subtly understand that they need to work on
weekends or holidays? And what does it mean by independently and
collaboratively at the same time. Or is this a template from HR
departments.

Was it always like this in science world or we too need to work like
amazon warehouse workers (you can google it and see the pain)?

Saddened...

Mark
(not trying to point out any single PI/person but overall it

Re: [ccp4bb] Open position - data management in biophysics

[Pearce, N.M. (Nick)]

Academia, one of the only careers where _success_ is rewarded with perpetual 
impending employment every two+ years.

Nick

On 22 Jan 2021, at 08:25, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
 wrote:

It is a long time since I had any practical concerns with this issue, but some 
funding bodies are more flexible than others. Welcome gives project grants then 
leaves it up to the recipient to hire and plan. And I guess the big research 
institutes like the crick and lmb have similar systems. It is obvious that this 
approach is much more productive than the shorter term grants - is there any 
mileage in someone doing a survey of “outcomes”(horrible word) and pointing out 
that productivity increases with more security?
And as for the national scandal of milking money fir visas from those who come 
here from abroad - already saving us from the cost of their education - I don’t 
know what to say!
Eleanor

On Fri, 22 Jan 2021 at 07:11, Frank von Delft 
mailto:frank.vonde...@cmd.ox.ac.uk>> wrote:
For me as hiring PI, what's repeatedly dismaying is that it's our funders and 
universities that set the terms, and only with extreme creativity can one shift 
the dial, and only on indidual recruitments, certainly not the high politics of 
the system as a whole.

No, I don't know what will break this - it exploits our fundamental weakness, 
that we go into science because we want to do it, and are already investiging 
all our energy at convincing a system that something else is worth doing 
(getting our mad science funded at all) -- so things like collective striking 
or unionising don't really come naturally.

I do hope the next wave of scientists (am I that old already?) have some 
aggressively constructive thoughts, because mine and the one before mine sure 
don't.


Frank



On 20/01/2021 23:38, Navdeep Sidhu wrote:

Dear Gerlind, Markus, All:

Well, sometimes the (written) promise of a 2-year contract also ends up
boiling down systematically (for some PIs) to only a 6-month contract
after all.--And that after you've spent half a year or more and multiple
trips to the country concerned trying to get a work visa and housing,
all at your own expense--particularly tough for migrants and their families:

"Many come here with a promise of a two-year contract, which later turns
out to be a six month scholarship, which is renewed six months at a
time. Many feel that they have been fooled."
 - From Palle Liljebaeck. "Postdoctoral fellows at KI must be given
better terms." Naturvetarna (Sweden), Nov. 7, 2013
.

(By the way, work contracts often entail health, pension and other
benefits which may be limited or unavailable on a scholarship.)

Fortunately, many PIs don't agree with such practices. But they do
occur, including unfortunately for jobs advertized on the CCP4 bulletin
board--and so perhaps the IUCr or other institutions can help set better
standards.

Cheers,
Navdeep


---
On 20.01.21 22:34, Gerlind Sulzenbacher wrote:


Dear Markus,

thank you for opening this discussion.

I'd like to add that in some countries, like France, where I work, this
goes often along with with 12 months contracts.
Imagine moving continent, eventually with family (yes, PostDocs happen
to have a family) just for a 12 months contract, under the conditions
you mentioned.
Sad, as you said, ... and I am quite sure that it has not always been
like that.
I wish all members of the BB a good mood,
Best,
gerlind


On 20/01/2021 21:48, Markus Heckmann wrote:


Dear PI s, and senior scientists' involved in recruitment,

Why do so many (especially postdoc) positions these days indicate:



Readiness for high workload
able to work independently but also effectively and collaboratively
with other lab member
Candidates should have a documented publication record in
peer-reviewed journals, able to work both independently and as an
effective team member.


Do the candidates need to subtly understand that they need to work on
weekends or holidays? And what does it mean by independently and
collaboratively at the same time. Or is this a template from HR
departments.

Was it always like this in science world or we too need to work like
amazon warehouse workers (you can google it and see the pain)?

Saddened...

Mark
(not trying to point out any single PI/person but overall it is the
same words repeated...)





We are opening a new position for an upcoming European project.

