Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac

[Peter Keller]

On Wed, 2015-05-20 at 16:09 -0600, James Stroud wrote:

> With that said, if you want to work behind a full-featured word
> processor and have access to the wonders of TeX typesetting,
> LibreOffice (OpenOffice) + TexMaths is the best for the author during
> preparation of a manuscript. At this point it is bug free (to my
> experience), embeds vector equations (SVG) or raster (PNG), is
> editable, and looks spectacular both when editing and when
> publishing/printing.

... as long as you don't use docx files: there are a lot of reported
docx-related problems (bugs and regressions) with LibreOffice. This URL
will show 500 of them:



There are many more docx-related issues on this bug tracker which have
been marked as fixed so a simple search like the above won't reveal
them, however they may not be fixed in the version of LibreOffice that
you happen to be using.

> The downside is that you have to collaborate with people you can’t
> force into using the best software. 

This brings us back to the original question, in which collaboration was
a factor. If you are able to use odt format for the containing document,
LibreOffice is fine and James' suggestion is a good one. It is probably
OK with doc format too, for most purposes. However, if you are
collaborating with people who are not able or willing to avoid the use
of docx format, using LibreOffice can be risky.

Regards,
Peter.

-- 
Peter Keller Tel.: +44 (0)1223 353033
Global Phasing Ltd., Fax.: +44 (0)1223 366889
Sheraton House,
Castle Park,
Cambridge CB3 0AX
United Kingdom

Re: [ccp4bb] SUMMARY: Equation Editor woes with Office 2011 for Mac

[Harry Powell]

hi

I haven't been following all the thread, so apologies if someone else has 
already mentioned this as a way round the original problem.

having had problems with equations "disappearing" in a variety of WP & 
presentation software over the years, I've taken to creating them in my program 
of choice, zooming in (using the tools available in whatever program I happen 
to be using), "grabbing" the on-screen image and save it in my graphics format 
of choice (at the moment I'm using PNG).

WFM...

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge, CB2 0QH
Chairman of International Union of Crystallography Commission on 
Crystallographic Computing
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 

> On 21 May 2015, at 03:12, Mooers, Blaine H.M. (HSC)  
> wrote:
> 
> I have had good experiences with MathJak for html. It too gives beautiful 
> renderings on webpages of equations 
> encoded in LaTeX. It is very easy to use. It grew out of jsMath.
> 
> http://www.mathjax.org/
> 
> Best regards,
> 
> Blaine Mooers
> 
> 
> 
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of William G. 
> Scott [wgsc...@ucsc.edu]
> Sent: Wednesday, May 20, 2015 7:32 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] SUMMARY: Equation Editor woes with Office 2011 for Mac
> 
>> On May 20, 2015, at 5:38 AM, Randy Read  wrote:
>> 
>> Thanks, as always, to everyone for a thoughtful discussion!
> 
> 
> Alternatively, as a scientific community, perhaps it is finally time for us 
> to untwist Clippy, bending him backwards and forwards until he snaps at those 
> horrid beady little eyeballs, ditch the Comic Sans, flip Redmond the bird, 
> HTFU and learn to use LaTeX equation markup, and ask that our journals do the 
> same.  It really isn’t any harder than learning basic HTML (and predates it 
> as one of the original mark-up languages). Journals and funding agencies 
> should not be demanding that we use crappy broken and restrictive proprietary 
> formats for submitting papers and proposals.
> 
> Ascii text documents provide the ultimate form of universal 
> interchangeability.
> 
> The syntax is actually quite straightforward and easy to learn (or look up), 
> eg:
> 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__en.wikibooks.org_wiki_LaTeX_Mathematics&d=AwIF-g&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=U-vNRZjPhftiaADvIzN7HNUo5rnv5-JKR6RwZjW0UDQ&s=Q3biyCgXkL73q4eLw0MovreIp6p923PLHLrEp3AiuBg&e=
> 
> LaTeX allows you to focus on content rather than document formatting.  
> Although it is definitely more badass to do this in vim, other ascii text 
> editors often have very useful LaTeX functionality.  (My favorite on OS X is 
> TextMate, version 2 of which is now free. If you code on OS X, you should 
> take a look at this.)
> 
> Once you make the small investment of time learning LaTeX, it makes other 
> tasks easier.  For example, you can use jsMath to embed LaTeX-encoded 
> equations (including chemistry symbols) in web pages, eg:
> 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.math.union.edu_-7Edpvc_jsmath_examples_welcome.html&d=AwIF-g&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=U-vNRZjPhftiaADvIzN7HNUo5rnv5-JKR6RwZjW0UDQ&s=UAkZG7nG6yJ1m41HFCqn3Ah_ifo-u-S4N8VwWbtbi3o&e=

