[ccp4bb] PSDI 2020

2020-06-10 Thread Djordje Musil 
Dear Friends and Colleagues,
We hope that you, your families and colleagues are all doing well in this time 
of COVID-19 pandemic.
The recent world-wide spread of the pandemic has, regretfully, led us to a 
decision to postpone this year's PSDI meeting till 2021. The conference will 
therefore return in May 2021 at the Marriott Hotel Lyon, France - the same 
venue as planned for this year. The exact dates for the conference have not yet 
been fully confirmed but are most likely to be from 23 to 25 May 2021.
In order to minimise the gap between two regular PSDI conferences we are 
preparing two half-day lecture and discussion slots via a video conference, 
which will take place on 9 and 10 November 2020 - so please keep these dates 
open. More details will follow soon.

The sponsorship options will be announced soon. If you are interested to 
receive some information on sponsorship ahead please contact us at 
psdi-exhibit...@list.embl.fr .
Best regards,
Djordje Musil (on behalf of PSDI 2020 Organising Committee)


Dr. Djordje Musil
Lab Head Protein Crystallography Darmstadt
Molecular Interactions and Biophysics, Discovery Technologies, R

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Re: [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms density

2020-06-10 Thread Jrh Gmail 
Dear Vito
I looked at the examples of I3C in 3e3d, 3e3s and 3e3t and certainly the latter 
two show clear 2Fo-Fc for several I3Cs at a range of occupancies. So my mention 
of the different difference maps’ effectiveness does not apply. 
Hermann and Eleanor suggestions hopefully will explain your I3C map visibility 
you showed
Best wishes
John 

Emeritus Professor of Chemistry John R Helliwell DSc_Physics 



> On 10 Jun 2020, at 09:39, John R Helliwell  wrote:
> 
> Dear Vito,
> The I3C isn't like the platins as a challenge to the 2Fo-Fc map.
> It maybe is more akin to the situation we described here:-
> https://onlinelibrary.wiley.com/doi/abs/10.1107/S0907444903004219
> ie what does your Fo-Fc map, with three iodines placed, at the correct 
> occupancy, look like? 
> Best wishes,
> John 
> 
> Emeritus Professor John R Helliwell DSc
> 
> 
> 
>>> On 10 Jun 2020, at 09:34, Vito Calderone  wrote:
>>> 
>> Dear Pierre,
>> I was in particular talking of 2FoFc refinement maps.
>> In the attached picture for example you can see the 2FoFc map contoured at 1
>> sigma level of an I3C molecule bound to a protein where for I3C the only
>> visible density is that of iodines whereas the density of the other atoms of
>> the ligand is insignificant.
>> Best regards
>> 
>> Vito
>> 
>> -Messaggio originale-
>> Da: CCP4 bulletin board  Per conto di LEGRAND Pierre
>> Inviato: mercoledì 10 giugno 2020 09:31
>> A: CCP4BB@JISCMAIL.AC.UK
>> Oggetto: Re: [ccp4bb] Heavy atom vs light atoms density
>> 
>> Dear Vito,
>> Could you precise in what kind of maps are you experiencing these effects:
>> 2FoFc refinement maps or experimental phasing ?
>> I had this kind of effects long ago in experiemental phasing due to Fourier
>> transform ripple effects. This could be due to scaling problems, low
>> resolution truncation or incompletness (maybe intensity overloads).
>> Another source condition could be local X-ray dose degradation due to the
>> high absoption of the metals.
>> Best regards,
>> Pierre Legrand
>> PROXIMA-1, SOLEIL
>> 
>> De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Vito
>> Calderone [calder...@cerm.unifi.it] Envoyé : mercredi 10 juin 2020 08:42 À :
>> CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Heavy atom vs light atoms density
>> 
>> Dear All,
>>   many of us have probably experienced that, in the diffraction
>> of protein ligands containing heavy atoms (cisPt, I3C, etc), the
>> overwhelming electron density of the metal can totally flatten that of the
>> light atoms around (or rather make it look insignificant).
>> Is anyone aware of an article/review (to use as a reference) in which this
>> is clearly stated/pointed out?
>> Best regards
>> 
>> Vito Calderone
>> 
>> 
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
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>> 
>> 
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Re: [ccp4bb] R: [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms density

2020-06-10 Thread Eleanor Dodson 
Hmm - of course heavy atoms will affect the sigma level of a map, but that
is easily adjusted - just scroll till the electron density looks sensible
for some well defined protein atoms. (Ideally I guess we should contour at
some absolute density level but choosing that to take account of resolution
is tricky..)