*We are looking for an expert in scientific programming with
experience in
scientific data processing for a European project focused on
Standards for
Data Archival and Exploitation. *

Job description:

We offer attractive work connected to development of 

[ccp4bb] protein web viewer that shows ADPs

[Pearce, N.M. (Nick)]

Hi all,

I’m looking for a web applet (preferably javascript) that can be used to show 
anisotropic displacement parameters (thermal ellipsoids) for atoms. 

Does anyone know of one that supports this? I’ve looked through the usual 
suspects but none of them seem to go beyond cartoon/sticks/etc.

Thanks,
Nick





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Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

[Pearce, N.M. (Nick)]

Hi,

I agree with Melanie and I think we should also go further...

We could require reviewers to tick a box on a PDB reviewer page to confirm they 
have “checked” the structure. Whether this box has been ticked could then be 
displayed on the PDB page (of course the reviewer would remain anonymous) or 
sent to the journal that published the paper (which could them prompt the 
reviewer to do so). It would be transparent for both depositors, editors, and 
users whether the structure had been reviewed. In papers with multiple 
reviewers, of course not all reviewers would be expected to look (i.e. 
interdisciplinary papers). As John says, many journals already require 
validation reports — this is only one small step further and wouldn’t unduly 
increase the work load for reviewers, since we already expect them to check the 
structure. 

I’m not saying it would completely solve the problem as people could just log 
on and click the button without reading, but it would at least be the start of 
accountability or at least record keeping. If you forced (assigned) reviewers 
to visit the PDB webpage, seeing a large array of red sliders might at least 
trigger a reviewer to look more carefully. Even better, a potential reviewer 
page could contain automatically generated electron density pictures for 
ligands (as are already available on the pdb websites, so generating them isn’t 
extra work) — this would avoid the problem where images in the paper are 
inaccurately or incorrectly generated. Again, it might trigger reviewer 
investigation if they’re forced to click a button on the websites for “I am ok 
with this structure and it is of appropriate quality for the conclusions of the 
paper”. 

This would of course require journals to require links to the pdb depositions 
on manuscript submission rather than asking for them if a reviewer requests it 
— I don’t think that’s a big ask.

Thanks,
Nick

> On 23 Jul 2019, at 09:52, "melanie.voll...@diamond.ac.uk" 
>  
> Dear John,
> 
> 
> Yes, I think the PDB should be stricter. The PDB is in the position to 
> enforce compliance with rules and if they are not followed then one doesn't 
> get a validation report and in turn it would be difficult to publish (most 
> journals require a validation report). For years it has been tried to make 
> adherence to standards voluntary but there are still examples, like the one 
> that started the discussion, where people just don't bother.
> 
> 
> For these particular structures I actually suspect that even if there were 
> all reports given to the referees they may not have looked carefully enough. 
> The journal where they were published in is heavy on the chemistry side so 
> perhaps the referees focused on the synthesis of the compounds rather than 
> the structure and the interaction within the protein. Aside from that, at a 
> resolution of 2.7A to 3A discussing detailed chemical interactions and 
> placing a compound with confidence is questionable anyway.
> 
> 
> Cheers
> 
> 
> M
> 
> 
> From: CCP4 bulletin board  on behalf of John 
> Berrisford 
> Sent: 22 July 2019 22:23:47
> To: ccp4bb
> Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
> 
> Dear Harry
> 
> We will be shortly making it mandatory for depositors to provide a value for 
> at least one of the merging statistics (Rmerge, Rpim, CC1/2 etc..). Most 
> depositors do, but we want to ensure that all depositors do provide at least 
> one value for a merging metric.
> 
> We would welcome feedback if we should be stricter and require a (or more 
> than one) specific metric (e.g. CC1/2) – please be aware that any required 
> metric must be available from all merging/scaling software.
> 
> Thanks
> 
> John
> 
> From: CCP4BB 
> Sent: 22 July 2019 11:32
> To: John Berrisford 
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
> 
> Hi John
> 
> These are great, but the things that make me suspicious are the values of 
> overall R(merge); these are tucked away in the full reports, rather than 
> highlighted with all the other structural metrics in the validation sliders. 
> It would be wonderful to be able to see at a glance where overall R(merge) 
> values like these fit in with those of other deposited structures (even 
> better if it could be drawn to the attention of authors before final 
> deposition).
> 
> Kay and Gérard have already pointed out that the data processing here may 
> have some issues.
> 
> Of course, those of us involved in teaching data processing have been 
> emphasizing the importance of CC(1/2) rather than relying on R(merge) for 
> yonks, but if CC(1/2) isn't given in the report it's all we have to go
> 
> Harry
> --
> Dr Harry Powell
> 
> On 22 Jul 2019, at 10:05, John Berrisford 
> mailto:j...@ebi.ac.uk>> wrote:
> Dear Daniel
> 
> The issues you mentioned are highlighted in the wwPDB validation report
> 

