[ccp4bb] Scientific Software Developer at RCSB PDB, UCSD

[Jose Duarte]

The RCSB PDB is seeking a Scientific Software Developer with skills as a
seasoned, experienced bioinformatics programming professional and a broad
understanding of computational algorithms.

The incumbent will develop, implement, and maintain complex scientific and
web-based software systems for the RCSB Protein Data Bank (PDB;
http://www.rcsb.org) at the University of California San Diego (UCSD).

The Scientific Software Developer will work closely and collaboratively
with other software developers and scientists at the San Diego
Supercomputer Center (SDSC) and the RCSB PDB partner sites to expand
RCSB.org's functionality and reliability as a premier biological data and
information resource. S/he will develop new scalable algorithms for the
mining and analysis of the rapidly growing PDB archive using leading edge
Big Data technologies, design and implement user interfaces for the query,
analysis, reporting, and visualization of 3D structural information and
associated annotations, as well as integrate external database resources
with RCSB PDB to provide a structural view of biology. The incumbent will
help lead the design of databases and data warehouses to store and aid in
the query of data and be actively involved in the software development
process, maintenance and system standards for analysis algorithms, tools,
and infrastructure.

Additionally, the incumbent will serve as an expert on relevant scientific
and technical aspects of the various web, web services, and database
components of the RCSB PDB. S/he will stay abreast of the latest
development in structural and computational biology and new technologies,
apply advanced bioinformatics concepts to design, develop, modify, debug,
and evaluate highly complex software programs and web tools, and translate
scientific problems into scalable and maintainable software solutions that
meet end-user needs. The incumbent will also further science through
Scientific Publications, written in collaboration with our team.

More information and how to apply at: https://www.rcsb.org/pages/jobs

---
Jose Duarte
RCSB Protein Data Bank
San Diego Supercomputing Center
UC San Diego



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[ccp4bb] Senior scientist position-Protein Expression at Evotec

[Stephanie Duclos]

Dear CCP4 community,

We are expanding our Structural Biology group at Evotec and we have many 
positions open in our Protein Science team.
If you are interested, please apply using this link:
https://evotecgroup.wd3.myworkdayjobs.com/en-US/Evotec_Career_Site/job/Abingdon/Mammalian-Expression-Scientist-Senior-Scientist_REQ-02534-1



Stephanie on behalf of Hara Black, Group Leader of Protein Science

[cid:image002.png@01D41934.D23B4340]
Stephanie Duclos, Ph.D.
Team Leader, Structural Biology
+44 (0)1235 44 1548  (Direct)
stephanie.duc...@evotec.com
www.evotec.com

Evotec (UK) Ltd.
114 Innovation Drive,
Milton Park
Abingdon
Oxfordshire
OX14 4RZ, UK



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This email and any attachments may contain confidential, proprietary, 
privileged and/or private information.  
If received in error, please notify us immediately by reply email and then 
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Evotec (UK) Ltd is a limited company registered in England and Wales. 
Registration number:2674265. Registered office: 114 Innovation Drive, Milton 
Park, Abingdon, Oxfordshire, OX14 4RZ, United Kingdom.



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[ccp4bb] Job Opportunity at NIH

[Esser, Lothar (NIH/NCI) [E]]

Hi,
on behalf of Dr. Di Xia, I am posting this interesting job opportunity:







We are looking for a young research scientist with a recent Ph.D. in structural 
biology with training in cryo-EM/X-ray crystallography to join our Section of 
Structural Biology of Membrane Proteins in the Laboratory of Cell Biology, 
Center for Cancer Research, National Cancer Institute, NIH to work on 
"Mechanistic investigation of cellular respiratory chain in drug resistance ".  
The project involves structural study of mitochondrial proteins that are 
targets of antimicrobial compounds.  It is anticipated that multiple structural 
techniques will be employed, involving the use of X-ray crystallography and 
Cryo-EM to illuminate structural aspects of target protein response to drug 
treatment.  Our group has assured access to a synchrotron beam line at APS and 
to an intramural EM facility equipped with a Krios microscope and Gatan K3 
detector.  While the candidate should have structural biology expertise, they 
are not expected to be proficient in all structural biology techniques. The 
successful candidate should have practical experiences in molecular biology and 
protein purification for target proteins production. Experience in 
mitochondrial proteins is a plus. NIH has a welcoming, collaborative and 
vibrant environment for biomedical research. Interested individuals should send 
their Applications, consisting of a CV, a statement of research interest, and 
three letters of recommendation, should be sent to Dr. Di Xia via Email at 
x...@mail.nih.gov