Re: [ccp4bb] SUMMARY: Equation Editor woes with Office 2011 for Mac

[Harry Powell]

oh... I should have said that once saved, I can then insert the image where I 
want in my doc(x).

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge, CB2 0QH
Chairman of International Union of Crystallography Commission on 
Crystallographic Computing
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 

> On 21 May 2015, at 11:51, Harry Powell  wrote:
> 
> hi
> 
> I haven't been following all the thread, so apologies if someone else has 
> already mentioned this as a way round the original problem.
> 
> having had problems with equations "disappearing" in a variety of WP & 
> presentation software over the years, I've taken to creating them in my 
> program of choice, zooming in (using the tools available in whatever program 
> I happen to be using), "grabbing" the on-screen image and save it in my 
> graphics format of choice (at the moment I'm using PNG).
> 
> WFM...
> 
> Harry
> --
> Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
> Cambridge Biomedical Campus, Cambridge, CB2 0QH
> Chairman of International Union of Crystallography Commission on 
> Crystallographic Computing
> Chairman of European Crystallographic Association SIG9 (Crystallographic 
> Computing) 
> 
>> On 21 May 2015, at 03:12, Mooers, Blaine H.M. (HSC) 
>>  wrote:
>> 
>> I have had good experiences with MathJak for html. It too gives beautiful 
>> renderings on webpages of equations 
>> encoded in LaTeX. It is very easy to use. It grew out of jsMath.
>> 
>> http://www.mathjax.org/
>> 
>> Best regards,
>> 
>> Blaine Mooers
>> 
>> 
>> 
>> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of William G. 
>> Scott [wgsc...@ucsc.edu]
>> Sent: Wednesday, May 20, 2015 7:32 PM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] SUMMARY: Equation Editor woes with Office 2011 for Mac
>> 
>>> On May 20, 2015, at 5:38 AM, Randy Read  wrote:
>>> 
>>> Thanks, as always, to everyone for a thoughtful discussion!
>> 
>> 
>> Alternatively, as a scientific community, perhaps it is finally time for us 
>> to untwist Clippy, bending him backwards and forwards until he snaps at 
>> those horrid beady little eyeballs, ditch the Comic Sans, flip Redmond the 
>> bird, HTFU and learn to use LaTeX equation markup, and ask that our journals 
>> do the same.  It really isn’t any harder than learning basic HTML (and 
>> predates it as one of the original mark-up languages). Journals and funding 
>> agencies should not be demanding that we use crappy broken and restrictive 
>> proprietary formats for submitting papers and proposals.
>> 
>> Ascii text documents provide the ultimate form of universal 
>> interchangeability.
>> 
>> The syntax is actually quite straightforward and easy to learn (or look up), 
>> eg:
>> 
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__en.wikibooks.org_wiki_LaTeX_Mathematics&d=AwIF-g&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=U-vNRZjPhftiaADvIzN7HNUo5rnv5-JKR6RwZjW0UDQ&s=Q3biyCgXkL73q4eLw0MovreIp6p923PLHLrEp3AiuBg&e=
>> 
>> LaTeX allows you to focus on content rather than document formatting.  
>> Although it is definitely more badass to do this in vim, other ascii text 
>> editors often have very useful LaTeX functionality.  (My favorite on OS X is 
>> TextMate, version 2 of which is now free. If you code on OS X, you should 
>> take a look at this.)
>> 
>> Once you make the small investment of time learning LaTeX, it makes other 
>> tasks easier.  For example, you can use jsMath to embed LaTeX-encoded 
>> equations (including chemistry symbols) in web pages, eg:
>> 
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.math.union.edu_-7Edpvc_jsmath_examples_welcome.html&d=AwIF-g&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=U-vNRZjPhftiaADvIzN7HNUo5rnv5-JKR6RwZjW0UDQ&s=UAkZG7nG6yJ1m41HFCqn3Ah_ifo-u-S4N8VwWbtbi3o&e=

