Re: [ccp4bb] Strange Pseudosymmetry Effects

[Tim Gruene]

Dear Eddie, dear all

According to ftp://ftp.ccp4.ac.uk/ccp4/newsletter/jun_95/, this article
appeare in Newsletter June 95. It is mentioned in the table of contents,
"Correction on perfection: primary extinction correction in protein
crystallography" by Polykarpov and Sawyer.
Unfortunately, the article itself is not there

Extinction is not the same as the dynamic effects that James mentioned,
but this seems the closest match.

Would anyone have a copy they can share with me?

Thanks a lot!

Best,

Tim 

On Thu, 28 May 2020 15:43:00 +
Edward Snell  wrote:

> This jogged my memory of a CCP4 newsletter article many years ago
> covering kinematical versus dynamic scattering in protein crystals
> and offering a correction that could be used. I think it was Lindsay
> Sawyer and Igor Polikarpov in the late 90’s. I apologize if I have
> the authors wrong but I thought it was a commentary well ahead of its
> time and with modern sources and low noise detectors, I am wondering
> if anyone has revisited this? Protein crystals are remarkably high
> quality until you cryocool them. Serial methods combined with
> instrument capabilities may rate a revisit to the use of the
> kinematical approximation versus application of dynamical theories?
> Certainly the computational power is available.
> 
> Just my 2 cents for the day.
> 
> Best,
> 
> Eddie
> 
> 
> Edward Snell Ph.D.
> 
> Director of the NSF BioXFEL Science and Technology Center
> President and CEO Hauptman-Woodward Medical Research Institute
> BioInnovations Chaired Professorship, University at Buffalo, SUNY
> 700 Ellicott Street, Buffalo, NY 14203-1102
> hwi.buffalo.edu
> Phone:   (716) 898 8631 Fax: (716) 898 8660
> Skype:eddie.snell Email:
> esn...@hwi.buffalo.edu Webpage:
> https://hwi.buffalo.edu/scientist-directory/snell/ [hwilogo]
> Heisenberg was probably here!
> 
> 
> 
> From: CCP4 bulletin board  On Behalf Of James
> Holton Sent: Thursday, May 28, 2020 11:34 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Strange Pseudosymmetry Effects
> 
> Be careful with electron diffraction and apparent absence violations.
> It is possible these weak spots are simply due to multiple
> scattering.  If so, you would see them relatively stronger with
> larger crystals,but much weaker relative to the strong reflections
> when the crystal is smaller. Do you?
> 
> -James Holton
> MAD Scientist
> On 5/27/2020 6:49 PM, Jessica Bruhn wrote:
> Hello,
> 
> I am wondering if pseudosymmetry can cause weak reflections that
> mimic the doubling of one unit cell axis' length. Has anyone seen
> something like this before?
> 
>  I am processing data from a small molecule sample collected with
> electron diffraction from multiple crystals. For the b axis, it is
> not clear if the length should be 10A or 20A. There are spots with
> the correct spacing for b=20A, but every other spot seems weaker than
> the spots along k if I choose b=10A (this extends beyond (0,k,0)). I
> am unable to phase the b=20 data. I have solved this structure in P1
> with b=10 and found four molecules in the ASU and in P212121 with
> b=10 resulting in one molecule in the ASU. In P1, three of the four
> molecules adopt the same conformation, but the fourth molecule is in
> an alternate conformation that causes only ~1/2 of the molecule to be
> consistent with the first three. In P212121 I see density for part of
> this alternative conformation, but the full molecule in this
> alternate conformation cannot pack properly in P212121. Based on
> these results and some orthogonal data, I think I should refine the
> solution in P1 with b=10. Does it seem reasonable that pseudosymmetry
> is causing these weak reflections along k hinting at a doubling of
> the b axis?
> 
> Thanks in advance!
> 
> Best,
> Jessica
> 
> --
> Jessica Bruhn, Ph.D
> Principal Scientist
> NanoImaging Services, Inc.
> 4940 Carroll Canyon Road, Suite 115
> San Diego, CA 92121
> Phone #: (888) 675-8261
> www.nanoimagingservices.com
> 
> 
> 
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-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG 

Re: [ccp4bb] visual mask editor - why

[Bernhard Rupp]

Yes I have already pilfered useful parts of it in the scripts.