Application deadline is 4th January 2021.







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Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

[Dorothee Liebschner]

Hi Nika,

- As Herman wrote, you should use common sense to interpret a polder map:
if the ligand is not there, this kind of map may show only bulk solvent. So
the appearance of some density in the area of the ligand does not "prove"
that the ligand is there. Also, map interpretation should be done while
keeping in mind data quality, data resolution and the state of the model
(how far along you are in refinement). Ligand density may not be clear yet
if the model is fresh out of MR, but it may become better once the model is
finalized. At high resolution, negative density may appear if the occupancy
is too high and it may disappear if you refine it (of course, don't let it
refine to unreasonably low occupancy...).

- There is no need to refine against a polder map. If the ligand is placed
in the model, the bulk solvent mask is calculated accordingly, so
refinement is aware that there is no bulk solvent in this area.

I wrote the polder tool, so if you want, I can have a look at the maps.
Send me the model with the refined ligand + data (+ cif restraints if
applicable). If you send files, be mindful to do so off-list (reply only to
me).

Best wishes,

Dorothee


On Tue, Nov 24, 2020 at 3:29 AM Nika Žibrat  wrote:

> Hello,
>
>
> I have a question about protein-ligand, of which ligand displays an
> ambiguous electron density. I am solving a structure of protein with
> ligand  which was obtained via soaking. Structural characteristics indicate
> the ligand is present however the electron density is quite vague and too
> small for the size of the whole ligand. I did a Polder map which showed
> much larger area of green density. After insertion of my ligand into the
> green density in Polder I ran phenix.refine and there is a lot of red on
> the spot where the ligand is which was to be expected. This leaves me
> wondering how, if even do I incorporate the polder map data into my refine
> input.
>
>
> My question is, how do I continue refining and validating the structure in
> this case?
>
>
> Thank you,
>
>
> Nika Žibrat
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>


-- 
Project Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org



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Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

[Bernhard Rupp]

In reasonably compact format, the discussion topic is summarized in this
CCP4 weekend introduction

https://journals.iucr.org/d/issues/2013/02/00/wd5191/index.html

 

As far as the solvent exclusion self-deception via low occupancy goes, fig 2
here:

https://febs.onlinelibrary.wiley.com/doi/epdf/10./febs.14320

 

Good luck, BR

 

From: CCP4 bulletin board  On Behalf Of Nika Žibrat
Sent: Tuesday, November 24, 2020 03:29
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] phenix.refine with ligand with ambiguous electron density

 

Hello, 

 

I have a question about protein-ligand, of which ligand displays an
ambiguous electron density. I am solving a structure of protein with ligand
which was obtained via soaking. Structural characteristics indicate the
ligand is present however the electron density is quite vague and too small
for the size of the whole ligand. I did a Polder map which showed much
larger area of green density. After insertion of my ligand into the green
density in Polder I ran phenix.refine and there is a lot of red on the spot
where the ligand is which was to be expected. This leaves me wondering how,
if even do I incorporate the polder map data into my refine input.

 

My question is, how do I continue refining and validating the structure in
this case? 

 

Thank you,

 

Nika Žibrat

 

 

  _  

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 =1 




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Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

[Dale Tronrud]

Dear Jon,

   I don't think we have any disagreement.  I just wanted to emphasize 
that you should have your plan thought out at the start.  You may have 
decided that you will compare your ligands shape with your map using a 
Real Space R Factor.  If you don't like that number the fault isn't in 
the RSR but in your density.