Re: [ccp4bb] fix b-factors/coordinates during refinement

[Pearce, N.M. (Nick)]

But no way to fix to a set of refined/parametrised Bfactors and refine? (That’s 
the one I wanted most). I.e. “refi coordsonly”.

Thanks,
Nick

On 20 Feb 2019, at 12:47, Jon Agirre 
mailto:jon.agi...@york.ac.uk>> wrote:

Hi Nick,

you can refine B-factors while leaving coordinates untouched by using the 'refi 
bonly' keywords. You can also preset an average (e.g. Wilson B) and have refmac 
do coordinate refinement 
(http://www.ccp4.ac.uk/html/refmac5/keywords/xray-principal.html#refi).

Cheers,
Jon

On Wed, 20 Feb 2019 at 11:29, Pearce, N.M. (Nick) 
mailto:n.m.pea...@uu.nl>> wrote:
Hi all,

Is it possible to fix the B-factors/coordinates of a model in refinement with 
REFMAC?

It’s trivial to do so in phenix.refine (strategy=…), but I can’t find an 
equivalent command line flag in refmac…

Thanks,
Nick

Post-doctoral Fellow,
Crystal and Structural Chemistry,
Utrecht University



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--
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Twitter: @alwaysonthejazz



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[ccp4bb] fix b-factors/coordinates during refinement

[Pearce, N.M. (Nick)]

Hi all, 

Is it possible to fix the B-factors/coordinates of a model in refinement with 
REFMAC? 

It’s trivial to do so in phenix.refine (strategy=…), but I can’t find an 
equivalent command line flag in refmac…

Thanks,
Nick

Post-doctoral Fellow,
Crystal and Structural Chemistry,
Utrecht University



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Re: [ccp4bb] visualising anis B factors

[Pearce, N.M. (Nick)]

in pymol you can just type “as ellipsoids”.

On 23 Jan 2019, at 16:17, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Is there any easy way to do this?

Coot? ccp4mg?

Eleanor Dodson



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Re: [ccp4bb] unmodeled blobs

[Pearce, N.M. (Nick)]

Hi,

I think it's unlikely to be “just one” molecule — It’s much more likely an 
average over multiple states in the crystal (i.e. that site is disordered).
Therefore, IMHO, modelling anything more than a couple of waters is highly 
misleading to anyone interpreting your model afterwards.

If you do try to model it with something, make sure check what the refined 
B-factor is — if they're much larger than the surroundings, then delete what 
you added and leave the site unmodelled because you "cannot determine the 
likely local model based on the quality of the crystallographic data and the 
local chemical environment”.

You don’t need to model every single blob in the crystal — only model the 
clearly resolved ones, or the ones for which you can construct a “sensible" 
model.

Nick

On 18 Jan 2019, at 12:03, Satvik Kumar 
mailto:kumarsatvi...@gmail.com>> wrote:

Dear Community,

I am solving a structure by MR at 2.1 A. I am unable to figure out what to fit 
in the two electron density blobs that I see.

The protein in Tris buffer and DTT was suplemented with sodium pyrophosphate 
before setting up the trays. The crystals were grown using MIB buffer (Malonic 
acid, Imidazole and Boric acid) and PEG 1500.

The images show the 2Fo-Fc electron density contoured at 1.3 sigma.

Can the experts kindly suggest what I can fit in these blobs?

