Re: [ccp4bb] A question of density

2020-03-09 Thread James Holton 
tion where I know it is real. Having a feeling of how much you
 have to contour the diff density at that point can give you a good
 feeling how much of noise is actually in your density right in
 between the waters..?

 best, matthias


 Dr. Matthias Barone

 AG Kuehne, Rational Drug Design

 Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
 Robert-Rössle-Strasse 10
 13125 Berlin

 Germany
 Phone: +49 (0)30 94793-284

 
 *From:* CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Jessica Besaw
 mailto:jbesaw1...@gmail.com>>
 *Sent:* Wednesday, March 4, 2020 6:42:34 PM
 *To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
 *Subject:* Re: [ccp4bb] A question of density
  
 Hey Nukri,


 Here are the details: Rwork/Rfree = 0.21 / 0.23 for a 2 Angstrom
 structure

 I absolutely agree with you on the refinement. I did previously do
 that, and I attached the picture.

 What is the BB?

 Cheers!

 Jessica






 On Wed, 4 Mar 2020 at 12:20, Nukri Sanishvili mailto:sannu...@gmail.com>> wrote:

 Hi Jessica,
 You do not say how well is the rest of the structure refined.
 First, you should refine the structure best you can, without
 placing anything in the unclear blob of your interest so to
 obtain the best possible phases and hopefully improve the blob
 density as well.
 Then you should let the BB see what that density looks like.
 Looking at only the list of possibilities has very little value
 without seeing the density itself.
 Best wishes,
 Nukri

 On Wed, Mar 4, 2020 at 11:10 AM Jessica Besaw
 mailto:jbesaw1...@gmail.com>> wrote:

 Hello friends,

 I have a "blob" of density in an active site of my protein.

 I am struggling to determine if I should place a water in
 this spot, if I should model it as a disordered water, if
 the density may be a ligand that I have not considered, or
 if it should be left as unaccounted for density. I would
 like to publish this structure without compromising the science.

 I have attached several possibilities that I have considered
 below.

 Any suggestions would be appreciated.

 Cheers!

 Jessica Besaw



 


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Re: [ccp4bb] A question of density

2020-03-05 Thread Bernhard Rupp 
A few figures in BMC re truncation effects:

 

http://www.ruppweb.org/Garland/gallery/Ch9/pages/Biomolecular_Crystallography_Fig_9-05_PART1.htm

http://www.ruppweb.org/Garland/gallery/Ch9/pages/Biomolecular_Crystallography_Fig_9-05_PART2.htm

http://www.ruppweb.org/Garland/gallery/Ch10/pages/Biomolecular_Crystallography_Fig_10-10.htm

 

Best, BR

 

From: CCP4 bulletin board  On Behalf Of 
0c2488af9525-dmarc-requ...@jiscmail.ac.uk
Sent: Thursday, March 5, 2020 12:21
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] A question of density

 

Hello, not sure if anyone has mentioned series termination errors in the 
vicinity of electron dense atoms. The attached is from Glusker & Trueblood and 
might be of interest.

Jon Cooper

 

On 5 Mar 2020 19:00, Jessica Besaw mailto:jbesaw1...@gmail.com> > wrote:

Hello Matthias,

 

Excellent point. Most of the the ordered water are easily visible at 2 rmsd. 
The central disordered (or partially occupied) water becomes visible only at 
1.3 - 1.4 rmsd, and it is very visible at 1 rmsd (which I have displayed all of 
the maps). In your opinion, do you think this would be noise? 

 

Jessica

 

On Wed, 4 Mar 2020 at 12:45, Barone, Matthias mailto:bar...@fmp-berlin.de> > wrote:

hey Jessica

a tip that might come up later on anyway: once you put every reasonable bit 
into the desity, what I like to to when facing such blobbs: I take a well 
defined water out to create a diff density at a position where I know it is 
real. Having a feeling of how much you have to contour the diff density at that 
point can give you a good feeling how much of noise is actually in your density 
right in between the waters..?

best, matthias

 

Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284

  _  

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> on behalf of Jessica Besaw mailto:jbesaw1...@gmail.com> >
Sent: Wednesday, March 4, 2020 6:42:34 PM
To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> 
Subject: Re: [ccp4bb] A question of density 

 

Hey Nukri, 

 

Here are the details: Rwork/Rfree = 0.21 / 0.23 for a 2 Angstrom structure

 

I absolutely agree with you on the refinement. I did previously do that, and I 
attached the picture. 