Thx, BR

 

From: Boaz Shaanan  
Sent: Thursday, May 28, 2020 11:59
To: b...@hofkristallamt.org
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] visual mask editor - why

 

Hi Bernhard,

Did you consider trying 'polder' in the phenix package? 

Boaz

Boaz Shaanan, Ph.D.
Department of Life Sciences
Ben Gurion University of the Negev
Beer Sheva
Israel

 

On May 28, 2020 21:17, Bernhard Rupp mailto:hofkristall...@gmail.com> > wrote:

Maybe I should explain an example: Say coot detects an unmodelled blob
(maybe a ligand). Now, I would like to do

a number of things without biasing towards a model. Like comparing these map
regions, excluding

intrusion of a solvent mask, etc.

 

Now could coot for example just generate a mask around what it already knows
are blobs?  

Possible useful items could be a solvent mask not including that regions, or
a density map

that includes only features with a certain boundary around that blob.

 

I pilfered some kludges together from different sources, but let's just say
inelegant would be a compliment.

 

Best, BR



Brief question: Does something like a visual density mask editor exist?

Thx, BR

--

Bernhard Rupp

http://www.hofkristallamt.org/

b...@hofkristallamt.org  

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 

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Re: [ccp4bb] visual mask editor - why

[Boaz Shaanan]

Hi Bernhard,
Did you consider trying 'polder' in the phenix package?
Boaz

Boaz Shaanan, Ph.D.
Department of Life Sciences
Ben Gurion University of the Negev
Beer Sheva
Israel



On May 28, 2020 21:17, Bernhard Rupp  wrote:




Maybe I should explain an example: Say coot detects an unmodelled blob (maybe a ligand). Now, I would like to do
a number of things without biasing towards a model. Like comparing these map regions, excluding
intrusion of a solvent mask, etc.
 
Now could coot for example just generate a mask around what it already knows are blobs?  
Possible useful items could be a solvent mask not including that regions, or a density map
that includes only features with a certain boundary around that blob.
 
I pilfered some kludges together from different sources, but let’s just say inelegant would be a compliment.
 
Best, BR

Brief question: Does something like a visual density mask editor exist?
Thx, BR
--
Bernhard Rupp
http://www.hofkristallamt.org/
b...@hofkristallamt.org
+1 925 209 7429
+43 676 571 0536
--
Many plausible ideas vanish 
at the presence of thought
--
 



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Re: [ccp4bb] visual mask editor - why

[Bernhard Rupp]

Looks like the density manipulation/carving tools might be useful.

Thx, BR

 

From: CCP4 bulletin board  On Behalf Of Jurgen Bosch
Sent: Thursday, May 28, 2020 11:29
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] visual mask editor - why

 

Give this a shot: https://www.eyesopen.com/afitt

 

At least in Vida from the same suite of programs, you can select such a blob as 
you describe and export it in a useful way.

Jürgen 

___

Jürgen Bosch, Ph.D.

Division of Pediatric Pulmonology and Allergy/Immunology
Case Western Reserve University

2109 Adelbert Rd, BRB 835

Cleveland, OH 44106

Phone: 216.368.7565

Fax: 216.368.4223

https://www.linkedin.com/in/jubosch/





CEO & Co-Founder at InterRayBio, LLC

 

Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology





On May 28, 2020, at 2:17 PM, Bernhard Rupp mailto:hofkristall...@gmail.com> > wrote:

 

Maybe I should explain an example: Say coot detects an unmodelled blob (maybe a 
ligand). Now, I would like to do

a number of things without biasing towards a model. Like comparing these map 
regions, excluding

intrusion of a solvent mask, etc.

 

Now could coot for example just generate a mask around what it already knows 
are blobs?  

Possible useful items could be a solvent mask not including that regions, or a 
density map

that includes only features with a certain boundary around that blob.