Thanks,
Satvik






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Re: [ccp4bb] PanDDA error revisiting old run

[Pearce, N.M. (Nick)]

Hi,

Yes, it is the case that newer pandda version may not be compatible with old 
pandda analyses. You’ll have to downgrade to the version you used originally. 

Thanks,
Nick

> On 20 Jun 2018, at 12:17, Chris Richardson  wrote:
> 
> One of our group has been using the newly updated PanDDA (0.2.12 in ccp4 
> 7.0.058) to look at some data previously processed with PanDDA.  It dies with 
> an error on unpickling a pickle file (see errors below).
> 
> My guess is that changes have left it unable to read some pickle files from 
> previous versions.  I’ve tried running pandda.analyse on the tutorial data 
> and it completes without errors.
> 
> Can anyone shed some light on this?
> 
> TIA,
> 
> Chris
> 
> ---%<---
> 
> PanDDA is running on Ubuntu 16.0.4 LTS with CCP4 7.0.058.  The command was:
> 
> pandda.analyse data_dirs="/work//foop/" 
> out_dir="//pandda/pandda_analyse" min_build_datasets=30 
> max_new_datasets=500 grid_spacing=0.5 cpus=8 events.order_by=cluster_size 
> pdb_style='pandda_in_*.pdb' mtz_style='pandda_in_*_map_coeffs.mtz' 
> recalculate_statistical_maps=no existing_datasets=reprocess 
> reference.pdb="/work//pandda/pandda_analyse/reference/reference.pdb"
>  
> reference.mtz="/work//pandda/pandda_analyse/reference/reference.mtz"
> 
> The error is:
> 
> <…>
> Checking for existing analyses
> ->>>
> Looking for pickled files from previous runs in: pickled_data
> -> Loading reference grid
> Unpickling File: pickled_data/grid.pickle
> -> Loading reference dataset
> Unpickling File: pickled_data/reference_dataset.pickle
> Runtime: 00 hours:00 minutes:00 seconds
> 
> ## <~~~> 
> ###
> ### PanDDA exited with an error   
>###
> ## <~~~> 
> ###
> 
> ->>>
> 
> Traceback (most recent call last):
>  File 
> "/common/app/ccp4/7.0.0/ccp4-7.0/lib/python2.7/site-packages/panddas-0.2.12-py2.7.egg/pandda/analyse/__init__.py",
>  line 1081, in run
>pandda_analyse_main(pandda=pandda)
>  File 
> "/common/app/ccp4/7.0.0/ccp4-7.0/lib/python2.7/site-packages/panddas-0.2.12-py2.7.egg/pandda/analyse/__init__.py",
>  line 1020, in pandda_analyse_main
>pandda.run_analysis_init()
>  File 
> "/common/app/ccp4/7.0.0/ccp4-7.0/lib/python2.7/site-packages/panddas-0.2.12-py2.7.egg/pandda/analyse/classes.py",
>  line 771, in run_analysis_init
>self.load_pickled_objects()
>  File 
> "/common/app/ccp4/7.0.0/ccp4-7.0/lib/python2.7/site-packages/panddas-0.2.12-py2.7.egg/pandda/analyse/classes.py",
>  line 821, in load_pickled_objects
>
> self.datasets.set_reference(dataset=self.unpickle(self.pickle_handler.get_file('reference_dataset')))
>  File 
> "/common/app/ccp4/7.0.0/ccp4-7.0/lib/python2.7/site-packages/panddas-0.2.12-py2.7.egg/giant/manager.py",
>  line 82, in unpickle
>return easy_pickle.load(pickle_file)
>  File 
> "/common/app/ccp4/7.0.0/ccp4-7.0/lib/py2/site-packages/cctbx_project/libtbx/easy_pickle.py",
>  line 80, in load
>return cPickle.loads(_open(file_name, "rb").read())
> AttributeError: 'module' object has no attribute 'ElectronDensityMap'
> 
> ->>>
> 
> ## <~~~> 
> ###
> ### PanDDA exited with an error   
>###
> ## <~~~> 
> ###
> -- 
> Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk
> 
> 
> 
> 
> 
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
> Limited by Guarantee, Registered in England under Company No. 534147 with its 
> Registered Office at 123 Old Brompton Road, London SW7 3RP.
> 
> This e-mail message is confidential and for use by the addressee only.  If 
> the message is received by anyone other than the addressee, please return the 
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> 
> 
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> 
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Re: [ccp4bb] AW: [ccp4bb] Pandda problems

[Pearce, N.M. (Nick)]

I agree completely for error messages regarding errors that the user can fix.