 

What is the BB?

 

Cheers!

 

Jessica 

 

 

 

 

 

 

On Wed, 4 Mar 2020 at 12:20, Nukri Sanishvili mailto:sannu...@gmail.com> > wrote:

Hi Jessica,

You do not say how well is the rest of the structure refined. 

First, you should refine the structure best you can, without placing anything 
in the unclear blob of your interest so to obtain the best possible phases and 
hopefully improve the blob density as well.

Then you should let the BB see what that density looks like. Looking at only 
the list of possibilities has very little value without seeing the density 
itself.

Best wishes,

Nukri

 

On Wed, Mar 4, 2020 at 11:10 AM Jessica Besaw mailto:jbesaw1...@gmail.com> > wrote:

Hello friends,  

 

I have a "blob" of density in an active site of my protein. 

 

I am struggling to determine if I should place a water in this spot, if I 
should model it as a disordered water, if the density may be a ligand that I 
have not considered, or if it should be left as unaccounted for density. I 
would like to publish this structure without compromising the science.

 

I have attached several possibilities that I have considered below. 

 

Any suggestions would be appreciated.

 

Cheers!

 

Jessica Besaw

 

 

 

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Re: [ccp4bb] A question of density

2020-03-05 Thread Dale Tronrud 
On 3/5/2020 11:00 AM, Jessica Besaw wrote:
> Hello Matthias,
> 
> Excellent point. Most of the the ordered water are easily visible at 2
> rmsd. The central disordered (or partially occupied) water becomes
> visible only at 1.3 - 1.4 rmsd, and it is very visible at 1 rmsd (which
> I have displayed all of the maps). In your opinion, do you think this
> would be noise? 

   "Noise" is a word that I hate.  Usually it is just a label we put on
something that we want an excuse to ignore.  If you decide to ignore
something you should be honest and have a specific reason.

   Personally, I think it is sufficient reason to not place an atom when
you are unsure if an atom should be placed.  With the density you have
shown, it is hard to imagine a consistent model that contains a
partially occupied water molecule in this little peak.  That "water
molecule" would be inconsistent with full occupancy of the atom to the
left, but that atom already has the lowest B factor when refined at full
occupancy.  These two atoms are too close together to both be present in
the same unit cell.

   Without a reasonable atomic model in mind, you can't build a
reasonable model.  Building a model is not simply the task of placing
atoms in peaks.  The resulting structure has to make physical sense.
What hydrogen bonding network are you proposing to exist when this rare
conformation is present?

   If you don't have confidence in a model, don't build it.  You will be
left with this little difference map peak, and you will take a tiny hit
on your R values.  Them's the breaks!  Putting in an atom you don't
believe would give you those slightly smaller R values, but is that
honest?   It seems to me that building a model that doesn't make
chemical sense just to lower R values borders on deception.

   Whether that makes this peak "noise" is irrelevant.  Maybe in five or
ten years someone will come up with a new tool for building overlapping,
partially occupied, water networks and this peak will be explained.
Would that change if this peak is "noise" or not?  All we have now is a
peak that we don't have a good way to interpret.

