Re: [ccp4bb] Resolution limit of index in XDS

2013-03-21 Thread Herman . Schreuder
Dear Tim,

It could be that COLSPOT does not rely on experimental setup parameters. 
However, XDS must have reasonably close starting values for distance, direct 
beam position etc., otherwise the autoindexing would fail, so the information 
to calculate an approximate TRUSTED_REGION is available.

For good data, a limited spot range usually works as well. However, for the 
weakly diffracting bad crystals with ice rings, salt spots, multiple 
diffraction patterns etc., one often needs the full range and often needs 
several tries with different parameters before indexing is successful. Since it 
is only cpu-time, it is the least of my worries and, as you mention, it is not 
bad to be forced to think once in a while instead of just clicking buttons in 
GUI's.

Best regards,
Herman



-Original Message-
From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] 
Sent: Wednesday, March 20, 2013 11:17 PM
To: Schreuder, Herman RD/DE
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Resolution limit of index in XDS

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Herman,

the short answer might be that at the stage of COLSPOT the term 'resolution' 
has a limited meaning because COLSPOT does not rely on the experimental setup 
like distance and beam direction, so the term 'resolution limit' is 
conceptually not applicable at this stage.

Indexing does often not require the full data set, you can reduce the 
SPOT_RANGE if you are worried about processing time, or by a multi-CPU 
machine.

One of the great advantages of XDS is that it asks you to think at a level 
higher than the average MS-Windows user while processing your data, so the 
effort to figure out the three  numbers to set the TRUSTED_REGION is in line 
with the philosphy of XDS as I understand it.

But you are right, I do not have access to the source of XDS and I am not the 
person to address a request to.

Kind regards,
Tim

On 03/20/2013 10:29 AM, herman.schreu...@sanofi.com wrote:
 Dear Tim, but probably I should adres this to Kai Diederichs,
 
 not including the resolution cutoff in COLSPOT and IDXREF is a feature 
 of XDS I do not understand at all. For most cases, it may not matter 
 since only the strong spots are used, but what are the advantages?
 
 In fact there are disadvantages, especially when dealing with poorly 
 diffracting difficult data sets: -when a crystallographer imposes a 
 resolution limit, there are usually good reasons for it.
 -outside the resolution limit, there may be ice rings or contaminating 
 salt spots, which make the autoindexing fail. -when processing 900 
 frame Pilatus data sets, running COLSPOT on the complete detector 
 surface takes significantly longer then running it only on the center 
 region.
 
 Of course, one could fudge a resolution cutoff by translating 
 resolution into pixels and then calculating a TRUSTED_REGION, or 
 manually editing the SPOT.XDS file, but this is a lot of extra and in 
 my view unneccessary work.
 
 I would really consider using the resolution cutoff for COLSPOT as 
 well.
 
 Best, Herman
 
 
 -Original Message- From: CCP4 bulletin board 
 [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent:
 Tuesday, March 19, 2013 11:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject:
 Re: [ccp4bb] Resolution limit of index in XDS
 
 Dear Niu,
 
 indexing relies on strong reflections only, that is (in very
 brieft) why INCLUDE_RESOLUTION_RANGE indeed does not affect the 
 relections collected in COLSPOT which in turn are used by IDXREF.
 You can work around this, however, by making use of TRUSTED_REGION and 
 set it to e.g. 0.7 or 0.6 (you can use adxv to translate resolution 
 into pixel and then calculate the fraction you need to set the second 
 number in TRUSTED_REGION to (or the first if you want to exclude the 
 inner resolution reflections - I remember one data set where this was 
 essential for indexing - DNA was involved
 there)
 
 Best, Tim
 
 On 03/19/2013 08:53 PM, Niu Tou wrote:
 Dear All,
 
 Is there any command can set the resolution limit for index step in 
 XDS? I only found a keyword INCLUDE_RESOLUTION_RANGE, but it looks to 
 be a definition of resolution range after index step as it says:
 
 INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by 
 DEFPIX,INTEGRATE,CORRECT
 
 Thanks! Niu
 
 
 

- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFRSjVtUxlJ7aRr7hoRApZhAJ9RFBs8D9NGjgLY3KOoNHhNtdOWggCgj7U0
zY7jEFDYZfl0Umb9E1Bzs1U=
=+HjR
-END PGP SIGNATURE-


Re: [ccp4bb] Resolution limit of index in XDS

2013-03-21 Thread Kay Diederichs
Dear Herman,

some pros and cons are documented at 
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Wishlist#Would_be_nice_to_have
 , and the workaround is at 
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Ice_rings . These 
XDSwiki articles are old, and nobody has contributed to the discussion since 
2007 (after all, is is a Wiki!), so there has not been much reason for a change.
Tim is right in that usage of INCLUDE_RESOLUTION_RANGE does not fit well at the 
COLSPOT stage, since COLSPOT knows nothing about wavelength, distance, pixel 
size and so on.
If there is agreement among XDS users that IDXREF should take 
INCLUDE_RESOLUTION_RANGE into account, there is a good chance that the next 
version of XDS will do that.

best,

Kay

On Wed, 20 Mar 2013 09:29:47 +, herman.schreu...@sanofi.com wrote:

Dear Tim, but probably I should adres this to Kai Diederichs,

not including the resolution cutoff in COLSPOT and IDXREF is a feature of XDS 
I do not understand at all. For most cases, it may not matter since only the 
strong spots are used, but what are the advantages?