[ccp4bb] CCP4-6.5 Update 010

[Charles Ballard]

Dear CCP4 Users

An update for the CCP4-6.5 series has just been released, consisting
of the following changes

 * refmac5 (all platforms)
 - various bug fixes and new program header2matr

 * prosmart (all)
 - fixed issue with degenerate PDB files

* pointless (all)
 - 1.9.31, allow real-space reindex operators

* aimless (all)
 - 0.5.9 make ABSORPTION  work. Bug fix in RESTORE with TILES

* ctruncate (all)
 - fix for output column names issue

 * blend (all)
 - 0.6.7, Fixed a bug responsible for the deletion of any file whose name 
includes "reference"

 * 'libg  (all)
 - dps for stacking planes of DNA/RNA

 * examples  (all)
 - corrections python.exam, pyrogen.exam and gere.seq

 * documentation (all) 
 - update aimless and pointless documentation

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team

Re: [ccp4bb] SUMMARY: Equation Editor woes with Office 2011 for Mac

[SIMON WESTRIP]

Perhaps one answer to the problem of using images might be to embed
the source LaTeX (or MathML, TeX, ...) in the image so that anyone with the 
appropriate tool

could then extract the source and edit the 'image' etc. 

Obviously this requires someone to provide the tools, but it coukd
free us of the restrictions imposed by word processors etc (images can be used 
anywhere...)

Just a thought...

Simon

S. P. Westrip
Developer for IUCr Journals


From: Harry Powell 
To: CCP4BB@JISCMAIL.AC.UK 
Sent: Thursday, 21 May 2015, 11:53
Subject: Re: [ccp4bb] SUMMARY: Equation Editor woes with Office 2011 for Mac



oh... I should have said that once saved, I can then insert the image where I 
want in my doc(x).


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge, CB2 0QH
Chairman of International Union of Crystallography Commission on 
Crystallographic Computing
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 



On 21 May 2015, at 11:51, Harry Powell  wrote:


hi

I haven't been following all the thread, so apologies if someone else has 
already mentioned this as a way round the original problem.

having had problems with equations "disappearing" in a variety of WP & 
presentation software over the years, I've taken to creating them in my program 
of choice, zooming in (using the tools available in whatever program I happen 
to be using), "grabbing" the on-screen image and save it in my graphics format 
of choice (at the moment I'm using PNG).

WFM...


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge, CB2 0QH
Chairman of International Union of Crystallography Commission on 
Crystallographic Computing
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 

On 21 May 2015, at 03:12, Mooers, Blaine H.M. (HSC)  
wrote:


I have had good experiences with MathJak for html. It too gives beautiful 
renderings on webpages of equations 
>encoded in LaTeX. It is very easy to use. It grew out of jsMath.
>
>http://www.mathjax.org/
>
>Best regards,
>
>Blaine Mooers
>
>
>
>From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of William G. 
>Scott [wgsc...@ucsc.edu]
>Sent: Wednesday, May 20, 2015 7:32 PM
>To: CCP4BB@JISCMAIL.AC.UK
>Subject: Re: [ccp4bb] SUMMARY: Equation Editor woes with Office 2011 for Mac
>
>
>On May 20, 2015, at 5:38 AM, Randy Read  wrote:
>>
>
>>
>Thanks, as always, to everyone for a thoughtful discussion!
>>
>
>Alternatively, as a scientific community, perhaps it is finally time for us to 
>untwist Clippy, bending him backwards and forwards until he snaps at those 
>horrid beady little eyeballs, ditch the Comic Sans, flip Redmond the bird, 
>HTFU and learn to use LaTeX equation markup, and ask that our journals do the 
>same.  It really isn’t any harder than learning basic HTML (and predates it as 
>one of the original mark-up languages). Journals and funding agencies should 
>not be demanding that we use crappy broken and restrictive proprietary formats 
>for submitting papers and proposals.
>
>Ascii text documents provide the ultimate form of universal interchangeability.
>
>The syntax is actually quite straightforward and easy to learn (or look up), 
>eg:
>
>https://urldefense.proofpoint.com/v2/url?u=http-3A__en.wikibooks.org_wiki_LaTeX_Mathematics&d=AwIF-g&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=U-vNRZjPhftiaADvIzN7HNUo5rnv5-JKR6RwZjW0UDQ&s=Q3biyCgXkL73q4eLw0MovreIp6p923PLHLrEp3AiuBg&e=
>
>LaTeX allows you to focus on content rather than document formatting.  
>Although it is definitely more badass to do this in vim, other ascii text 
>editors often have very useful LaTeX functionality.  (My favorite on OS X is 
>TextMate, version 2 of which is now free. If you code on OS X, you should take 
>a look at this.)
>
>Once you make the small investment of time learning LaTeX, it makes other 
>tasks easier.  For example, you can use jsMath to embed LaTeX-encoded 
>equations (including chemistry symbols) in web pages, eg:
>
>https://urldefense.proofpoint.com/v2/url?u=http-3A__www.math.union.edu_-7Edpvc_jsmath_examples_welcome.html&d=AwIF-g&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=U-vNRZjPhftiaADvIzN7HNUo5rnv5-JKR6RwZjW0UDQ&s=UAkZG7nG6yJ1m41HFCqn3Ah_ifo-u-S4N8VwWbtbi3o&e=
>

[ccp4bb] PhD positions available in the Hamburg Centre for Ultrafast Imaging

[Arwen Pearson]

Two PhD positions are open in the laboratory of Prof. Arwen Pearson in 
the Hamburg Centre for Ultrafast Imaging 
(http://www.cui.uni-hamburg.de/en/about-us/who-we-are/research-group-arwen-pearson/). 



a) the development of new photochemical tools for time-resolved 
structural biology

http://www.uni-hamburg.de/uhh/stellenangebote/wissenschaftliches-personal/cui-physik-15-6-2015.pdf

b) a nanoscale chip based membrane protein production platform.
http://www.uni-hamburg.de/uhh/stellenangebote/wissenschaftliches-personal/cui-physik-15-6-15.pdf

Application deadline is June 15th 2015.

Informal enquries can be sent to arwen.pear...@cfel.de

PS: A number of my colleagues in the Centre for Ultrafast Imaging also 
have positions open (both PhD and postdoc). You can see the full list of 
current opportunities here: http://www.cui.uni-hamburg.de/en/openpositions/

[ccp4bb] Point group

[Mohamed Noor]

Dear all

I can process my 3.8 A dataset in either P4 or P422 point groups. MR searches 
and refinement in SG P41 and P41212 results in R/Rfree of around 30/35 % with 8 
and 4 NCS copies, respectively. Pointless doesn't seem to complain but Xtriage 
suggests 25 % twinning in the former (refinement was done without twin law) and 
that the true point group could be P422. So do I go with P422? 

Secondly, where can I find the DIALS equivalent to XDS FRAME.cbf? The 
statistics are slightly better but I prefer to confirm it visually. I recently 
had a case of pseudosymmetry which makes me suspicious of automated processing 
suggestions.

Thanks.

Re: [ccp4bb] Point group

[David Schuller]

On 05/21/15 11:56, Mohamed Noor wrote:

Dear all

I can process my 3.8 A dataset in either P4 or P422 point groups.
Do the scaling statistics look similar for both? If so, go with P422. 
Trying to enforce an incorrect symmetry operator would blow up your stats.