However that is not the case with this error, which was an “unexpected” error — 
perhaps I will add a “contact developer” message to those errors to make this 
clear.

Thanks,
Nick

On 25 May 2018, at 16:22, 
"herman.schreu...@sanofi.com<mailto:herman.schreu...@sanofi.com>" 
<herman.schreu...@sanofi.com<mailto:herman.schreu...@sanofi.com>> wrote:

Dear Nick,

Thank you for your reply. I am looking forward to test a new Pandda version 
that is hopefully compatible with the latest CCP4 version.

Concerning the error messages: I think they are very useful for developers, to 
trace back in the code what had happened, but not for users, who need 
information how to change the input files and/or parameters to fix the problem. 
However, Charles Ballard send me an email that the problem could also have been 
caused by old .pyc files and gave instructions how to remove these.

If the alignment is to get a superposition, you could consider aligning on 
sequence numbers, which is trivial and which should be identical for all data 
sets.

Best regards and have a nice weekend!
Herman




Von: Pearce, N.M. (Nick) [mailto:n.m.pea...@uu.nl]
Gesendet: Freitag, 25. Mai 2018 15:59
An: Schreuder, Herman /DE
Cc: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Betreff: [EXTERNAL] Re: [ccp4bb] Pandda problems

Hi,

Yes, that’s not a very useful error message — sorry. I am still in the process 
of intermittently rewriting the pandda code to be …better.

I don’t think you’ve necessarily done anything wrong — pandda has not been 
extensively tested on running on series of structures that are not identical 
(we normally refine one reference structure against all datasets).

However, your timing is pretty good, because I will (today) release a new 
version of pandda that should work with the latest version of ccp4. I think it 
should fix the particular problem that you have.

I’m just running tests now, but on Monday you should be able to update your 
ccp4 to the newest update and then update your version of pandda using pip, 
following the instructions on the website 
(https://pandda.bitbucket.io<https://urldefense.proofpoint.com/v2/url?u=https-3A__pandda.bitbucket.io=DwMGaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=pIVoj_vY0iZI7b1jCo9sKCstLJBflXDxeehLO9PEB9U=aiR_cyVICaVVLw8M5Uh4UIcY4TROi_XWnKii9xF65KA=>).

If that doesn’t work on Monday, let me know if you have any more problems.

Thanks,
Nick


On 25 May 2018, at 14:36, 
herman.schreu...@sanofi.com<mailto:herman.schreu...@sanofi.com> wrote:

Dear bulletin board,

I am trying to run Pandda on a set of about 50 data sets. I asked our system 
manager to roll back to CCP4 update 047 and by using unique and refmac, I could 
fix the problem of a few missing low resolution reflections.

However, then Pandda crashes apparently during alignment of the structures with 
the following – for me not very helpful – error messages:

Failed to align dataset x10
Traceback (most recent call last):
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/pandda/analyse/functions.py",
 line 68, in run
alignment = model.align_to(other_hierarchy=other.hierarchy, method=method, 
require_hierarchies_identical=False)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/dataset.py",
 line 96, in align_to
self.alignment = align_structures_flexible(mov_hierarchy=self.hierarchy, 
ref_hierarchy=other_hierarchy, **kwargs)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/structure/align.py",
 line 254, in align_structures_flexible
l_ali = align_chains_flexible(chn_mov=chn_mov, chn_ref=chn_ref, 
altlocs=altlocs, cutoff_radius=cutoff_radius)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/structure/align.py",
 line 285, in align_chains_flexible
chn_ref_cr, chn_mov_cr = common_residues(chn_ref_cb, chn_mov_cb)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/structure/select.py",
 line 79, in common_residues
assert (max(m_seq_1)<len(alignment.a)) and (max(m_seq_2)<len(alignment.b)), 
'Something has gone wrong: selecting residue index greater than chain length'
AssertionError: Something has gone wrong: selecting residue index greater than 
chain length

The same message is repeated for 47 more data sets.

