Re: [ccp4bb] include corners in mosflm

2017-09-27 Thread Tim Gruene 
Dear JPK,

the CSD holds about 8x more crystal structures than the PDB. Taking ICSD into 
account as well as many non-published structures, it is probably safe to say 
that the majority of structures did require 'swung out mode' - 'atypical' may 
be a little a narrow view of crystallography.
At many synchrotron beamlines, that often do not provide a 2theta arm, it is 
often borderline to get to the Acta Cryst C limit for publication, i.e. 0.84A 
complete data.

Best,
Tim


On Wednesday, September 27, 2017 12:09:47 PM CEST Keller, Jacob wrote:
> You’ve got a point about including data, but on the other hand, I would
> assume one would (almost always) set the collection parameters so as not to
> require use of the corners. And “swung out” mode is pretty atypical, so
> would be strange to set a default for it.
 
> JPK
> 
> From: herman.schreu...@sanofi.com [mailto:herman.schreu...@sanofi.com]
> Sent: Wednesday, September 27, 2017 2:44 AM
> To: Keller, Jacob <kell...@janelia.hhmi.org>; CCP4BB@JISCMAIL.AC.UK
> Subject: AW: [ccp4bb] include corners in mosflm
> 
> With a detector in swing-out position, one has to include the corners. Also,
> why should one discard potential data during processing? Based on the
> statistics, one can always discard data afterwards if it is not good or too
> incomplete.
 
> HS
> 
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
> Keller, Jacob
 Gesendet: Dienstag, 26. September 2017 22:14
> An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
> Betreff: Re: [ccp4bb] include corners in mosflm
> 
> Why on earth would one want that to be the *default*? I understand that
> there may be the odd unrepeatable dataset collected too close, or there may
> be occasionally be hardward limitations, but I cannot understand how this
> would be a recurring problem….
 
> JPK
> 
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> CCP4BB
 Sent: Tuesday, September 26, 2017 4:11 PM
> To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
> Subject: Re: [ccp4bb] include corners in mosflm
> 
> Hi Ed
> 
> I'm afraid not; that's one thing that can't be changed to a different
> default.
 Harry
> --
> Dr Harry Powell
> Chairman of European Crystallographic Association SIG9 (Crystallographic
> Computing)
 
> On 26 Sep 2017, at 20:34, Edwin Pozharski
> <pozharsk...@gmail.com<mailto:pozharsk...@gmail.com>> wrote:
 By default,
> iMosflm excludes corners from processing.  Is there a simple way to make it
> the default to go all the way to the corner instead of detector edge?  I
> could of course set the max resolution for processing to some outrageous
> value that is guaranteed to be outside of the image, but perhaps I am
> missing a more intelligent option in the gui.  (I vaguely recall HKL2000
> having a Edge/Corner/Other) radiobutton). 
> There is a whole separate question as to wisdom of including corners, of
> course.  Yes, adding a resolution shell with robust data will improve model
> quality even if such shell is woefully incomplete. On the other hand, it's
> possible that fill-in option for missing reflections in map calculation may
> make maps more biased. A reasonable solution to this would be to use 2
> different resolution limits in refinement and map calculation - not hard to
> script for that yet I don't know if any refinement software provides such
> option natively.
 Ed.
-- 
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Principal Investigator
Biology and Chemistry
OFLC/104
CH-5232 Villigen PSI

Phone: +41 (0)56 310 5297

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Re: [ccp4bb] include corners in mosflm

2017-09-27 Thread Keller, Jacob 
You’ve got a point about including data, but on the other hand, I would assume 
one would (almost always) set the collection parameters so as not to require 
use of the corners. And “swung out” mode is pretty atypical, so would be 
strange to set a default for it.

JPK

From: herman.schreu...@sanofi.com [mailto:herman.schreu...@sanofi.com]
Sent: Wednesday, September 27, 2017 2:44 AM
To: Keller, Jacob <kell...@janelia.hhmi.org>; CCP4BB@JISCMAIL.AC.UK
Subject: AW: [ccp4bb] include corners in mosflm

With a detector in swing-out position, one has to include the corners. Also, 
why should one discard potential data during processing? Based on the 
statistics, one can always discard data afterwards if it is not good or too 
incomplete.

HS

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Keller, 
Jacob
Gesendet: Dienstag, 26. September 2017 22:14
An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Betreff: Re: [ccp4bb] include corners in mosflm

Why on earth would one want that to be the *default*? I understand that there 
may be the odd unrepeatable dataset collected too close, or there may be 
occasionally be hardward limitations, but I cannot understand how this would be 
a recurring problem….

JPK

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of CCP4BB
Sent: Tuesday, September 26, 2017 4:11 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] include corners in mosflm

Hi Ed

I'm afraid not; that's one thing that can't be changed to a different default.
Harry
--
Dr Harry Powell
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing)

On 26 Sep 2017, at 20:34, Edwin Pozharski 
<pozharsk...@gmail.com<mailto:pozharsk...@gmail.com>> wrote:
By default, iMosflm excludes corners from processing.  Is there a simple way to 
make it the default to go all the way to the corner instead of detector edge?  
I could of course set the max resolution for processing to some outrageous 
value that is guaranteed to be outside of the image, but perhaps I am missing a 
more intelligent option in the gui.  (I vaguely recall HKL2000 having a 
Edge/Corner/Other) radiobutton).

There is a whole separate question as to wisdom of including corners, of 
course.  Yes, adding a resolution shell with robust data will improve model 
quality even if such shell is woefully incomplete. On the other hand, it's 
possible that fill-in option for missing reflections in map calculation may 
make maps more biased. A reasonable solution to this would be to use 2 
different resolution limits in refinement and map calculation - not hard to 
script for that yet I don't know if any refinement software provides such 
option natively.
Ed.