   Of course you could have decided ahead of time to use a correlation 
coefficient.  Or you could have planed to calculate both and defined 
some weighting scheme to use the two in making the decision.  The error 
comes in if you decision tree depends on how well the analysis justifies 
your desired outcome.


   Like your test set, how you make your decisions should be kept 
isolated from your actual analysis.  The power of the human mind to bend 
its choices toward a rewarding outcome, even unconsciously, is enormous.


   I was trying to stay away from the particulars of what that decision 
tree would look like.  That topic has been discussed many times on the 
BB.  I certainly agree with my good friend Blaine Moors that the Fo-Fo 
map is the gold standard for deciding if something bound and gives a map 
that is unbiased by modeling.  In addition, Fo-Fo maps between the 
crystals of varying occupancy, even very small changes in occupancy, are 
surprisingly informative.  They tend to be highly isomorphorus and 
provide direct information for deconvoluting multiple conformations 
which is vital in partial occupancy binding.


Dale Tronrud

P.S. Changing the contour level does not change the map. That is simply 
a representation issue due to the difficulty of presenting all the 
information in a map.  Sharpening or blurring a map makes a new map, and 
since the sharpening factor is a continuous number that dial wheel 
creates an infinite number of different maps.  If your only means of 
selecting which one is "best" is how well the map fits your ligand, that 
map can't be used to justify your interpretation.


This could be made rigorous by, for example, deciding on the factor by 
looking at the quality of the map in some uncontroversial region -- If 
you decide on the means of choosing that region ahead of time.


On 11/24/2020 8:20 PM, Jon Cooper wrote:
Hello Dale, the statistical rigour you describe is, of course, 
excellent, but in a learning environment, if someone gets a negative 
result, you have to go into overdrive to check that everything has been 
done correctly, since there is a fair chance that human error is the 
cause. It may be a terrible practice, but it would seem to be an 
important part of the process? Even as a relative newcomer to the field 
(well, since the mid-80's ;-) I have seen many people getting nothing in 
their initial difference maps, even if the ligand is there. Frequently 
it was just the contour level being too high and, depending on how far 
back you go, the solution varied from showing someone how to roll the 
mouse wheel in Coot to having the map recontoured at a computer centre 
200 miles away and posted back on a magnetic tape, which took about 10 
days - a timescale on which some people just gave up and did something 
else! I can't help thinking it would be a shame to robotically accept 
every negative result at face value, not least if you're doing something 
important like curing a pandemic. However, back to the original question 
which I think was whether polder map coefficients could be used as 
refinement targets and I think the answer to that one is probably 'no', 
at least in the X-ray field ;-)


Best wishes, Jon Cooper



 Original Message 
On 24 Nov 2020, 16:02, Dale Tronrud < de...@daletronrud.com> wrote:


Hi,

To me, this sounds like a very dangerous way to use this tool decide
if a ligand has bound. I would be very reluctant to modify my map with
a range of arbitrary parameters until it looked like what I wanted to
see. The sharpening and blurring of this tool is not guided or limited
by theory or data.

As you describe it, your choice of map is driven by its agreement
with your ligand, and the proper way to make this decision is the other
way around.

The original poster has the problem that their density does not have
the appearance they desire. They have chosen to run around trying to
find some way to modify the map to get a variant that does. This is a
terrible practice, since the final choice of map is being made in a
fashion that is dominated by bias.

I have no idea what sort of "structural characteristics" have
convinced this poster of the presence of their ligand despite the
absence of clear electron density. What other evidence does a
diffraction pattern give? The map is your best and only source of
information about your structure that you can get from the diffraction
pattern. (Mass spec and other experimental techniques could, of course,
be applied.)

I think we, as a community, could learn a few things from the

Re: [ccp4bb] Coot 0.9.2 in CCP4 - quad-buffered stereo broken?