 

I pilfered some kludges together from different sources, but let’s just say 
inelegant would be a compliment.

 

Best, BR



Brief question: Does something like a visual density mask editor exist?

Thx, BR

--

Bernhard Rupp

  http://www.hofkristallamt.org/

  b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 

  _  

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] visual mask editor - why

[Jurgen Bosch]

Give this a shot: https://www.eyesopen.com/afitt 


At least in Vida from the same suite of programs, you can select such a blob as 
you describe and export it in a useful way.
Jürgen 
___
Jürgen Bosch, Ph.D.
Division of Pediatric Pulmonology and Allergy/Immunology
Case Western Reserve University
2109 Adelbert Rd, BRB 835
Cleveland, OH 44106
Phone: 216.368.7565
Fax: 216.368.4223
https://www.linkedin.com/in/jubosch/

CEO & Co-Founder at InterRayBio, LLC

Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology

> On May 28, 2020, at 2:17 PM, Bernhard Rupp  wrote:
> 
> Maybe I should explain an example: Say coot detects an unmodelled blob (maybe 
> a ligand). Now, I would like to do
> a number of things without biasing towards a model. Like comparing these map 
> regions, excluding
> intrusion of a solvent mask, etc.
>  
> Now could coot for example just generate a mask around what it already knows 
> are blobs?  
> Possible useful items could be a solvent mask not including that regions, or 
> a density map
> that includes only features with a certain boundary around that blob.
>  
> I pilfered some kludges together from different sources, but let’s just say 
> inelegant would be a compliment.
>  
> Best, BR
> 
> Brief question: Does something like a visual density mask editor exist?
> Thx, BR
> --
> Bernhard Rupp
> http://www.hofkristallamt.org/ 
> b...@hofkristallamt.org 
> +1 925 209 7429
> +43 676 571 0536
> --
> Many plausible ideas vanish 
> at the presence of thought
> --
>  
> 
> 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] visual mask editor?

[Jurgen Bosch]

Sehr geehrter Herr Hofkristallamt,

Depending on your learning style, you might want to look into blender.
https://www.blender.org/download/ 
Together with eMPV you can do some magic from scratch. 

You could also use any other CAD program end export the file one of the Uppsala 
Software Suite programs can read and convert them into masks.

Jürgen 


___
Jürgen Bosch, Ph.D.
Division of Pediatric Pulmonology and Allergy/Immunology
Case Western Reserve University
2109 Adelbert Rd, BRB 835
Cleveland, OH 44106
Phone: 216.368.7565
Fax: 216.368.4223
https://www.linkedin.com/in/jubosch/

CEO & Co-Founder at InterRayBio, LLC

Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology

> On May 28, 2020, at 1:57 PM, Bernhard Rupp  wrote:
> 
> Yes, there are some ways to do it, more or less cumbersome.
> But after being already reprimanded for using old ccp4 stuff I was looking 
> for a 21st century solution…sort of matrix-style…put you shades on, wave your 
> hands, and done.
>  
> Cheers, BR
> From: CCP4 bulletin board  On Behalf Of Soisson, 
> Stephen M
> Sent: Thursday, May 28, 2020 09:57
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] visual mask editor?
>  
> You used to be able to do this in O (dating myself)
>  
> From: CCP4 bulletin board  > On Behalf Of Bernhard Rupp
> Sent: Thursday, May 28, 2020 12:39 PM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: [ccp4bb] visual mask editor?
>  
> EXTERNAL EMAIL – Use caution with any links or file attachments.
> Brief question: Does something like a visual density mask editor exist?
> Thx, BR
> --
> Bernhard Rupp
> http://www.hofkristallamt.org/ 
> b...@hofkristallamt.org 
> +1 925 209 7429
> +43 676 571 0536
> --
> Many plausible ideas vanish 
> at the presence of thought
> --
>  
>  
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 
> 
> Notice:  This e-mail message, together with any attachments, contains
> information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, 
> New Jersey, USA 07033), and/or its affiliates Direct contact information
> for affiliates is available at 
> http://www.merck.com/contact/contacts.html 
> ) that may be confidential,
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[ccp4bb] visual mask editor - why

[Bernhard Rupp]

Maybe I should explain an example: Say coot detects an unmodelled blob
(maybe a ligand). Now, I would like to do

a number of things without biasing towards a model. Like comparing these map
regions, excluding

intrusion of a solvent mask, etc.