[ccp4bb] AW: [ccp4bb] include corners in mosflm

2017-09-27 Thread Herman . Schreuder 
With a detector in swing-out position, one has to include the corners. Also, 
why should one discard potential data during processing? Based on the 
statistics, one can always discard data afterwards if it is not good or too 
incomplete.

HS

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Keller, 
Jacob
Gesendet: Dienstag, 26. September 2017 22:14
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] include corners in mosflm

Why on earth would one want that to be the *default*? I understand that there 
may be the odd unrepeatable dataset collected too close, or there may be 
occasionally be hardward limitations, but I cannot understand how this would be 
a recurring problem….

JPK

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of CCP4BB
Sent: Tuesday, September 26, 2017 4:11 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] include corners in mosflm

Hi Ed

I'm afraid not; that's one thing that can't be changed to a different default.
Harry
--
Dr Harry Powell
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing)

On 26 Sep 2017, at 20:34, Edwin Pozharski 
<pozharsk...@gmail.com<mailto:pozharsk...@gmail.com>> wrote:
By default, iMosflm excludes corners from processing.  Is there a simple way to 
make it the default to go all the way to the corner instead of detector edge?  
I could of course set the max resolution for processing to some outrageous 
value that is guaranteed to be outside of the image, but perhaps I am missing a 
more intelligent option in the gui.  (I vaguely recall HKL2000 having a 
Edge/Corner/Other) radiobutton).

There is a whole separate question as to wisdom of including corners, of 
course.  Yes, adding a resolution shell with robust data will improve model 
quality even if such shell is woefully incomplete. On the other hand, it's 
possible that fill-in option for missing reflections in map calculation may 
make maps more biased. A reasonable solution to this would be to use 2 
different resolution limits in refinement and map calculation - not hard to 
script for that yet I don't know if any refinement software provides such 
option natively.
Ed.

Re: [ccp4bb] include corners in mosflm

2017-09-26 Thread Keller, Jacob 
Why on earth would one want that to be the *default*? I understand that there 
may be the odd unrepeatable dataset collected too close, or there may be 
occasionally be hardward limitations, but I cannot understand how this would be 
a recurring problem….

JPK

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of CCP4BB
Sent: Tuesday, September 26, 2017 4:11 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] include corners in mosflm

Hi Ed

I'm afraid not; that's one thing that can't be changed to a different default.
Harry
--
Dr Harry Powell
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing)

On 26 Sep 2017, at 20:34, Edwin Pozharski 
<pozharsk...@gmail.com<mailto:pozharsk...@gmail.com>> wrote:
By default, iMosflm excludes corners from processing.  Is there a simple way to 
make it the default to go all the way to the corner instead of detector edge?  
I could of course set the max resolution for processing to some outrageous 
value that is guaranteed to be outside of the image, but perhaps I am missing a 
more intelligent option in the gui.  (I vaguely recall HKL2000 having a 
Edge/Corner/Other) radiobutton).

There is a whole separate question as to wisdom of including corners, of 
course.  Yes, adding a resolution shell with robust data will improve model 
quality even if such shell is woefully incomplete. On the other hand, it's 
possible that fill-in option for missing reflections in map calculation may 
make maps more biased. A reasonable solution to this would be to use 2 
different resolution limits in refinement and map calculation - not hard to 
script for that yet I don't know if any refinement software provides such 
option natively.
Ed.

Re: [ccp4bb] include corners in mosflm

2017-09-26 Thread CCP4BB 
Hi Ed

I'm afraid not; that's one thing that can't be changed to a different default.

Harry
--
Dr Harry Powell
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 

> On 26 Sep 2017, at 20:34, Edwin Pozharski  wrote:
> 
> By default, iMosflm excludes corners from processing.  Is there a simple way 
> to make it the default to go all the way to the corner instead of detector 
> edge?  I could of course set the max resolution for processing to some 
> outrageous value that is guaranteed to be outside of the image, but perhaps I 
> am missing a more intelligent option in the gui.  (I vaguely recall HKL2000 
> having a Edge/Corner/Other) radiobutton).
> 
> There is a whole separate question as to wisdom of including corners, of 
> course.  Yes, adding a resolution shell with robust data will improve model 
> quality even if such shell is woefully incomplete. On the other hand, it's 
> possible that fill-in option for missing reflections in map calculation may 
> make maps more biased. A reasonable solution to this would be to use 2 
> different resolution limits in refinement and map calculation - not hard to 
> script for that yet I don't know if any refinement software provides such 
> option natively.
> 
> Ed.

[ccp4bb] include corners in mosflm

2017-09-26 Thread Edwin Pozharski 
By default, iMosflm excludes corners from processing.  Is there a simple
way to make it the default to go all the way to the corner instead of
detector edge?  I could of course set the max resolution for processing to
some outrageous value that is guaranteed to be outside of the image, but
perhaps I am missing a more intelligent option in the gui.  (I vaguely
recall HKL2000 having a Edge/Corner/Other) radiobutton).

There is a whole separate question as to wisdom of including corners, of
course.  Yes, adding a resolution shell with robust data will improve model
quality even if such shell is woefully incomplete. On the other hand, it's
possible that fill-in option for missing reflections in map calculation may
make maps more biased. A reasonable solution to this would be to use 2
different resolution limits in refinement and map calculation - not hard to
script for that yet I don't know if any refinement software provides such
option natively.

Ed.