[Christian Becke]

Hi Paul,

Am 25.11.20 um 17:14 schrieb Paul Emsley:
I have committed 30ec64cc9906a5f19142a87d88b522f6f65409fa which I 
think/hope should fix the problem (undoing the breaking). Just to be 
clear, this commit doesn't require that you have backed out 
5043f6adbbbc5725149e6c53bbbc6a85f3c5e8af.



30ec64cc9906a5f19142a87d88b522f6f65409fa fixes the problems introduced 
by 5043f6adbbbc5725149e6c53bbbc6a85f3c5e8af. Or so I hope.


with commit 30ec64 hardware stereo works again for me, thank you for the 
quick fix!


Christian



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Re: [ccp4bb] Coot 0.9.2 in CCP4 - quad-buffered stereo broken?

[Pedro Matias]

Hi All,

How can a noob user do that? Will CCP4 release a patched Coot binary?

Pedro

Às 15:25 de 25/11/2020, Christian Becke escreveu:

Dear Paul,

Am 25.11.20 um 12:05 schrieb Paul Emsley:

On 23/11/2020 15:21, Pedro Matias wrote:


In the latest coot update (to 0.9.2) in CCP4 the quad-buffered 
stereo doesn't seem to work. The NVIDIA emitter turns on but the 
stereo picture does not appear when the glasses are turned on. 
Strangely enough, the only coot update I can find in the updates 
list is to 0.9.1 in 7.1.007 dated 23-10-2020.


I don't have NVIDIA stereo setup at home and the equipment at work is 
installed on communal workstations. I'm not inclined to touch them at 
the moment.


I have reviewed my commits between 0.9 and 0.9.2 and find that this 
one might have broken NVIDIA stereo:

5043f6adbbbc5725149e6c53bbbc6a85f3c5e8af
So try backing that out if you wish to pursue this.


I am facing the same issue with home-built coot from latest git. 
Reverting the commit you mentioned fixes hardware stereo for me.


Cheers,

Christian



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--

Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
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Universidade Nova de Lisboa
Av. da República
2780-157 Oeiras
PORTUGAL

ITQB NOVA, a great choice for your PhD
https://youtu.be/de6j-aaTWNQ

Master Programme in Biochemistry for Health
https://youtu.be/UKstDCFjYI8



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Re: [ccp4bb] Coot 0.9.2 in CCP4 - quad-buffered stereo broken?

[Christian Becke]

Dear Paul,

Am 25.11.20 um 12:05 schrieb Paul Emsley:

On 23/11/2020 15:21, Pedro Matias wrote:


In the latest coot update (to 0.9.2) in CCP4 the quad-buffered stereo 
doesn't seem to work. The NVIDIA emitter turns on but the stereo 
picture does not appear when the glasses are turned on. Strangely 
enough, the only coot update I can find in the updates list is to 
0.9.1 in 7.1.007 dated 23-10-2020.


I don't have NVIDIA stereo setup at home and the equipment at work is 
installed on communal workstations. I'm not inclined to touch them at 
the moment.


I have reviewed my commits between 0.9 and 0.9.2 and find that this 
one might have broken NVIDIA stereo:

5043f6adbbbc5725149e6c53bbbc6a85f3c5e8af
So try backing that out if you wish to pursue this.


I am facing the same issue with home-built coot from latest git. 
Reverting the commit you mentioned fixes hardware stereo for me.


Cheers,

Christian



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

[Mooers, Blaine H.M. (HSC)]

Dear Nika,

The question is about a Fo-Fc map and the replies have been focused on such 
maps.
However, I question why you are bothering with Fo-Fc maps.
The ligand was soaked into the crystal. There is probably an isomorphous apo 
data set available. 
A [Fo(ligand complex) - Fo(apo)]*exp(alpha_apo,calc) map should be consulted in 
preference to various Fo-Fc maps corrected for phase bias.
It would be even better to substitute in the experimental phases for the apo 
structure if
they are available.