  MR searches and refinement in SG P41 and P41212 results in R/Rfree of around 
30/35 % with 8 and 4 NCS copies, respectively. Pointless doesn't seem to 
complain but Xtriage suggests 25 % twinning in the former (refinement was done 
without twin law) and that the true point group could be P422. So do I go with 
P422?

Secondly, where can I find the DIALS equivalent to XDS FRAME.cbf? The 
statistics are slightly better but I prefer to confirm it visually. I recently 
had a case of pseudosymmetry which makes me suspicious of automated processing 
suggestions.

Thanks.



--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

Re: [ccp4bb] Point group

[Keller, Jacob]

>> I can process my 3.8 A dataset in either P4 or P422 point groups.
>Do the scaling statistics look similar for both? If so, go with P422. 
>Trying to enforce an incorrect symmetry operator would blow up your stats.

...But in the case of twinning, lower space groups can masquerade as higher 
ones. I say try out P4 with twin refinement, see how your stats go.

JPK














-- 
===
All Things Serve the Beam
===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu

Re: [ccp4bb] Point group

[frazao]

On 05/21/2015 05:23 PM, Keller, Jacob wrote:

I can process my 3.8 A dataset in either P4 or P422 point groups.

Do the scaling statistics look similar for both? If so, go with P422.
Trying to enforce an incorrect symmetry operator would blow up your stats.

...But in the case of twinning, lower space groups can masquerade as higher 
ones. I say try out P4 with twin refinement, see how your stats go.

JPK
Or eventually even to further lower symmetry... I had once an example of 
true P21212 crystals that processed nicely as P4212, due to a twinning 
two-fold axis parallel to the a,b diagonal


Carlos

--
**
Dr. Carlos Frazao
Structural Biology Laboratory -
Macromolecular Crystallography Unit
ITQB-UNL, Av Republica, Apartado 127
2781-901 Oeiras, Portugal

Phone:  (351)-214469666/609
FAX:(351)-214433644
e-mail: fra...@itqb.unl.pt
www.itqb.unl.pt

[ccp4bb] Early registration deadline is May 31 for ACA Annual meeting in Philadelphia July 25-19

[Terwilliger, Thomas Charles]

Hi CCP4 users!

A message from the American Crystallographic Association:

Early registration for the ACA annual meeting in Philadelphia July 25-29 is 
open until May 31.  

See http://www.amercrystalassn.org/2015-mtg-homepage for details!

All the best,
Tom T
Vice-President, ACA

[ccp4bb] X-rays and matter (the particle-wave picture)

[Murpholino Peligro]

Hello Everybody!
I was trying to make some sense from  Bernhard Rupp's book page 251.

I will copy the relevant part...

When photons travel through a crystal, either of two things can happen: (i)
nothing, which happens over 99% of the time; (ii) the electric field vector
induces oscillations in all the electrons coherently within* the photon's
coherence length* ranging from a few 1000 Angstroms for X-ray emission
lines to several microns for modern synchrotron sources. At this point, the
photon ceases to exist, and we can imagine that the electrons themselves
emanate *virtual waves*, which constructively overlap in certain
directions, and interfere destructively in others. The scattered photon
then *appears again in some direction*, with the probability of that
appearance proportional to the amplitude of the combined, resultant
scattered wave in that particular direction...The sum of all scattering
events of independent, single photons then generates the diffraction
pattern.

I underlined the problematic parts...

can anyone shed some light on this ..or point me in the right direction?


Thanks in advance

Re: [ccp4bb] X-rays and matter (the particle-wave picture)

[Keller, Jacob]

Excellent and interesting question—I’d love to hear an answer as well. Creatio 
ex nihilo at the synchrotron?

I’d also love to hear what the evidence in the literature is for this, although 
I suspect much of it would be hopelessly encoded in bristling equations. 
(Nothing against equations, but they don’t do too much for the imagination or 
mental picture.)