But ripples around heavier atoms are more likely due to some error. Data
incompleteness? (not so common nowadays). Wrong occupancy for heavier
atoms? That should show up as a residual peak or hole in the difference
map..

I like to look at the plot of  &   v resolution - it is in the
REFMAC log after the rfactor v resolution. If there are gross differences
between the two means that indicates a problem - maybe measurement - maybe
scaling.. And of course that will be reflected ni the map
 Eleanor


On Wed, 10 Jun 2020 at 10:06, LEGRAND Pierre <
pierre.legr...@synchrotron-soleil.fr> wrote:

> Dear Vito,
> In that case, and from what I can see from the picture you shared, I would
> guess that it is mainly the effect of the low occupancy of this I3C. The
> peak height of the iodide atoms seems low.
> Pierre
>
>
> *De :* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Vito
> Calderone [calder...@cerm.unifi.it]
> *Envoyé :* mercredi 10 juin 2020 10:54
> *À :* CCP4BB@JISCMAIL.AC.UK
> *Objet :* [ccp4bb] R: [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms
> density
>
> Dear John,
>
>I would say that in that case the FoFc is basically flat.
>
>
>
> Vito
>
>
>
> *Da:* CCP4 bulletin board  *Per conto di *John R
> Helliwell
> *Inviato:* mercoledì 10 giugno 2020 10:40
> *A:* CCP4BB@JISCMAIL.AC.UK
> *Oggetto:* Re: [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms density
>
>
>
> Dear Vito,
>
> The I3C isn't like the platins as a challenge to the 2Fo-Fc map.
>
> It maybe is more akin to the situation we described here:-
>
> https://onlinelibrary.wiley.com/doi/abs/10.1107/S0907444903004219
>
> ie what does your Fo-Fc map, with three iodines placed, at the correct
> occupancy, look like?
>
> Best wishes,
>
> John
>
> Emeritus Professor John R Helliwell DSc
>
>
>
>
>
>
>
> On 10 Jun 2020, at 09:34, Vito Calderone  wrote:
>
> Dear Pierre,
> I was in particular talking of 2FoFc refinement maps.
> In the attached picture for example you can see the 2FoFc map contoured at
> 1
> sigma level of an I3C molecule bound to a protein where for I3C the only
> visible density is that of iodines whereas the density of the other atoms
> of
> the ligand is insignificant.
> Best regards
>
> Vito
>
> -Messaggio originale-
> Da: CCP4 bulletin board  Per conto di LEGRAND
> Pierre
> Inviato: mercoledì 10 giugno 2020 09:31
> A: CCP4BB@JISCMAIL.AC.UK
> Oggetto: Re: [ccp4bb] Heavy atom vs light atoms density
>
> Dear Vito,
> Could you precise in what kind of maps are you experiencing these effects:
> 2FoFc refinement maps or experimental phasing ?
> I had this kind of effects long ago in experiemental phasing due to Fourier
> transform ripple effects. This could be due to scaling problems, low
> resolution truncation or incompletness (maybe intensity overloads).
> Another source condition could be local X-ray dose degradation due to the
> high absoption of the metals.
> Best regards,
> Pierre Legrand
> PROXIMA-1, SOLEIL
> 
> De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Vito
> Calderone [calder...@cerm.unifi.it] Envoyé : mercredi 10 juin 2020 08:42
> À :
> CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Heavy atom vs light atoms density
>
> Dear All,
>   many of us have probably experienced that, in the diffraction
> of protein ligands containing heavy atoms (cisPt, I3C, etc), the
> overwhelming electron density of the metal can totally flatten that of the
> light atoms around (or rather make it look insignificant).
> Is anyone aware of an article/review (to use as a reference) in which this
> is clearly stated/pointed out?
> Best regards
>
> Vito Calderone
>
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
> 
>
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> 
>
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>
>
>

Re: [ccp4bb] R: [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms density

2020-06-10 Thread LEGRAND Pierre 
Dear Vito,
In that case, and from what I can see from the picture you shared, I would 
guess that it is mainly the effect of the low occupancy of this I3C. The peak 
height of the iodide atoms seems low.
Pierre


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Vito Calderone 
[calder...@cerm.unifi.it]
Envoyé : mercredi 10 juin 2020 10:54
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] R: [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms density

Dear John,
   I would say that in that case the FoFc is basically flat.