Fo-Fo maps may be nosier than Fo-Fc maps. but they are more reliable when you 
are
trying to decide if a ligand is present. 

I recommend reading the following book chapter:

@incollection{rould2003isomorphous,
  title={Isomorphous difference methods},
  author={Rould, Mark A and Carter Jr, Charles W},
  booktitle={Methods in enzymology},
  volume={374},
  pages={145--163},
  year={2003},
  publisher={Elsevier}
}

I second Robbie's "bloody obvious" rule. 
Sounds like you have an occupancy issue.
If you collected data from multiple crystals of the complex
as is the standard practice these days,
process and check each one. There can be large differences 
in ligand occupancy between crystals from different drops. 

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of John R Helliwell 
[jrhelliw...@gmail.com]
Sent: Wednesday, November 25, 2020 4:36 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] phenix.refine with ligand with ambiguous 
electron density

Hello Robbie,
Yes exactly, I agree. I thought that was what the poster faced: density with 
insufficient detail and not extending sufficiently for the whole ligand.
To make the discussion thread more focussed a screenshot or two would assist us.
Greetings,
John

Emeritus Professor John R Helliwell DSc




On 25 Nov 2020, at 09:03, Robbie Joosten  wrote:


I’m with Dale on this, the scientifically prudent thing is to set the rules and 
then play by them. Not to change the rules as you go. Of course, in a teaching 
environment where you know the correct answer, it is good to be educational and 
learn how to dig a bit more.

However, in a scientific setting this digging is not to come to a strong 
conclusion, but only to see if you should pursue the project and do additional 
experiments (e.g. longer soaks or using a higher ligand concentration). In this 
case the topic starter has poor density and fitting the ligand and refining 
gives negative difference density. Surely that is not enough evidence to reject 
the null hypothesis “the ligand is not bound”. In other words, there is no 
strong evidence that the ligand is bound. Perhaps you can look at the occupancy 
, but that is probably as far as you should go. The polder map is useful to get 
rid of the effect of the solvent mask blurring actual ligand density. But after 
fitting the ligand you shouldn’t need the polder map. Blurring and sharpening 
is something to make sense of the density shape to better fit your ligand, not 
to conclude whether or not you ligand is there.

On a whole, for ligands we should try to stick to the so-called “bloody 
obvious” test: if the density is not bloody obvious, your ligand is not there. 
At least not all the time.

Cheers,
Robbie


From: CCP4 bulletin board  On Behalf Of Jon Cooper
Sent: Wednesday, November 25, 2020 05:20
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Hello Dale, the statistical rigour you describe is, of course, excellent, but 
in a learning environment, if someone gets a negative result, you have to go 
into overdrive to check that everything has been done correctly, since there is 
a fair chance that human error is the cause. It may be a terrible practice, but 
it would seem to be an important part of the process? Even as a relative 
newcomer to the field (well, since the mid-80's ;-) I have seen many people 
getting nothing in their initial difference maps, even if the ligand is there. 
Frequently it was just the contour level being too high and, depending on how 
far back you go, the solution varied from showing someone how to roll the mouse 
wheel in Coot to having the map recontoured at a computer centre 200 miles away 
and posted back on a magnetic tape, which took about 10 days - a timescale on 
which some people just gave up and did something else! I can't help thinking it 
would be a shame to robotically accept every negative result at face value, not 
least if you're doing something important like curing a pandemic. However, back 
to the original question which I think was whether polder map coefficients 
could be used as refinement targets 

[ccp4bb] PhD position in Drug Discovery

[Groves, Matthew]

Dear All,

An ITN PhD position is currently available in my laboratory in the field of
drug discovery. Within the MepAnti ITN we aim to develop and test novel
anti-infectives targeting malaria, tuberculosis and other infectious
diseases. The ideal candidate will have Xray experience, but we are also
hoping to fill this position as soon as possible.

Further details:
http://mepanti.hips-wordpress.helmholtz-hzi.de/
http://mepanti.hips-wordpress.helmholtz-hzi.de/?page_id=179

Please contact me off this list for further information (m.r.gro...@rug.nl).