 

Now could coot for example just generate a mask around what it already knows
are blobs?  

Possible useful items could be a solvent mask not including that regions, or
a density map

that includes only features with a certain boundary around that blob.

 

I pilfered some kludges together from different sources, but let's just say
inelegant would be a compliment.

 

Best, BR



Brief question: Does something like a visual density mask editor exist?

Thx, BR

--

Bernhard Rupp

http://www.hofkristallamt.org/

b...@hofkristallamt.org  

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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Re: [ccp4bb] visual mask editor?

[Bernhard Rupp]

Yes, there are some ways to do it, more or less cumbersome.

But after being already reprimanded for using old ccp4 stuff I was looking for 
a 21st century solution…sort of matrix-style…put you shades on, wave your 
hands, and done.

 

Cheers, BR

From: CCP4 bulletin board  On Behalf Of Soisson, Stephen 
M
Sent: Thursday, May 28, 2020 09:57
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] visual mask editor?

 

You used to be able to do this in O (dating myself)

 

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> On Behalf Of Bernhard Rupp
Sent: Thursday, May 28, 2020 12:39 PM
To: CCP4BB@JISCMAIL.AC.UK  
Subject: [ccp4bb] visual mask editor?

 

EXTERNAL EMAIL – Use caution with any links or file attachments.

Brief question: Does something like a visual density mask editor exist?

Thx, BR

--

Bernhard Rupp

http://www.hofkristallamt.org/

b...@hofkristallamt.org  

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 

  _  

To unsubscribe from the CCP4BB list, click the following link:
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Notice:  This e-mail message, together with any attachments, contains
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Re: [ccp4bb] visual mask editor?

[Reza Khayat]

?You can generate maps using UCSF Chimera then convert these to binary masks. 
This means you can drag PDB around to generate a mask where ever you like.


Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031

From: CCP4 bulletin board  on behalf of Soisson, Stephen 
M <338a268c4763-dmarc-requ...@jiscmail.ac.uk>
Sent: Thursday, May 28, 2020 12:57 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] visual mask editor?

You used to be able to do this in O (dating myself)

From: CCP4 bulletin board  On Behalf Of Bernhard Rupp
Sent: Thursday, May 28, 2020 12:39 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] visual mask editor?

EXTERNAL EMAIL - Use caution with any links or file attachments.
Brief question: Does something like a visual density mask editor exist?
Thx, BR
--
Bernhard Rupp
http://www.hofkristallamt.org/
b...@hofkristallamt.org
+1 925 209 7429
+43 676 571 0536
--
Many plausible ideas vanish
at the presence of thought
--




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Re: [ccp4bb] visual mask editor?

[Soisson, Stephen M]

You used to be able to do this in O (dating myself)

From: CCP4 bulletin board  On Behalf Of Bernhard Rupp
Sent: Thursday, May 28, 2020 12:39 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] visual mask editor?

EXTERNAL EMAIL – Use caution with any links or file attachments.
Brief question: Does something like a visual density mask editor exist?
Thx, BR
--
Bernhard Rupp
http://www.hofkristallamt.org/
b...@hofkristallamt.org
+1 925 209 7429
+43 676 571 0536
--
Many plausible ideas vanish
at the presence of thought
--




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[ccp4bb] visual mask editor?

[Bernhard Rupp]

Brief question: Does something like a visual density mask editor exist?

Thx, BR

--

Bernhard Rupp

  http://www.hofkristallamt.org/

  b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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Re: [ccp4bb] Strange Pseudosymmetry Effects

[Edward Snell]

This jogged my memory of a CCP4 newsletter article many years ago covering 
kinematical versus dynamic scattering in protein crystals and offering a 
correction that could be used. I think it was Lindsay Sawyer and Igor 
Polikarpov in the late 90’s. I apologize if I have the authors wrong but I 
thought it was a commentary well ahead of its time and with modern sources and 
low noise detectors, I am wondering if anyone has revisited this? Protein 
crystals are remarkably high quality until you cryocool them. Serial methods 
combined with instrument capabilities may rate a revisit to the use of the 
kinematical approximation versus application of dynamical theories? Certainly 
the computational power is available.