JPK

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
Murpholino Peligro
Sent: Thursday, May 21, 2015 9:44 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] X-rays and matter (the particle-wave picture)

Hello Everybody!
I was trying to make some sense from  Bernhard Rupp's book page 251.
I will copy the relevant part...
When photons travel through a crystal, either of two things can happen: (i) 
nothing, which happens over 99% of the time; (ii) the electric field vector 
induces oscillations in all the electrons coherently within the photon's 
coherence length ranging from a few 1000 Angstroms for X-ray emission lines to 
several microns for modern synchrotron sources. At this point, the photon 
ceases to exist, and we can imagine that the electrons themselves emanate 
virtual waves, which constructively overlap in certain directions, and 
interfere destructively in others. The scattered photon then appears again in 
some direction, with the probability of that appearance proportional to the 
amplitude of the combined, resultant scattered wave in that particular 
direction...The sum of all scattering events of independent, single photons 
then generates the diffraction pattern.
I underlined the problematic parts...

can anyone shed some light on this ..or point me in the right direction?

Thanks in advance

Re: [ccp4bb] X-rays and matter (the particle-wave picture)

[Zbyszek Otwinowski]

The answer to your questions depends on the level of understanding of
quantum mechanics. I am sending info where to find the subject discussed
in more details.

Bernhard Rupp's book page 251 necessarily simplifies a rather complex
subject of the photon's interaction with multiple particles. Quantum
mechanical wave function can be considered virtual from the measurement
process point of view, as the photon (a single quantum) appears in the
detector during the measurement process, but not on the way to it.


> the photon's coherence length

The concept of photon's coherence length involves quantum mechanics mixed
state. For introduction see:
http://en.wikipedia.org/wiki/Quantum_state#Mixed_states

> virtual waves
Quantum mechanical wave function is "virtual" in certain sense. The
Feynman Lectures on Physics Vol 3 covers this subject quite well.

> appears again in some direction
This refers to quantum mechanical wave-particle duality


> Hello Everybody!
> I was trying to make some sense from  Bernhard Rupp's book page 251.
>
> I will copy the relevant part...
>
> When photons travel through a crystal, either of two things can happen: (i)
> nothing, which happens over 99% of the time; (ii) the electric field vector
> induces oscillations in all the electrons coherently within* the
photon's coherence length* ranging from a few 1000 Angstroms for X-ray
emission lines to several microns for modern synchrotron sources. At
this point, the
> photon ceases to exist, and we can imagine that the electrons themselves
emanate *virtual waves*, which constructively overlap in certain
directions, and interfere destructively in others. The scattered photon
then *appears again in some direction*, with the probability of that
appearance proportional to the amplitude of the combined, resultant
scattered wave in that particular direction...The sum of all
scattering
> events of independent, single photons then generates the diffraction
pattern.
>
> I underlined the problematic parts...
>
> can anyone shed some light on this ..or point me in the right direction?
>
>
> Thanks in advance
>


Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353



Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353

Re: [ccp4bb] Point group

[dhaval patel]

Even I have the same problem my crystals get processed in to P212121 as
well as P4212 and I am currently analysing the data but not able to
conclude the space group. Any idea? Both structure while refining is giving
around same R/Rfree. Any help will be appreciable.

Dhaval Patel
PhD Student,
Bioinformatics &
Structural Biology
Indian Institute of
Advanced Research
+91-9925450504

On Thu, May 21, 2015 at 10:57 PM, frazao  wrote:

> On 05/21/2015 05:23 PM, Keller, Jacob wrote:
>
>> I can process my 3.8 A dataset in either P4 or P422 point groups.