Cheers,

Matthew



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Re: [ccp4bb] Coot 0.9.2 in CCP4 - quad-buffered stereo broken?

[Paul Emsley]

On 23/11/2020 15:21, Pedro Matias wrote:


In the latest coot update (to 0.9.2) in CCP4 the quad-buffered stereo doesn't seem to work. The NVIDIA 
emitter turns on but the stereo picture does not appear when the glasses are turned on. Strangely enough, 
the only coot update I can find in the updates list is to 0.9.1 in 7.1.007 dated 23-10-2020.


I don't have NVIDIA stereo setup at home and the equipment at work is 
installed on communal workstations. I'm not inclined to touch them at 
the moment.


I have reviewed my commits between 0.9 and 0.9.2 and find that this one 
might have broken NVIDIA stereo:

5043f6adbbbc5725149e6c53bbbc6a85f3c5e8af
So try backing that out if you wish to pursue this.


I noticed that 0.9.3 is already up on Paul's site but I couldn't get it to work 
in standalone mode.


:-(

Paul.



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Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

[John R Helliwell]

Hello Robbie,
Yes exactly, I agree. I thought that was what the poster faced: density with 
insufficient detail and not extending sufficiently for the whole ligand. 
To make the discussion thread more focussed a screenshot or two would assist 
us. 
Greetings,
John 

Emeritus Professor John R Helliwell DSc




> On 25 Nov 2020, at 09:03, Robbie Joosten  wrote:
> 
> 
> I’m with Dale on this, the scientifically prudent thing is to set the rules 
> and then play by them. Not to change the rules as you go. Of course, in a 
> teaching environment where you know the correct answer, it is good to be 
> educational and learn how to dig a bit more.
>  
> However, in a scientific setting this digging is not to come to a strong 
> conclusion, but only to see if you should pursue the project and do 
> additional experiments (e.g. longer soaks or using a higher ligand 
> concentration). In this case the topic starter has poor density and fitting 
> the ligand and refining gives negative difference density. Surely that is not 
> enough evidence to reject the null hypothesis “the ligand is not bound”. In 
> other words, there is no strong evidence that the ligand is bound. Perhaps 
> you can look at the occupancy , but that is probably as far as you should go. 
> The polder map is useful to get rid of the effect of the solvent mask 
> blurring actual ligand density. But after fitting the ligand you shouldn’t 
> need the polder map. Blurring and sharpening is something to make sense of 
> the density shape to better fit your ligand, not to conclude whether or not 
> you ligand is there.
>  
> On a whole, for ligands we should try to stick to the so-called “bloody 
> obvious” test: if the density is not bloody obvious, your ligand is not 
> there. At least not all the time.
>  
> Cheers,
> Robbie
>  
>  
> From: CCP4 bulletin board  On Behalf Of Jon Cooper
> Sent: Wednesday, November 25, 2020 05:20
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] phenix.refine with ligand with ambiguous electron 
> density
>  
> Hello Dale, the statistical rigour you describe is, of course, excellent, but 
> in a learning environment, if someone gets a negative result, you have to go 
> into overdrive to check that everything has been done correctly, since there 
> is a fair chance that human error is the cause. It may be a terrible 
> practice, but it would seem to be an important part of the process? Even as a 
> relative newcomer to the field (well, since the mid-80's ;-) I have seen many 
> people getting nothing in their initial difference maps, even if the ligand 
> is there. Frequently it was just the contour level being too high and, 
> depending on how far back you go, the solution varied from showing someone 
> how to roll the mouse wheel in Coot to having the map recontoured at a 
> computer centre 200 miles away and posted back on a magnetic tape, which took 
> about 10 days - a timescale on which some people just gave up and did 
> something else! I can't help thinking it would be a shame to robotically 
> accept every negative result at face value, not least if you're doing 
> something important like curing a pandemic. However, back to the original 
> question which I think was whether polder map coefficients could be used as 
> refinement targets and I think the answer to that one is probably 'no', at 
> least in the X-ray field ;-)
> 
> Best wishes, Jon Cooper
> 
> 
> 
>  Original Message 
> On 24 Nov 2020, 16:02, Dale Tronrud < de...@daletronrud.com> wrote:
>  
> Hi,
> 
> To me, this sounds like a very dangerous way to use this tool decide
> if a ligand has bound. I would be very reluctant to modify my map with
> a range of arbitrary parameters until it looked like what I wanted to
> see. The sharpening and blurring of this tool is not guided or limited
> by theory or data.
> 
> As you describe it, your choice of map is driven by its agreement
> with your ligand, and the proper way to make this decision is the other
> way around.
> 
> The original poster has the problem that their density does not have
> the appearance they desire. They have chosen to run around trying to
> find some way to modify the map to get a variant that does. This is a
> terrible practice, since the final choice of map is being made in a
> fashion that is dominated by bias.
> 
> I have no idea what sort of "structural characteristics" have
> convinced this poster of the presence of their ligand despite the
> absence of clear electron density. What other evidence does a
> diffraction pattern give? The map is your best and only source of
> information about your structure that you can get from the diffraction
> pattern. (Mass spec and other experimental techniques could, of course,
> be applied.)
> 
> I think we, as a community, could learn a few things from the
> vaccine trial studies that are so much in the news now. In a modern
> clinical trial, to avoid bias in the interpretation of the results, all
> of the statistical 