Dale Tronrud


> 
> Jessica
> 
> On Wed, 4 Mar 2020 at 12:45, Barone, Matthias  <mailto:bar...@fmp-berlin.de>> wrote:
> 
> hey Jessica
> 
> a tip that might come up later on anyway: once you put every
> reasonable bit into the desity, what I like to to when facing such
> blobbs: I take a well defined water out to create a diff density at
> a position where I know it is real. Having a feeling of how much you
> have to contour the diff density at that point can give you a good
> feeling how much of noise is actually in your density right in
> between the waters..?
> 
> best, matthias
> 
> 
> Dr. Matthias Barone
> 
> AG Kuehne, Rational Drug Design
> 
> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> Robert-Rössle-Strasse 10
> 13125 Berlin
> 
> Germany
> Phone: +49 (0)30 94793-284
> 
> 
> *From:* CCP4 bulletin board  <mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Jessica Besaw
> mailto:jbesaw1...@gmail.com>>
> *Sent:* Wednesday, March 4, 2020 6:42:34 PM
> *To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
> *Subject:* Re: [ccp4bb] A question of density
>  
> Hey Nukri,
> 
> Here are the details: Rwork/Rfree = 0.21 / 0.23 for a 2 Angstrom
> structure
> 
> I absolutely agree with you on the refinement. I did previously do
> that, and I attached the picture. 
> 
> What is the BB?
> 
> Cheers!
> 
> Jessica 
> 
> 
> 
> 
> 
> 
> On Wed, 4 Mar 2020 at 12:20, Nukri Sanishvili  <mailto:sannu...@gmail.com>> wrote:
> 
> Hi Jessica,
> You do not say how well is the rest of the structure refined.
> First, you should refine the structure best you can, without
> placing anything in the unclear blob of your interest so to
> obtain the best possible phases and hopefully improve the blob
> density as well.
> Then you should let the BB see what that density looks like.
> Looking at only the list of possibilities has very little value
> without seeing the density itself.
> Best wishes,
> Nukri
> 
> On Wed, Mar 4, 2020 at 11:10 AM Jessica Besaw
> mailto:jbesaw1...@gmail.com>> wrote:
> 
> Hello friends, 
> 
> I have a "blob" of density in an active site of my protein. 
> 
> I am struggling to determ

Re: [ccp4bb] A question of density

2020-03-05 Thread Dale Tronrud 
   Series termination is a problem when you leave out Fourier
coefficients that have significant amplitude.  Back in the old days when
we cut data aggressively it was something to worry about.  Now that most
everyone integrates down to very weak intensities it shouldn't be much
of a problem.

   Besides, as Glusker and Tureblood noted, a peak in a difference map
(the green blob in this discussion) cannot be caused by series
termination.  If there is series termination the shape of a difference
map peak can be affected, but not the presence of the peak itself.

Dale Tronrud

On 3/5/2020 12:20 PM, 0c2488af9525-dmarc-requ...@jiscmail.ac.uk wrote:
> Hello, not sure if anyone has mentioned series termination errors in the
> vicinity of electron dense atoms. The attached is from Glusker &
> Trueblood and might be of interest.
> 
> Jon Cooper
> 
> On 5 Mar 2020 19:00, Jessica Besaw  wrote:
> 
> Hello Matthias,
> 
> Excellent point. Most of the the ordered water are easily visible at
> 2 rmsd. The central disordered (or partially occupied) water becomes
> visible only at 1.3 - 1.4 rmsd, and it is very visible at 1 rmsd
> (which I have displayed all of the maps). In your opinion, do you
> think this would be noise? 
> 
> Jessica
> 
> On Wed, 4 Mar 2020 at 12:45, Barone, Matthias  <mailto:bar...@fmp-berlin.de>> wrote:
> 
> hey Jessica
> 
> a tip that might come up later on anyway: once you put every
> reasonable bit into the desity, what I like to to when facing
> such blobbs: I take a well defined water out to create a diff
> density at a position where I know it is real. Having a feeling
> of how much you have to contour the diff density at that point
> can give you a good feeling how much of noise is actually in
> your density right in between the waters..?
> 
> best, matthias
> 
> 
> Dr. Matthias Barone
> 
> AG Kuehne, Rational Drug Design
> 
> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> Robert-Rössle-Strasse 10
> 13125 Berlin
> 
> Germany
> Phone: +49 (0)30 94793-284
> 
> 
> 
> *From:* CCP4 bulletin board  <mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Jessica Besaw
> mailto:jbesaw1...@gmail.com>>
> *Sent:* Wednesday, March 4, 2020 6:42:34 PM
> *To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
> *Subject:* Re: [ccp4bb] A question of density
>  
> Hey Nukri,
> 
> Here are the details: Rwork/Rfree = 0.21 / 0.23 for a 2 Angstrom
> structure
> 
> I absolutely agree with you on the refinement. I did previously
> do that, and I attached the picture. 
> 
> What is the BB?
> 
> Cheers!
> 
> Jessica 
> 
> 
> 
> 
> 
> 
> On Wed, 4 Mar 2020 at 12:20, Nukri Sanishvili
> mailto:sannu...@gmail.com>> wrote:
> 
> Hi Jessica,
> You do not say how well is the rest of the structure refined.
> First, you should refine the structure best you can, without
> placing anything in the unclear blob of your interest so to
> obtain the best possible phases and hopefully improve the
> blob density as well.
> Then you should let the BB see what that density looks like.
> Looking at only the list of possibilities has very little
> value without seeing the density itself.
> Best wishes,
> Nukri
> 
> On Wed, Mar 4, 2020 at 11:10 AM Jessica Besaw
> mailto:jbesaw1...@gmail.com>> wrote:
> 
> Hello friends, 
> 
> I have a "blob" of density in an active site of my protein. 
> 
> I am struggling to determine if I should place a water
> in this spot, if I should model it as a disordered
> water, if the density may be a ligand that I have not
> considered, or if it should be left as unaccounted for
> density. I would like to publish this structure without
> compromising the science.
> 
> I have attached several possibilities that I have
> considered below. 
> 
> Any suggestions would be appreciated.
> 
> Cheers!
> 
> Jessica Besaw
> 
> 
> 
> 
>