Does anyone has an idea what the problem is? Did the rollback to update 047 
fail? All pdb files have the same sequence, but there may sometimes be one or 
two residues missing at the N- or C-terminus. Also in some cases, some 
side-chains may be missing. There is only a single protein chain and a few 
calcium ions. In most cases, the calcium ions have the same chainID as the 
protein (as in the reference pdb file), but sometimes the calcium ions have a 
separate chainID.

Any help will be greatly appreciated!
Herman

Re: [ccp4bb] Pandda problems

[Pearce, N.M. (Nick)]

Hi,

Yes, that’s not a very useful error message — sorry. I am still in the process 
of intermittently rewriting the pandda code to be …better.

I don’t think you’ve necessarily done anything wrong — pandda has not been 
extensively tested on running on series of structures that are not identical 
(we normally refine one reference structure against all datasets).

However, your timing is pretty good, because I will (today) release a new 
version of pandda that should work with the latest version of ccp4. I think it 
should fix the particular problem that you have.

I’m just running tests now, but on Monday you should be able to update your 
ccp4 to the newest update and then update your version of pandda using pip, 
following the instructions on the website (https://pandda.bitbucket.io).

If that doesn’t work on Monday, let me know if you have any more problems.

Thanks,
Nick

On 25 May 2018, at 14:36, 
herman.schreu...@sanofi.com wrote:

Dear bulletin board,

I am trying to run Pandda on a set of about 50 data sets. I asked our system 
manager to roll back to CCP4 update 047 and by using unique and refmac, I could 
fix the problem of a few missing low resolution reflections.

However, then Pandda crashes apparently during alignment of the structures with 
the following – for me not very helpful – error messages:

Failed to align dataset x10
Traceback (most recent call last):
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/pandda/analyse/functions.py",
 line 68, in run
alignment = model.align_to(other_hierarchy=other.hierarchy, method=method, 
require_hierarchies_identical=False)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/dataset.py",
 line 96, in align_to
self.alignment = align_structures_flexible(mov_hierarchy=self.hierarchy, 
ref_hierarchy=other_hierarchy, **kwargs)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/structure/align.py",
 line 254, in align_structures_flexible
l_ali = align_chains_flexible(chn_mov=chn_mov, chn_ref=chn_ref, 
altlocs=altlocs, cutoff_radius=cutoff_radius)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/structure/align.py",
 line 285, in align_chains_flexible
chn_ref_cr, chn_mov_cr = common_residues(chn_ref_cb, chn_mov_cb)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/structure/select.py",
 line 79, in common_residues
assert (max(m_seq_1)

[ccp4bb] Abstract deadline is TOMORROW for Diffraction Methods in Structural Biology GRS

[Pearce, N.M. (Nick)]

Dear BB,

Tomorrow is the abstract deadline for the Gordon Research Seminar in 
Diffraction Methods 2018 at Bates College, Maine (28-29th July 2018).
Applications/abstracts received after this date (28th April) will still be able 
to attend and present posters, but will not be considered for oral 
presentations.

This year’s title is Crystallography 2.0: Restructuring the Field Around a New 
Wave of Experiments

We want to have as many young scientists (Post-docs, PhD candidates & Master’s 
students) at the GRS (and associated GRC) as possible. For Jessica and myself, 
the 2016 Diffraction Methods GRS & GRC was the best conference we’ve attended 
during our PhDs, since it allowed us to present our research directly to our 
peers in a relaxed setting; it also gave many of us the opportunity to gain 
first-hand experience as session chairs -- an opportunity that is difficult to 
find as a young scientist. On top of this, the intimate nature and relatively 
small size of Gordon conferences helped us to build more long-lasting 
international connections than at any other conference we have attended.

Of course, the GRS can only be truly successful if a wide variety of viewpoints 
are represented — so please consider attending.
We would greatly appreciate it if you could also forward this invitation to any 
young scientists for whom you think this conference might be valuable.

You can apply for the seminar (GRS) here: 
https://www.grc.org/diffraction-methods-in-structural-biology-grs-conference/2018/.
On this page you can also find a link to the associated Gordon Research 
Conference (GRC).