Re: [ccp4bb] Apple Silicon / XQuartz / X11 / CCP4

[Wie-Cuhn Koa]

Hello,

I just tested some structural biology programs on my MacMini with M1 chip (base 
model, MacOS 11.0.1). After installing Xcode command line tools 12.2 and 
Xquartz 2.7.11, open source pymol 2.4.0 (via homebrew), coot 0.8.9.3 (W. 
Scott's binary) and UCSF chimeraX 1.1 (official dmg) are all working and 
operations such as dragging, zooming with map seem to be quite fast. There was 
a short delay when starting the program and I have heard that this is typical 
when rosetta 2 is called.

Below is a brief pymol rendering benchmark for the same figure. MacMini M1 
behaves quite reasonably. The purpose is merely to compare the performance of 
my devices so I apologise for the limited data available ;-)

MacMini M1 8 core: 17.2 frames/ h
MacMini 2018 (i5 3.0 GHz) 6 core: 13.0 frames/ h
MacBook Pro 2012 (i7 2.16 GHz) 8 core: 6.4 frames/ h
CentOS7 (i7 3.2 GHz desktop) 12 core: 13.8 frames/ h




Fig. 1: Open source pymol 2.4.0 starting message from MacMini M1 (upper panel) 
and MacMini 2018 (lower panel).


Greetings,

Wei-Chun

—

Dr. rer. nat. Wei-Chun Kao
wei-chun@biochemie.uni-freiburg.de 

TEL: +49-761-203-5277 
orcid.org/-0001-8687-6334 


Institute for Biochemistry and Molecular Biology
AG Carola Hunte
Albert-Ludwigs-Universitaet Freiburg
Stefan-Meier-Str. 17
D-79104 Freiburg im Breisgau
Germany

> On 11. Nov 2020, at 10:21, Antony Oliver  wrote:
> 
> Perhaps this is a little too soon, but does anyone know if the new M1 
> system-on-a-chip will continue to run XQuartz/X11 + the CCP4 program suite + 
> other crystallography / EM software? Will CCP4 continue to support the 
> platform?
> 
> (a quick check of the GitHub page indicates that there is already an ARM64 
> implementation of XQuartz)
> 
> I am not in a rush to purchase the newly announced computers, but am keen to 
> understand if we are going to need to future-proof ourselves when the entire 
> family moves over to the new hardware.
> 
> With thanks,
> 
> Antony.
> 
> 
> 
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Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

[Robbie Joosten]

I’m with Dale on this, the scientifically prudent thing is to set the rules and 
then play by them. Not to change the rules as you go. Of course, in a teaching 
environment where you know the correct answer, it is good to be educational and 
learn how to dig a bit more.