Vito

Da: CCP4 bulletin board  Per conto di John R Helliwell
Inviato: mercoledì 10 giugno 2020 10:40
A: CCP4BB@JISCMAIL.AC.UK
Oggetto: Re: [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms density

Dear Vito,
The I3C isn't like the platins as a challenge to the 2Fo-Fc map.
It maybe is more akin to the situation we described here:-
https://onlinelibrary.wiley.com/doi/abs/10.1107/S0907444903004219
ie what does your Fo-Fc map, with three iodines placed, at the correct 
occupancy, look like?
Best wishes,
John
Emeritus Professor John R Helliwell DSc




On 10 Jun 2020, at 09:34, Vito Calderone 
mailto:calder...@cerm.unifi.it>> wrote:
Dear Pierre,
I was in particular talking of 2FoFc refinement maps.
In the attached picture for example you can see the 2FoFc map contoured at 1
sigma level of an I3C molecule bound to a protein where for I3C the only
visible density is that of iodines whereas the density of the other atoms of
the ligand is insignificant.
Best regards

Vito

-Messaggio originale-
Da: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
Per conto di LEGRAND Pierre
Inviato: mercoledì 10 giugno 2020 09:31
A: CCP4BB@JISCMAIL.AC.UK
Oggetto: Re: [ccp4bb] Heavy atom vs light atoms density

Dear Vito,
Could you precise in what kind of maps are you experiencing these effects:
2FoFc refinement maps or experimental phasing ?
I had this kind of effects long ago in experiemental phasing due to Fourier
transform ripple effects. This could be due to scaling problems, low
resolution truncation or incompletness (maybe intensity overloads).
Another source condition could be local X-ray dose degradation due to the
high absoption of the metals.
Best regards,
Pierre Legrand
PROXIMA-1, SOLEIL

De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Vito
Calderone [calder...@cerm.unifi.it] Envoyé : mercredi 10 juin 2020 08:42 À :
CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Heavy atom 
vs light atoms density

Dear All,
  many of us have probably experienced that, in the diffraction
of protein ligands containing heavy atoms (cisPt, I3C, etc), the
overwhelming electron density of the metal can totally flatten that of the
light atoms around (or rather make it look insignificant).
Is anyone aware of an article/review (to use as a reference) in which this
is clearly stated/pointed out?
Best regards

Vito Calderone





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[ccp4bb] AW: [EXTERNAL] [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms density

2020-06-10 Thread Schreuder, Herman /DE 
Dear Vito,

I have also worked with iodinated and brominated compounds and in general the 
light atoms are not flattened out. As John Helliwell pointed out, you may look 
at series termination effects. However, since your map does not appear to be of 
extremely high resolution, I guess all useful data will have been collected and 
included.

The other thing to look at is occupancy. If your ligand is bound at partial 
occupancy, the iodides will still have very strong density, but the lighter 
atoms may fall below the 1 sigma threshold. You can test this by refining a 
group occupancy for your ligand and also by scrolling down the contour level in 
coot to see if some density appears at lower contour levels. 

Good luck!
Herman 

-Ursprüngliche Nachricht-
Von: CCP4 bulletin board  Im Auftrag von Vito Calderone
Gesendet: Mittwoch, 10. Juni 2020 10:34
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms density

EXTERNAL : Real sender is  owner-ccp...@jiscmail.ac.uk   



Dear Pierre,
 I was in particular talking of 2FoFc refinement maps.
In the attached picture for example you can see the 2FoFc map contoured at 1 
sigma level of an I3C molecule bound to a protein where for I3C the only 
visible density is that of iodines whereas the density of the other atoms of 
the ligand is insignificant.
Best regards

Vito

-Messaggio originale-
Da: CCP4 bulletin board  Per conto di LEGRAND Pierre
Inviato: mercoledì 10 giugno 2020 09:31
A: CCP4BB@JISCMAIL.AC.UK
Oggetto: Re: [ccp4bb] Heavy atom vs light atoms density

Dear Vito,
Could you precise in what kind of maps are you experiencing these effects:
2FoFc refinement maps or experimental phasing ?
I had this kind of effects long ago in experiemental phasing due to Fourier 
transform ripple effects. This could be due to scaling problems, low resolution 
truncation or incompletness (maybe intensity overloads).
Another source condition could be local X-ray dose degradation due to the high 
absoption of the metals.
Best regards,
Pierre Legrand
PROXIMA-1, SOLEIL

De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Vito Calderone 
[calder...@cerm.unifi.it] Envoyé : mercredi 10 juin 2020 08:42 À :
CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Heavy atom vs light atoms density

Dear All,
   many of us have probably experienced that, in the diffraction of 
protein ligands containing heavy atoms (cisPt, I3C, etc), the overwhelming 
electron density of the metal can totally flatten that of the light atoms 
around (or rather make it look insignificant).
Is anyone aware of an article/review (to use as a reference) in which this is 
clearly stated/pointed out?
Best regards

Vito Calderone





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[ccp4bb] R: [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms density

2020-06-10 Thread Vito Calderone 
Dear John,

   I would say that in that case the FoFc is basically flat.