Just my 2 cents for the day.

Best,

Eddie


Edward Snell Ph.D.

Director of the NSF BioXFEL Science and Technology Center
President and CEO Hauptman-Woodward Medical Research Institute
BioInnovations Chaired Professorship, University at Buffalo, SUNY
700 Ellicott Street, Buffalo, NY 14203-1102
hwi.buffalo.edu
Phone:   (716) 898 8631 Fax: (716) 898 8660
Skype:eddie.snell Email: 
esn...@hwi.buffalo.edu
Webpage: https://hwi.buffalo.edu/scientist-directory/snell/
[hwilogo]
Heisenberg was probably here!



From: CCP4 bulletin board  On Behalf Of James Holton
Sent: Thursday, May 28, 2020 11:34 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Strange Pseudosymmetry Effects

Be careful with electron diffraction and apparent absence violations. It is 
possible these weak spots are simply due to multiple scattering.  If so, you 
would see them relatively stronger with larger crystals,but much weaker 
relative to the strong reflections when the crystal is smaller. Do you?

-James Holton
MAD Scientist
On 5/27/2020 6:49 PM, Jessica Bruhn wrote:
Hello,

I am wondering if pseudosymmetry can cause weak reflections that mimic the 
doubling of one unit cell axis' length. Has anyone seen something like this 
before?

 I am processing data from a small molecule sample collected with electron 
diffraction from multiple crystals. For the b axis, it is not clear if the 
length should be 10A or 20A. There are spots with the correct spacing for 
b=20A, but every other spot seems weaker than the spots along k if I choose 
b=10A (this extends beyond (0,k,0)). I am unable to phase the b=20 data. I have 
solved this structure in P1 with b=10 and found four molecules in the ASU and 
in P212121 with b=10 resulting in one molecule in the ASU. In P1, three of the 
four molecules adopt the same conformation, but the fourth molecule is in an 
alternate conformation that causes only ~1/2 of the molecule to be consistent 
with the first three. In P212121 I see density for part of this alternative 
conformation, but the full molecule in this alternate conformation cannot pack 
properly in P212121. Based on these results and some orthogonal data, I think I 
should refine the solution in P1 with b=10. Does it seem reasonable that 
pseudosymmetry is causing these weak reflections along k hinting at a doubling 
of the b axis?

Thanks in advance!

Best,
Jessica

--
Jessica Bruhn, Ph.D
Principal Scientist
NanoImaging Services, Inc.
4940 Carroll Canyon Road, Suite 115
San Diego, CA 92121
Phone #: (888) 675-8261
www.nanoimagingservices.com



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Re: [ccp4bb] Refmac and hydrogens -developers

[James Holton]

The first thing you want to do when debugging hydrogens in refmac5 is to 
make sure it outputs whatever it was doing:

MAKE HOUT Y

This is not the default.  Normally, refmac will take a PDB file without 
any hydrogens in it, quietly add them before doing refinement, and then 
delete them before outputting the final coordinates.  Why so secretive?  
Probably because someone complained about having to look at all that 
fuzzy hydrogen nonsense in the graphics.  In fact, I know some 
crystallographers who refuse to believe that the element hydrogen even 
exists. Never seen it. Including them in refinement has even been called 
"too many parameters". Nowadays, of course, we know having hydrogens 
involved in the geometry is a good thing.  This is especially true at 
poor resolution.