Re: [ccp4bb] A question of density

2020-03-05 Thread Jessica Besaw 
Hello Matthias,

Excellent point. Most of the the ordered water are easily visible at 2
rmsd. The central disordered (or partially occupied) water becomes visible
only at 1.3 - 1.4 rmsd, and it is very visible at 1 rmsd (which I have
displayed all of the maps). In your opinion, do you think this would be
noise?

Jessica

On Wed, 4 Mar 2020 at 12:45, Barone, Matthias  wrote:

> hey Jessica
>
> a tip that might come up later on anyway: once you put every reasonable
> bit into the desity, what I like to to when facing such blobbs: I take a
> well defined water out to create a diff density at a position where I know
> it is real. Having a feeling of how much you have to contour the diff
> density at that point can give you a good feeling how much of noise is
> actually in your density right in between the waters..?
>
> best, matthias
>
>
> Dr. Matthias Barone
>
> AG Kuehne, Rational Drug Design
>
> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> Robert-Rössle-Strasse 10
> 13125 Berlin
>
> Germany
> Phone: +49 (0)30 94793-284
> --
> *From:* CCP4 bulletin board  on behalf of Jessica
> Besaw 
> *Sent:* Wednesday, March 4, 2020 6:42:34 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] A question of density
>
> Hey Nukri,
>
> Here are the details: Rwork/Rfree = 0.21 / 0.23 for a 2 Angstrom structure
>
> I absolutely agree with you on the refinement. I did previously do that,
> and I attached the picture.
>
> What is the BB?
>
> Cheers!
>
> Jessica
>
>
>
>
>
>
> On Wed, 4 Mar 2020 at 12:20, Nukri Sanishvili  wrote:
>
>> Hi Jessica,
>> You do not say how well is the rest of the structure refined.
>> First, you should refine the structure best you can, without placing
>> anything in the unclear blob of your interest so to obtain the best
>> possible phases and hopefully improve the blob density as well.
>> Then you should let the BB see what that density looks like. Looking at
>> only the list of possibilities has very little value without seeing the
>> density itself.
>> Best wishes,
>> Nukri
>>
>> On Wed, Mar 4, 2020 at 11:10 AM Jessica Besaw 
>> wrote:
>>
>>> Hello friends,
>>>
>>> I have a "blob" of density in an active site of my protein.
>>>
>>> I am struggling to determine if I should place a water in this spot, if
>>> I should model it as a disordered water, if the density may be a ligand
>>> that I have not considered, or if it should be left as unaccounted for
>>> density. I would like to publish this structure without compromising the
>>> science.
>>>
>>> I have attached several possibilities that I have considered below.
>>>
>>> Any suggestions would be appreciated.
>>>
>>> Cheers!
>>>
>>> Jessica Besaw
>>>
>>>
>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>>
>>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>