We hope to see you in July,
Nicholas Pearce & Jessica Besaw

Chair & Co-Chair,
Gordon Research Seminar in Diffraction Methods, 2018

[ccp4bb] Abstract deadline is 28th April for Diffraction Methods in Structural Biology GRS

[Pearce, N.M. (Nick)]

Dear BB,

There are five more days until the abstract deadline for the Gordon Research 
Seminar in Diffraction Methods 2018 at Bates College, Maine (28-29th July 2018).
Applications/abstracts received after this date (28th April) will still be able 
to attend and present posters, but will not be considered for oral 
presentations.

This year’s title is Crystallography 2.0: Restructuring the Field Around a New 
Wave of Experiments

We want to have as many young scientists (Post-docs, PhD candidates & Master’s 
students) at the GRS (and associated GRC) as possible. For Jessica and myself, 
the 2016 Diffraction Methods GRS & GRC was the best conference we’ve attended 
during our PhDs, since it allowed us to present our research directly to our 
peers in a relaxed setting; it also gave many of us the opportunity to gain 
first-hand experience as session chairs -- an opportunity that is difficult to 
find as a young scientist. On top of this, the intimate nature and relatively 
small size of Gordon conferences helped us to build more long-lasting 
international connections than at any other conference we have attended.

Of course, the GRS can only be truly successful if a wide variety of viewpoints 
are represented — so please consider attending.
We would greatly appreciate it if you could also forward this invitation to any 
young scientists for whom you think this conference might be valuable.

You can apply for the seminar (GRS) here: 
https://www.grc.org/diffraction-methods-in-structural-biology-grs-conference/2018/.
On this page you can also find a link to the associated Gordon Research 
Conference (GRC).

We hope to see you in July,
Nicholas Pearce & Jessica Besaw

Chair & Co-Chair,
Gordon Research Seminar in Diffraction Methods, 2018

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

[Pearce, N.M. (Nick)]

Oh, sorry, I'm with you — thanks for clarifying. I thought you were suggesting 
some other effect (that I was unaware of) than standard systematic absences.

I don’t think this is the problem in our case, but you’re right the spacegroup 
issue is an interesting one to look out for if any reindexing occurs.

Thanks,
Nick

On 6 Apr 2018, at 02:02, James Holton 
<jmhol...@slac.stanford.edu<mailto:jmhol...@slac.stanford.edu>> wrote:


I say "putative" because I don't know what your space group is.

In P212121 the reflection h,k,l = 0,0,1 is absent, but in P222 it is not 
absent.  So, if your unit cell is a=30 b=40 c=60 the lowest-angle hkl you will 
get is at 60 A resolution (0,0,1) in P222, but the lowest-angle reflection you 
will get out of P212121 will be (0,1,1), at 33.3 A resolution.  This is because 
0,1,0 is also absent.  So, if you ever specify P212121 in your pipeline the 
0,0,1 reflection will be lost.  Same thing happens with most any 
screw-vs-rotation axis assignment.

You loose other reflections to absences too, of course, but the lowest-order 
ones have an annoying habit of defining the "resolution range", and this can 
sometimes get set at one point in the pipeline and applied to subsequent 
operations, even if you change the space group back.  This could also be 
happening to you?

It is also possible to a subtle change in unit cell can move your lowest-order 
(and also the highest order) reflections across the defined "resolution range" 
boundaries.  Sometimes even round-off error can be enough.

So, if low-resolution is important it is always a good idea to replace the 
low-angle resolution limit with  A.  Just be sure your beamstop was 
properly masked off.

-James Holton
MAD Scientist


On 4/5/2018 10:55 AM, Pearce, N.M. (Nick) wrote:
Could you expand a bit on what you mean by a “putative” systematic absence? 
(e.g. why only the lowest order hkl?)



On 5 Apr 2018, at 19:39, James Holton 
<jmhol...@slac.stanford.edu<mailto:jmhol...@slac.stanford.edu>> wrote:


You need to be careful with the exact space group at the particular stage in 
your pipeline here.  Often the lowest-order hkl is a putative systematic 
absence, so if you uniqueify in P222 you will get it, but if you uniqueify in 
P212121, then you won't.  That sort of thing.  Note that it doesn't matter what 
the "true" space group is, it only matters what is in the mtz header when you 
run uniqueify.