 

Vito

 

Da: CCP4 bulletin board  Per conto di John R Helliwell
Inviato: mercoledì 10 giugno 2020 10:40
A: CCP4BB@JISCMAIL.AC.UK
Oggetto: Re: [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms density

 

Dear Vito,

The I3C isn't like the platins as a challenge to the 2Fo-Fc map.

It maybe is more akin to the situation we described here:-

https://onlinelibrary.wiley.com/doi/abs/10.1107/S0907444903004219

ie what does your Fo-Fc map, with three iodines placed, at the correct 
occupancy, look like? 

Best wishes,

John 

Emeritus Professor John R Helliwell DSc

 

 





On 10 Jun 2020, at 09:34, Vito Calderone mailto:calder...@cerm.unifi.it> > wrote:

Dear Pierre,
I was in particular talking of 2FoFc refinement maps.
In the attached picture for example you can see the 2FoFc map contoured at 1
sigma level of an I3C molecule bound to a protein where for I3C the only
visible density is that of iodines whereas the density of the other atoms of
the ligand is insignificant.
Best regards

Vito

-Messaggio originale-
Da: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> > 
Per conto di LEGRAND Pierre
Inviato: mercoledì 10 giugno 2020 09:31
A: CCP4BB@JISCMAIL.AC.UK  
Oggetto: Re: [ccp4bb] Heavy atom vs light atoms density

Dear Vito,
Could you precise in what kind of maps are you experiencing these effects:
2FoFc refinement maps or experimental phasing ?
I had this kind of effects long ago in experiemental phasing due to Fourier
transform ripple effects. This could be due to scaling problems, low
resolution truncation or incompletness (maybe intensity overloads).
Another source condition could be local X-ray dose degradation due to the
high absoption of the metals.
Best regards,
Pierre Legrand
PROXIMA-1, SOLEIL

De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Vito
Calderone [calder...@cerm.unifi.it] Envoyé : mercredi 10 juin 2020 08:42 À :
CCP4BB@JISCMAIL.AC.UK   Objet : [ccp4bb] Heavy 
atom vs light atoms density

Dear All,
  many of us have probably experienced that, in the diffraction
of protein ligands containing heavy atoms (cisPt, I3C, etc), the
overwhelming electron density of the metal can totally flatten that of the
light atoms around (or rather make it look insignificant).
Is anyone aware of an article/review (to use as a reference) in which this
is clearly stated/pointed out?
Best regards

Vito Calderone





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Re: [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms density

2020-06-10 Thread John R Helliwell 
Dear Vito,
The I3C isn't like the platins as a challenge to the 2Fo-Fc map.
It maybe is more akin to the situation we described here:-
https://onlinelibrary.wiley.com/doi/abs/10.1107/S0907444903004219
ie what does your Fo-Fc map, with three iodines placed, at the correct 
occupancy, look like? 
Best wishes,
John 

Emeritus Professor John R Helliwell DSc



> On 10 Jun 2020, at 09:34, Vito Calderone  wrote:
> 
> Dear Pierre,
> I was in particular talking of 2FoFc refinement maps.
> In the attached picture for example you can see the 2FoFc map contoured at 1
> sigma level of an I3C molecule bound to a protein where for I3C the only
> visible density is that of iodines whereas the density of the other atoms of
> the ligand is insignificant.
> Best regards
> 
> Vito
> 
> -Messaggio originale-
> Da: CCP4 bulletin board  Per conto di LEGRAND Pierre
> Inviato: mercoledì 10 giugno 2020 09:31
> A: CCP4BB@JISCMAIL.AC.UK
> Oggetto: Re: [ccp4bb] Heavy atom vs light atoms density
> 
> Dear Vito,
> Could you precise in what kind of maps are you experiencing these effects:
> 2FoFc refinement maps or experimental phasing ?
> I had this kind of effects long ago in experiemental phasing due to Fourier
> transform ripple effects. This could be due to scaling problems, low
> resolution truncation or incompletness (maybe intensity overloads).
> Another source condition could be local X-ray dose degradation due to the
> high absoption of the metals.
> Best regards,
> Pierre Legrand
> PROXIMA-1, SOLEIL
> 
> De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Vito
> Calderone [calder...@cerm.unifi.it] Envoyé : mercredi 10 juin 2020 08:42 À :
> CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Heavy atom vs light atoms density
> 
> Dear All,
>   many of us have probably experienced that, in the diffraction
> of protein ligands containing heavy atoms (cisPt, I3C, etc), the
> overwhelming electron density of the metal can totally flatten that of the
> light atoms around (or rather make it look insignificant).
> Is anyone aware of an article/review (to use as a reference) in which this
> is clearly stated/pointed out?
> Best regards
> 
> Vito Calderone
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
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> 
> 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
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> 
> 
> 
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Re: [ccp4bb] Heavy atom vs light atoms density