>>> Do the scaling statistics look similar for both? If so, go with P422.
>>> Trying to enforce an incorrect symmetry operator would blow up your
>>> stats.
>>>
>> ...But in the case of twinning, lower space groups can masquerade as
>> higher ones. I say try out P4 with twin refinement, see how your stats go.
>>
>> JPK
>>
> Or eventually even to further lower symmetry... I had once an example of
> true P21212 crystals that processed nicely as P4212, due to a twinning
> two-fold axis parallel to the a,b diagonal
>
> Carlos
>
> --
> **
> Dr. Carlos Frazao
> Structural Biology Laboratory -
> Macromolecular Crystallography Unit
> ITQB-UNL, Av Republica, Apartado 127
> 2781-901 Oeiras, Portugal
>
> Phone:  (351)-214469666/609
> FAX:(351)-214433644
> e-mail: fra...@itqb.unl.pt
> www.itqb.unl.pt
>

Re: [ccp4bb] Point group

[Graeme Winter]

Dear Mohamed

You can get the equivalent of frame.CBF by using the duals image viewer
with datablock or experiments.json and integrated.pickle. this will allow
you to step through the frames looking at the actual integration boxes.

Best wishes Graeme
On 21 May 2015 17:02, "Mohamed Noor"  wrote:

> Dear all
>
> I can process my 3.8 A dataset in either P4 or P422 point groups. MR
> searches and refinement in SG P41 and P41212 results in R/Rfree of around
> 30/35 % with 8 and 4 NCS copies, respectively. Pointless doesn't seem to
> complain but Xtriage suggests 25 % twinning in the former (refinement was
> done without twin law) and that the true point group could be P422. So do I
> go with P422?
>
> Secondly, where can I find the DIALS equivalent to XDS FRAME.cbf? The
> statistics are slightly better but I prefer to confirm it visually. I
> recently had a case of pseudosymmetry which makes me suspicious of
> automated processing suggestions.
>
> Thanks.
>

Re: [ccp4bb] X-rays and matter (the particle-wave picture)

[William G. Scott]

I also find that a bit confusing.

If you want to think about it in terms of quantum approach (i.e., individual 
photons), the following points are worth keeping in mind:

(1) All of this is elastic scattering, falling within the first-order Born 
approximation.  What this means physically is a photon is elastically scattered 
from a spherically-symmetric potential — effectively a billiard ball. It 
neither absorbs or emits energy.  Scattering from a single point yields a 
spherical wave, but that wave in the single-photon quantum limit has to be 
interpreted as a probability amplitude, not an electric field vector.

(2) A single photon only interferes with itself.

(3) A photon scattering from a given atom within a macromolecule in the crystal 
feels the scattering contribution only from the other identical, 
crystallographic symmetry-related atoms in the other asymmetric units of the 
crystal that are exposed to the X-ray beam, and all of these contribute equally 
to the diffraction pattern. (The diffraction pattern is in essence the 
spherically scattered wave sampled by the reciprocal lattice).

(4) This is physically the same problem as a single photon scattering from a 
multiple (effectively infinite) slit diffraction grating.  Classically, we 
would assume the photon only goes through one of the slits, but 
quantum-mechanically, we have to consider all of them in order to correctly 
predict the diffraction pattern.  (My guess is what Bernhard wrote is a way of 
describing this non-classical behavior).

BTW that really has to be the ickiest user name alias in the history of the 
CCP4 BB.


William G. Scott

http://scottlab.ucsc.edu/~wgscott

> On May 21, 2015, at 6:43 PM, Murpholino Peligro  wrote:
> 
> Hello Everybody! 
> I was trying to make some sense from  Bernhard Rupp's book page 251.
> 
> I will copy the relevant part...
> 
> When photons travel through a crystal, either of two things can happen: (i) 
> nothing, which happens over 99% of the time; (ii) the electric field vector 
> induces oscillations in all the electrons coherently within the photon's 
> coherence length ranging from a few 1000 Angstroms for X-ray emission lines 
> to several microns for modern synchrotron sources. At this point, the photon 
> ceases to exist, and we can imagine that the electrons themselves emanate 
> virtual waves, which constructively overlap in certain directions, and 
> interfere destructively in others. The scattered photon then appears again in 
> some direction, with the probability of that appearance proportional to the 
> amplitude of the combined, resultant scattered wave in that particular 
> direction...The sum of all scattering events of independent, single 
> photons then generates the diffraction pattern.
> 
> I underlined the problematic parts...
> 
> can anyone shed some light on this ..or point me in the right direction? 
> 
> 
> Thanks in advance
> 
>