Could that be what is going on?

-James Holton

MAD Scisntist

On 4/5/2018 3:52 AM, Frank von Delft wrote:

Hello - can anybody shed light on this mystery:

We need (for PanDDA analysis) a lot of datasets each to have the complete set 
of low resolution indices, whether measured or not.  (Refmac adds the estimates 
as DFc, which is crucial when comparing maps.)

In ccp4, there are two obvious ways to get these indices complete:

  *   uniqueify
  *   CAD using the keyword "RESOLUTION FILE 1 999 "  (999 is the low 
resolution limit).

Mystifyingly, in ~1% of datasets, one or the other route misses one or two 
indices.  Our work-around is to go belt-and-braces and run both for each 
dataset.


It does however remain a bug.  Does anybody have any idea what's happening?  We 
can send example datasets to any volunteers who want to fiddle with it.

phx

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

[Pearce, N.M. (Nick)]

Could you expand a bit on what you mean by a “putative” systematic absence? 
(e.g. why only the lowest order hkl?)



On 5 Apr 2018, at 19:39, James Holton 
> wrote:


You need to be careful with the exact space group at the particular stage in 
your pipeline here.  Often the lowest-order hkl is a putative systematic 
absence, so if you uniqueify in P222 you will get it, but if you uniqueify in 
P212121, then you won't.  That sort of thing.  Note that it doesn't matter what 
the "true" space group is, it only matters what is in the mtz header when you 
run uniqueify.

Could that be what is going on?

-James Holton

MAD Scisntist

On 4/5/2018 3:52 AM, Frank von Delft wrote:

Hello - can anybody shed light on this mystery:

We need (for PanDDA analysis) a lot of datasets each to have the complete set 
of low resolution indices, whether measured or not.  (Refmac adds the estimates 
as DFc, which is crucial when comparing maps.)

In ccp4, there are two obvious ways to get these indices complete:

  *   uniqueify
  *   CAD using the keyword "RESOLUTION FILE 1 999 "  (999 is the low 
resolution limit).

Mystifyingly, in ~1% of datasets, one or the other route misses one or two 
indices.  Our work-around is to go belt-and-braces and run both for each 
dataset.


It does however remain a bug.  Does anybody have any idea what's happening?  We 
can send example datasets to any volunteers who want to fiddle with it.

phx

Re: [ccp4bb] Overlapping ligand electron density

[Pearce, N.M. (Nick)]

It’s definitely possible to have a superposition of states: 
https://www.ncbi.nlm.nih.gov/m/pubmed/28291761/

You need to use alternate conformers to generate the different states of the 
crystal.

Thanks,
Nick

On 13 Dec 2017, at 20:12, Matthew Bratkowski 
> wrote:

Hello all,

I am working on a ligand binds near the active site of the protein, such that 
part of the ligand would clash with part of the natural substrate.  I recently 
co-crystallized the enzyme with both molecules and solved the crystal structure 
to high resolution (around 1.4 angstrom).  Surprisingly, the structure appears 
to contain both molecules.  A few atoms from both molecules are located only 
~1.4 A apart and are clashing (although not overlapping).  The electron density 
between them looks connected, but based on the two groups that are clashing (a 
methyl group and a carbonyl oxygen), I do not think that a covalent adduct 
occurs.  I had a few questions.

1) My guess is that the crystal is "sampling" two different conformational 
states and that both are visible due to the high diffraction resolution.  The 
substrate contains a ring that shows a characteristic "hole" in the electron 
density and binds in the exact substrate binding site, suggesting that it is 
not a different molecule (no molecules with ring structures were included in 
the sample, crystallization buffer, or cry-protectant).  One of the two 
proteins in the ASU contains electron density for whole substrate, while the 
other site has only density around the ring.  However, a sizable amount of red 
FoFc density is present around the substrate, suggesting that it is only 
partially occupied.

Does this explanation seem plausible?

2) How would I go about modeling these two molecules in the structure?  Should 
I include both molecules (in their entirety) in the structure?  I suspect that 
neither the ligand nor substrate are completely occupied, so should I modify 
the occupancies to reflect this?

Thanks,
Matt