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Re: [ccp4bb] A question of density

2020-03-04 Thread James Holton 
Looks to me like those two waters are just close enough to push the bulk 
solvent mask out of that region. Have you tried optimizing your bulk 
solvent parameters? (keyword "solvent optimize" in refmac; 
"optimize_mask=True" in phenix).


Also, try exporting your bulk solvent mask (MSKOUT in refmac; use 
phenix.fmodel with "solvent_radius" and "shrink truncation radius" taken 
from phenix.refine log), and looking to see where it begins and ends.


-James Holton
MAD Scientist

On 3/4/2020 6:04 PM, Jessica Besaw wrote:

Hello friends,

I have a "blob" of density in an active site of my protein.

I am struggling to determine if I should place a water in this spot, 
if I should model it as a disordered water, if the density may be a 
ligand that I have not considered, or if it should be left as 
unaccounted for density. I would like to publish this structure 
without compromising the science.


I have attached several possibilities that I have considered below.

Any suggestions would be appreciated.

Cheers!

Jessica Besaw





To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] A question of density

2020-03-04 Thread mesters 

Hello Jessica,

options to test (in order to judge what is going on in the active site):

1) Take all the water/ion molecules out of the pocket and refine the 
rest of the structure as good as you can (without overfitting 
everything) and calculate a sigma A-weighed *3Fo-2Fc* map. Since you 
already refined the atoms, there may be some memory effect (if you do 
not use the correct/older mtz file), so shake all coordinates/B-factors 
a bit before starting the refinement (reset B-factors to 30 and/or 
slightly shift the atom coordinates randomly).

2) Consider to use an alternative refinement program (may save the day).
3) Since you have built a model, you can calculate maps on an absolute 
scale (i.e. electrons/Å3) - the absence of an atom should result in a 
peak of a particular height, but will not be consistent when viewed in 
sigma’s.
4) Calculate a "polder" map and/or AK (averaged kicked) map instead of 
the classical maps that have there shortcomings.
5) Finally, could be you are facing a partial occupation or alternative 
position of a water molecule that will never materialize... You could 
spend weeks for little to no progress. In this case, it is better to not 
refine anything in that position and write down all your efforts in the 
manuscript…..


Cheers,
Jeroen


Am 04.03.20 um 19:04 schrieb Jessica Besaw:


Hey Roger,

I believe the Chloride spot is a negatively changed anion because it 
has more density that water and it is close to an arginine. Does this 
chloride binding coordination look reasonable?


All of the other water are coordinated to two other side-chains, and 
do not depend on the partially occupied water


Cheers!

Jessica



On Wed, 4 Mar 2020 at 12:27, Roger Rowlett > wrote:


In addition, one should carefully consider the chemistry and
coordination geometry around the putative chloride ion. Not only
do candidates have to be consistent with the observed omit
density, but they must also make chemical interaction and geometry
sense. I suspect a partial occupancy water may make the most sense
from the limited data provided, but only if all the other placed
solvent molecules have clearly defined interactions that do not
depend solely on the partially occupied water. What does the
chloride coordination geometry look like? Is it clearly a chloride
ion and not a cation?

Roger Rowlett
Gordon & Dorothy Kline Professor, Emeritus
Colgate University

On Wed, Mar 4, 2020, 12:20 PM Nukri Sanishvili mailto:sannu...@gmail.com>> wrote:

Hi Jessica,
You do not say how well is the rest of the structure refined.
First, you should refine the structure best you can, without
placing anything in the unclear blob of your interest so to
obtain the best possible phases and hopefully improve the blob
density as well.
Then you should let the BB see what that density looks like.
Looking at only the list of possibilities has very little
value without seeing the density itself.
Best wishes,
Nukri

On Wed, Mar 4, 2020 at 11:10 AM Jessica Besaw
mailto:jbesaw1...@gmail.com>> wrote:

Hello friends,

I have a "blob" of density in an active site of my protein.