The other important hydrogen keyword to know is:
MAKE HYDR A

This is the default.  "A" means add all hydrogens, regardless of what is 
in the input pdb file.  Normally, these get deleted before output, so 
you don't notice it.  The other choices are:
MAKE HYDR N: which is basically "do not do the hydrogen thing".  Any 
hydrogens in the input file will be ignored, and they will also not be 
in the output file (even if you use MAKE HOUT Y), because they were 
never there.
MAKE HYDR Y : this is the one that will use the hydrogens listed in the 
pdb file.  Here there lies a danger!  Not every program names hydrogens 
the same way, so some might be quietly ignored.  The only way to know if 
they were is to use MAKE HOUT Y.


So, if you want to define and use your own hydrogens through many rounds 
of refmac, you want to use:

MAKE HYDR Y
MAKE HOUT Y

But, if your starting PDB has no hydrogens in it you want your first 
round to have:

MAKE HYDR A
MAKE HOUT Y

If you inspect the occupancies of the output hydrogens you may find that 
some are zero, and every once ina while one is somewhere between 1 and 
0.  I have not seen documentation for this, but it appears that refmac 
might be quietly doing some sort of occupancy refinement on hydrogens 
that may or may not be there.  Titratable ones for example.  The 
philisophy explained to me once by Garib is that since it is twice as 
bad to put in an electron that isn't there vs leaving out one that is 
you want to err on the side of dropping hydrogens that don't seem to fit.


HTH,

-James Holton
MAD Scientist


On 5/20/2020 7:07 PM, Bernhard Rupp wrote:


Hi Fellows,

for an experiment, I am running 0.9 A data with unrestrained Refmac 
(yes I know should/could use SHELXL, but let’s drop that for now).


When I select ‘ignore even if present in file’ in a PDB that has 
hydrogens, I get the identical results than with ’use if present’ or 
‘generate all’.


The log informs me that the instructions were properly issued, the 
output PDB does not have Hs, but Rs and map are exactly the same


as with selection of if present or generate all H. Does not seem to 
make sense.


If I cull the hydrogens from the input PDB and ‘use if present’ or 
‘ignore’, the stats and map are different and no H in output as 
requested -  all as expected.


Maybe that can be reproduced and, if it is not a feature, fixed.

Best, BR

--

Bernhard Rupp

http://www.hofkristallamt.org/

b...@hofkristallamt.org 

+1 925 209 7429

+43 676 571 0536

--

Real knowledge is to know

the extent of one's ignorance

--




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Re: [ccp4bb] Strange Pseudosymmetry Effects

[James Holton]

Be careful with electron diffraction and apparent absence violations. It 
is possible these weak spots are simply due to multiple scattering.  If 
so, you would see them relatively stronger with larger crystals,but much 
weaker relative to the strong reflections when the crystal is smaller. 
Do you?


-James Holton
MAD Scientist

On 5/27/2020 6:49 PM, Jessica Bruhn wrote:

Hello,

I am wondering if pseudosymmetry can cause weak reflections that mimic 
the doubling of one unit cell axis' length. Has anyone seen something 
like this before?


 I am processing data from a small molecule sample collected with 
electron diffraction from multiple crystals. For the b axis, it is not 
clear if the length should be 10A or 20A. There are spots 
with the correct spacing for b=20A, but every other spot seems weaker 
than the spots along k if I choose b=10A (this extends beyond 
(0,k,0)). I am unable to phase the b=20 data. I have solved this 
structure in P1 with b=10 and found four molecules in the ASU and in 
P212121 with b=10 resulting in one molecule in the ASU. In P1, three 
of the four molecules adopt the same conformation, but the fourth 
molecule is in an alternate conformation that causes only ~1/2 of the 
molecule to be consistent with the first three. In P212121 I see 
density for part of this alternative conformation, but the full 
molecule in this alternate conformation cannot pack properly in 
P212121. Based on these results and some orthogonal data, I think I 
should refine the solution in P1 with b=10. Does it seem reasonable 
that pseudosymmetry is causing these weak reflections along k hinting 
at a doubling of the b axis?


Thanks in advance!

Best,
Jessica

--
Jessica Bruhn, Ph.D
Principal Scientist
NanoImaging Services, Inc.
4940 Carroll Canyon Road, Suite 115
San Diego, CA 92121
Phone #: (888) 675-8261
www.nanoimagingservices.com 



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