However, in a scientific setting this digging is not to come to a strong 
conclusion, but only to see if you should pursue the project and do additional 
experiments (e.g. longer soaks or using a higher ligand concentration). In this 
case the topic starter has poor density and fitting the ligand and refining 
gives negative difference density. Surely that is not enough evidence to reject 
the null hypothesis “the ligand is not bound”. In other words, there is no 
strong evidence that the ligand is bound. Perhaps you can look at the occupancy 
, but that is probably as far as you should go. The polder map is useful to get 
rid of the effect of the solvent mask blurring actual ligand density. But after 
fitting the ligand you shouldn’t need the polder map. Blurring and sharpening 
is something to make sense of the density shape to better fit your ligand, not 
to conclude whether or not you ligand is there.

On a whole, for ligands we should try to stick to the so-called “bloody 
obvious” test: if the density is not bloody obvious, your ligand is not there. 
At least not all the time.

Cheers,
Robbie


From: CCP4 bulletin board  On Behalf Of Jon Cooper
Sent: Wednesday, November 25, 2020 05:20
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Hello Dale, the statistical rigour you describe is, of course, excellent, but 
in a learning environment, if someone gets a negative result, you have to go 
into overdrive to check that everything has been done correctly, since there is 
a fair chance that human error is the cause. It may be a terrible practice, but 
it would seem to be an important part of the process? Even as a relative 
newcomer to the field (well, since the mid-80's ;-) I have seen many people 
getting nothing in their initial difference maps, even if the ligand is there. 
Frequently it was just the contour level being too high and, depending on how 
far back you go, the solution varied from showing someone how to roll the mouse 
wheel in Coot to having the map recontoured at a computer centre 200 miles away 
and posted back on a magnetic tape, which took about 10 days - a timescale on 
which some people just gave up and did something else! I can't help thinking it 
would be a shame to robotically accept every negative result at face value, not 
least if you're doing something important like curing a pandemic. However, back 
to the original question which I think was whether polder map coefficients 
could be used as refinement targets and I think the answer to that one is 
probably 'no', at least in the X-ray field ;-)

Best wishes, Jon Cooper



 Original Message 
On 24 Nov 2020, 16:02, Dale Tronrud < 
de...@daletronrud.com> wrote:


Hi,

To me, this sounds like a very dangerous way to use this tool decide
if a ligand has bound. I would be very reluctant to modify my map with
a range of arbitrary parameters until it looked like what I wanted to
see. The sharpening and blurring of this tool is not guided or limited
by theory or data.

As you describe it, your choice of map is driven by its agreement
with your ligand, and the proper way to make this decision is the other
way around.

The original poster has the problem that their density does not have
the appearance they desire. They have chosen to run around trying to
find some way to modify the map to get a variant that does. This is a
terrible practice, since the final choice of map is being made in a
fashion that is dominated by bias.

I have no idea what sort of "structural characteristics" have
convinced this poster of the presence of their ligand despite the
absence of clear electron density. What other evidence does a
diffraction pattern give? The map is your best and only source of
information about your structure that you can get from the diffraction
pattern. (Mass spec and other experimental techniques could, of course,
be applied.)

I think we, as a community, could learn a few things from the
vaccine trial studies that are so much in the news now. In a modern
clinical trial, to avoid bias in the interpretation of the results, all
of the statistical procedures are decided upon BEFORE the study is even
began. This protocol is written down and peer reviewed at the start.
Then the study is performed and the protocol is followed exactly. If
the results don't pass the test, the treatment is not supported. There
is no hunting around, after the fact, for a "better" statistical measure
until one is found that "works".

This way of handling data analysis in clinical trials was adopted
after the hard lesson was learned that many trails could be reproduced,
their results were not.