I am struggling to determine if I should place a water in
this spot, if I should model it as a disordered water, if
the density may be a ligand that I have not considered, or
if it should be left as unaccounted for density. I would
like to publish this structure without compromising the
science.

I have attached several possibilities that I have
considered below.

Any suggestions would be appreciated.

Cheers!

Jessica Besaw






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--
*Dr.math. et dis. nat.Jeroen R. Mesters*
Deputy, Lecturer, Program Coordinator /Infection Biology
/ 
Visiting 
Professorship (South Bohemian Univ

Re: [ccp4bb] A question of density

2020-03-04 Thread Roger Rowlett 
Chloride coordination spheres are typically tetrahedral (CN=4) or square
pyramidal (CN=5), and occasionally octahedral (CN=6). Arg and His and well
as amide nitrogens are common protein ligands, and it is possible but not
common to see carboxylates in the coordination sphere.

Roger Rowlett

On Wed, Mar 4, 2020, 1:05 PM Jessica Besaw  wrote:

>
> Hey Roger,
>
> I believe the Chloride spot is a negatively changed anion because it has
> more density that water and it is close to an arginine. Does this chloride
> binding coordination look reasonable?
>
> All of the other water are coordinated to two other side-chains, and do
> not depend on the partially occupied water
>
> Cheers!
>
> Jessica
>
>
>
> On Wed, 4 Mar 2020 at 12:27, Roger Rowlett  wrote:
>
>> In addition, one should carefully consider the chemistry and coordination
>> geometry around the putative chloride ion. Not only do candidates have to
>> be consistent with the observed omit density, but they must also make
>> chemical interaction and geometry sense. I suspect a partial occupancy
>> water may make the most sense from the limited data provided, but only if
>> all the other placed solvent molecules have clearly defined interactions
>> that do not depend solely on the partially occupied water. What does the
>> chloride coordination geometry look like? Is it clearly a chloride ion and
>> not a cation?
>>
>> Roger Rowlett
>> Gordon & Dorothy Kline Professor, Emeritus
>> Colgate University
>>
>> On Wed, Mar 4, 2020, 12:20 PM Nukri Sanishvili 
>> wrote:
>>
>>> Hi Jessica,
>>> You do not say how well is the rest of the structure refined.
>>> First, you should refine the structure best you can, without placing
>>> anything in the unclear blob of your interest so to obtain the best
>>> possible phases and hopefully improve the blob density as well.
>>> Then you should let the BB see what that density looks like. Looking at
>>> only the list of possibilities has very little value without seeing the
>>> density itself.
>>> Best wishes,
>>> Nukri
>>>
>>> On Wed, Mar 4, 2020 at 11:10 AM Jessica Besaw 
>>> wrote:
>>>
 Hello friends,

 I have a "blob" of density in an active site of my protein.

 I am struggling to determine if I should place a water in this spot, if
 I should model it as a disordered water, if the density may be a ligand
 that I have not considered, or if it should be left as unaccounted for
 density. I would like to publish this structure without compromising the
 science.

 I have attached several possibilities that I have considered below.

 Any suggestions would be appreciated.

 Cheers!

 Jessica Besaw



 --

 To unsubscribe from the CCP4BB list, click the following link:
 https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>
>



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Re: [ccp4bb] A question of density

2020-03-04 Thread Barone, Matthias 
hey Jessica

a tip that might come up later on anyway: once you put every reasonable bit 
into the desity, what I like to to when facing such blobbs: I take a well 
defined water out to create a diff density at a position where I know it is 
real. Having a feeling of how much you have to contour the diff density at that 
point can give you a good feeling how much of noise is actually in your density 
right in between the waters..?

best, matthias


Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284


From: CCP4 bulletin board  on behalf of Jessica Besaw 

Sent: Wednesday, March 4, 2020 6:42:34 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] A question of density

Hey Nukri,

Here are the details: Rwork/Rfree = 0.21 / 0.23 for a 2 Angstrom structure

I absolutely agree with you on the refinement. I did previously do that, and I 
attached the picture.