2020-06-10 Thread John R Helliwell 
Dear Vito,
We accumulated quite a good deal of knowledge of this type of complex, firstly 
the platins, then later, led by Dr Alice Brink, rhenium complexes with 
proteins. This review describes some of this:-  
https://pubs.rsc.org/en/content/articlelanding/2017/mt/c7mt00219j#!divAbstract 
The flattening of electron density that you refer to was not an issue but does 
become a problem though with uranyl hydrides (not involving proteins to my 
knowledge), solved by using neutrons, work led by the late Prof Bob Bau. 
Exchange of the ligands in the often quite complex biochemical mix of a protein 
crystal can be more challenging to decipher however. Chlorine versus ammine in 
platins can be distinguished with high enough resolution data but confounded at 
lower resolution. Sharing of raw diffraction data has proved very informative 
and by sharing all of our raw data in the platins new improved details have 
been squeezed out, with Prof Kay Diederichs leading us and also through Dr Ivan 
Shabalin and colleagues‘ helpful and expert work, in a very broad study, we 
learnt more about our platins and stimulated us in yet more detailed analyses 
with Dr Loes Kroon-Batenburg and Dr Toine Schreurs in Utrecht.
It is all a most interesting topic especially given the wide medicinal roles of 
these heavy metals which “must bind somewhere in us”, and not only used as 
tools for solving our phase problem!
Best wishes,
John
Emeritus Professor John R Helliwell DSc




> On 10 Jun 2020, at 07:42, Vito Calderone  wrote:
> 
> 
> Dear All,
>many of us have probably experienced that, in the diffraction 
> of protein ligands containing heavy atoms (cisPt, I3C, etc), the overwhelming 
> electron density of the metal can totally flatten that of the light atoms 
> around (or rather make it look insignificant).
> Is anyone aware of an article/review (to use as a reference) in which this is 
> clearly stated/pointed out?
> Best regards
>  
> Vito Calderone
>  
>  
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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Re: [ccp4bb] Heavy atom vs light atoms density

2020-06-10 Thread LEGRAND Pierre 
Dear Vito,
Could you precise in what kind of maps are you experiencing these effects: 
2FoFc refinement maps or experimental phasing ?
I had this kind of effects long ago in experiemental phasing due to Fourier 
transform ripple effects. This could be due to scaling problems, low resolution 
truncation or incompletness (maybe intensity overloads).
Another source condition could be local X-ray dose degradation due to the high 
absoption of the metals.
Best regards,
Pierre Legrand
PROXIMA-1, SOLEIL

De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Vito Calderone 
[calder...@cerm.unifi.it]
Envoyé : mercredi 10 juin 2020 08:42
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Heavy atom vs light atoms density

Dear All,
   many of us have probably experienced that, in the diffraction of 
protein ligands containing heavy atoms (cisPt, I3C, etc), the overwhelming 
electron density of the metal can totally flatten that of the light atoms 
around (or rather make it look insignificant).
Is anyone aware of an article/review (to use as a reference) in which this is 
clearly stated/pointed out?
Best regards

Vito Calderone





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[ccp4bb] Heavy atom vs light atoms density

2020-06-10 Thread Vito Calderone 
Dear All,

   many of us have probably experienced that, in the diffraction
of protein ligands containing heavy atoms (cisPt, I3C, etc), the
overwhelming electron density of the metal can totally flatten that of the
light atoms around (or rather make it look insignificant).

Is anyone aware of an article/review (to use as a reference) in which this
is clearly stated/pointed out? 

Best regards

 

Vito Calderone

 

 




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