Re: [ccp4bb] Strange Pseudosymmetry Effects

2020-05-29 Thread John R Helliwell
Hello Eddie,
I believe this article from Robert Huber and coauthors was the first to
discuss dynamical effects in a protein crystal:-
Acta Cryst. <https://journals.iucr.org/b> (1980). B*36*
<https://journals.iucr.org/b/contents/backissues.html>, 621-627
Greetings,
John

On Thu, May 28, 2020 at 4:44 PM 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/
>
> [image: 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
>
>
> --
>
> 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
>


-- 
Professor John R Helliwell DSc



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

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 
https://www.jiscmail.ac.uk/policyandsecurity/


Re: [ccp4bb] Strange Pseudosymmetry Effects

2020-05-29 Thread Harry Powell - CCP4BB
Hi Tim

You could send out an SOS to some of the other authors in the same issue, who 
might have kept a copy - several are “regular" posters on this forum, e.g.  

Sacha Urzhumtsev
Gerard Kleywegt
Eleanor Dodson

There’s a good chance they’ll be stuck at home at the moment with plenty of 
time to search through old boxes…

Harry

> On 28 May 2020, at 21:04, Tim Gruene  wrote:
> 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 



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

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 
https://www.jiscmail.ac.uk/policyandsecurity/


Re: [ccp4bb] Strange Pseudosymmetry Effects

2020-05-28 Thread 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<http://hwi.buffalo.edu/>
> Phone:   (716) 898 8631 Fax: (716) 898 8660
> Skype:eddie.snell Email:
> esn...@hwi.buffalo.edu<mailto: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<http://www.nanoimagingservices.com>
> 
> 
> 
> 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

Re: [ccp4bb] Strange Pseudosymmetry Effects

2020-05-28 Thread 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<http://hwi.buffalo.edu/>
Phone:   (716) 898 8631 Fax: (716) 898 8660
Skype:eddie.snell Email: 
esn...@hwi.buffalo.edu<mailto: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<http://www.nanoimagingservices.com>



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

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 
https://www.jiscmail.ac.uk/policyandsecurity/


Re: [ccp4bb] Strange Pseudosymmetry Effects

2020-05-28 Thread 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 



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

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 
https://www.jiscmail.ac.uk/policyandsecurity/


Re: [ccp4bb] Strange Pseudosymmetry Effects

2020-05-27 Thread Eleanor Dodson
Yes - in P1 if you have two molecules approximately related by
X y z. And x+ 1/2 y z say then the spots along the axis a* will have h=2n
weak.  And the sections with h even will have very weak spots. If you
calculate a Patterson for the data there will be a strong peak st 1/2, 0,0.
  But you say you can find a reasonable solution in p21 21 21? Have you
tried symmetry p21 with the 2fd axis along a* or c*?   Also it is possible
if you have multiple crystals the merging has combined crystals with
similar symmetry - is your 2 fold axes- but not exact. Look at the data
analysis to see if some crystals agree better than others.

On Thu, 28 May 2020 at 03:49, Ethan A Merritt  wrote:

> On Wednesday, 27 May 2020 18:49:23 PDT 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?
>
> Yes.
>
> >  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?
>
> This description makes me think also of a supercell.  This can happen
> when, say, the position of one copy N is not compatible with all (N-1) of
> the others positions.  Some unit cells contain (N-1) copies but not the
> problematic N; other cells contain the N copy but miss one or more of
> the others to make room.  This gives you a stochastic mix of cell
> contents.  If it were truly random you'd see spots for a small cell
> but the contents would have to be described by partially occupied sites.
> But if there is a bias towards alternation of cells +N -N +N -N you
> get a pseudo-doubling of that cell edge, matching your description.
>
> Suggested reading:
> Lovelace J, Petrícek V, Murshudov G, Borgstahl GEO.
> Supercell refinement: a cautionary tale. Acta Crystallogr D Struct Biol.
> 2019 Sep 1;75(Pt 9):852-860.
> doi: 10.1107/S2059798319011082. Epub 2019 Aug 28. PMID: 31478908; PMCID:
> PMC6719663.
>
> I've had to deal with these in macromolecular crystals.
> I would imagine that the same can happen for electron diffraction
> but I can't point to any prior examples in the literature.
>
> good luck!
>
> Ethan
>
> > Thanks in advance!
> >
> > Best,
> > Jessica
> >
> >
>
>
> --
> Ethan A Merritt
> Biomolecular Structure Center,  K-428 Health Sciences Bldg
> MS 357742,   University of Washington, Seattle 98195-7742
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
> 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 https://www.jiscmail.ac.uk/policyandsecurity/
>



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

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 
https://www.jiscmail.ac.uk/policyandsecurity/


Re: [ccp4bb] Strange Pseudosymmetry Effects

2020-05-27 Thread Ethan A Merritt
On Wednesday, 27 May 2020 18:49:23 PDT 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?

Yes.

>  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?

This description makes me think also of a supercell.  This can happen
when, say, the position of one copy N is not compatible with all (N-1) of
the others positions.  Some unit cells contain (N-1) copies but not the
problematic N; other cells contain the N copy but miss one or more of
the others to make room.  This gives you a stochastic mix of cell
contents.  If it were truly random you'd see spots for a small cell
but the contents would have to be described by partially occupied sites.
But if there is a bias towards alternation of cells +N -N +N -N you
get a pseudo-doubling of that cell edge, matching your description.

Suggested reading:
Lovelace J, Petrícek V, Murshudov G, Borgstahl GEO.
Supercell refinement: a cautionary tale. Acta Crystallogr D Struct Biol. 2019 
Sep 1;75(Pt 9):852-860. 
doi: 10.1107/S2059798319011082. Epub 2019 Aug 28. PMID: 31478908; PMCID: 
PMC6719663.

I've had to deal with these in macromolecular crystals.
I would imagine that the same can happen for electron diffraction
but I can't point to any prior examples in the literature.

good luck!

Ethan

> Thanks in advance!
> 
> Best,
> Jessica
> 
> 


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



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

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 
https://www.jiscmail.ac.uk/policyandsecurity/


Re: [ccp4bb] Strange Pseudosymmetry Effects

2020-05-27 Thread Petrus Zwart
Hi Jessica,

If you see spots and they fit a lattice, you should use them.  Use the b=10
solution in P1 that you have with 3 models (or two if one is iffy) and use
that as a start model for MR in b=20 and start searching for the rest.
Alternatively, use the b=10 model with stuff that looks decent and generate
a model for b=20 by adding in the lattice translations. This can be tricky,
especially when you are not in P1, so perhaps try the first option first.

Pseudo translational symmetry will do this to you btw:
https://journals.iucr.org/d/issues/2008/01/00/ba5111/ba5111.pdf , section
3.4.2

Regards
Peter


On Wed, May 27, 2020 at 7:00 PM Jessica Bruhn <
450e5de75376-dmarc-requ...@jiscmail.ac.uk> 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
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>


-- 

P.H. Zwart
Staff Scientist
Molecular Biophysics and Integrated Bioimaging &
Center for Advanced Mathematics for Energy Research Applications
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246

PHENIX:   http://www.phenix-online.org
CAMERA: http://camera.lbl.gov/
-



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

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 
https://www.jiscmail.ac.uk/policyandsecurity/


[ccp4bb] Strange Pseudosymmetry Effects

2020-05-27 Thread Jessica Bruhn
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



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

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 
https://www.jiscmail.ac.uk/policyandsecurity/