What is the BB?

Cheers!

Jessica






On Wed, 4 Mar 2020 at 12:20, Nukri Sanishvili 
mailto:sannu...@gmail.com>> wrote:
Hi Jessica,
You do not say how well is the rest of the structure refined.
First, you should refine the structure best you can, without placing anything 
in the unclear blob of your interest so to obtain the best possible phases and 
hopefully improve the blob density as well.
Then you should let the BB see what that density looks like. Looking at only 
the list of possibilities has very little value without seeing the density 
itself.
Best wishes,
Nukri

On Wed, Mar 4, 2020 at 11:10 AM Jessica Besaw 
mailto:jbesaw1...@gmail.com>> wrote:
Hello friends,

I have a "blob" of density in an active site of my protein.

I am struggling to determine if I should place a water in this spot, if I 
should model it as a disordered water, if the density may be a ligand that I 
have not considered, or if it should be left as unaccounted for density. I 
would like to publish this structure without compromising the science.

I have attached several possibilities that I have considered below.

Any suggestions would be appreciated.

Cheers!

Jessica Besaw





To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1



To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] A question of density

2020-03-04 Thread Roger Rowlett 
In addition, one should carefully consider the chemistry and coordination
geometry around the putative chloride ion. Not only do candidates have to
be consistent with the observed omit density, but they must also make
chemical interaction and geometry sense. I suspect a partial occupancy
water may make the most sense from the limited data provided, but only if
all the other placed solvent molecules have clearly defined interactions
that do not depend solely on the partially occupied water. What does the
chloride coordination geometry look like? Is it clearly a chloride ion and
not a cation?

Roger Rowlett
Gordon & Dorothy Kline Professor, Emeritus
Colgate University

On Wed, Mar 4, 2020, 12:20 PM Nukri Sanishvili  wrote:

> Hi Jessica,
> You do not say how well is the rest of the structure refined.
> First, you should refine the structure best you can, without placing
> anything in the unclear blob of your interest so to obtain the best
> possible phases and hopefully improve the blob density as well.
> Then you should let the BB see what that density looks like. Looking at
> only the list of possibilities has very little value without seeing the
> density itself.
> Best wishes,
> Nukri
>
> On Wed, Mar 4, 2020 at 11:10 AM Jessica Besaw 
> wrote:
>
>> Hello friends,
>>
>> I have a "blob" of density in an active site of my protein.
>>
>> I am struggling to determine if I should place a water in this spot, if I
>> should model it as a disordered water, if the density may be a ligand that
>> I have not considered, or if it should be left as unaccounted for density.
>> I would like to publish this structure without compromising the science.
>>
>> I have attached several possibilities that I have considered below.
>>
>> Any suggestions would be appreciated.
>>
>> Cheers!
>>
>> Jessica Besaw
>>
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] A question of density

2020-03-04 Thread Nukri Sanishvili 
Hi Jessica,
You do not say how well is the rest of the structure refined.
First, you should refine the structure best you can, without placing
anything in the unclear blob of your interest so to obtain the best
possible phases and hopefully improve the blob density as well.
Then you should let the BB see what that density looks like. Looking at
only the list of possibilities has very little value without seeing the
density itself.
Best wishes,
Nukri

On Wed, Mar 4, 2020 at 11:10 AM Jessica Besaw  wrote:

> Hello friends,
>
> I have a "blob" of density in an active site of my protein.
>
> I am struggling to determine if I should place a water in this spot, if I
> should model it as a disordered water, if the density may be a ligand that
> I have not considered, or if it should be left as unaccounted for density.
> I would like to publish this structure without compromising the science.
>
> I have attached several possibilities that I have considered below.
>
> Any suggestions would be appreciated.
>
> Cheers!
>
> Jessica Besaw
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>



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