In fact there are disadvantages, especially when dealing with poorly 
diffracting difficult data sets:
-when a crystallographer imposes a resolution limit, there are usually good 
reasons for it.
-outside the resolution limit, there may be ice rings or contaminating salt 
spots, which make the autoindexing fail.
-when processing 900 frame Pilatus data sets, running COLSPOT on the complete 
detector surface takes significantly longer then running it only on the center 
region.

Of course, one could fudge a resolution cutoff by translating resolution into 
pixels and then calculating a TRUSTED_REGION, or manually editing the SPOT.XDS 
file, but this is a lot of extra and in my view unneccessary work.

I would really consider using the resolution cutoff for COLSPOT as well.

Best,
Herman
 

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim 
Gruene
Sent: Tuesday, March 19, 2013 11:06 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Resolution limit of index in XDS

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Niu,

indexing relies on strong reflections only, that is (in very brieft) why 
INCLUDE_RESOLUTION_RANGE indeed does not affect the relections collected in 
COLSPOT which in turn are used by IDXREF. You can work around this, however, 
by making use of TRUSTED_REGION and set it to e.g. 0.7 or 0.6 (you can use 
adxv to translate resolution into pixel and then calculate the fraction you 
need to set the second number in TRUSTED_REGION to (or the first if you want 
to exclude the inner resolution reflections - I remember one data set where 
this was essential for indexing - DNA was involved there)

Best,
Tim

On 03/19/2013 08:53 PM, Niu Tou wrote:
 Dear All,
 
 Is there any command can set the resolution limit for index step in 
 XDS? I only found a keyword INCLUDE_RESOLUTION_RANGE, but it looks to 
 be a definition of resolution range after index step as it
 says:
 
 INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by 
 DEFPIX,INTEGRATE,CORRECT
 
 Thanks! Niu
 

- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFRSOFJUxlJ7aRr7hoRAo6TAKC+BePgeODbDyngO7N8vCE4CnjxmQCfS5cP
srShHNz1sDK0EMHSbE3fDwA=
=kAwf
-END PGP SIGNATURE-


Re: [ccp4bb] Resolution limit of index in XDS

2013-03-21 Thread Kay Diederichs
On Thu, 21 Mar 2013 08:28:27 +, herman.schreu...@sanofi.com wrote:

Dear Tim,

It could be that COLSPOT does not rely on experimental setup parameters. 
However, XDS must have reasonably close starting values for distance, direct 
beam position etc., otherwise the autoindexing would fail, so the information 
to calculate an approximate TRUSTED_REGION is available.

TRUSTED_REGION and INCLUDE_RESOLUTION_RANGE are orthogonal concepts; both are 
input by the user and not calculated by the program.


For good data, a limited spot range usually works as well. However, for the 
weakly diffracting bad crystals with ice rings, salt spots, multiple 
diffraction patterns etc., one often needs the full range and often needs 
several tries with different parameters before indexing is successful. Since 
it is only cpu-time, it is the least of my worries and, as you mention, it is 
not bad to be forced to think once in a while instead of just clicking buttons 
in GUI's.

Nevertheless I plan to release a GUI for xds soon; among other things, this 
enables to visualize and change TRUSTED_REGION and INCLUDE_RESOLUTION_RANGE .

best,

Kay


Best regards,
Herman



-Original Message-
From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] 
Sent: Wednesday, March 20, 2013 11:17 PM
To: Schreuder, Herman RD/DE
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Resolution limit of index in XDS

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Herman,

the short answer might be that at the stage of COLSPOT the term 'resolution' 
has a limited meaning because COLSPOT does not rely on the experimental setup 
like distance and beam direction, so the term 'resolution limit' is 
conceptually not applicable at this stage.

Indexing does often not require the full data set, you can reduce the 
SPOT_RANGE if you are worried about processing time, or by a multi-CPU 
machine.

One of the great advantages of XDS is that it asks you to think at a level 
higher than the average MS-Windows user while processing your data, so the 
effort to figure out the three  numbers to set the TRUSTED_REGION is in line 
with the philosphy of XDS as I understand it.

But you are right, I do not have access to the source of XDS and I am not the 
person to address a request to.

Kind regards,
Tim

On 03/20/2013 10:29 AM, herman.schreu...@sanofi.com wrote:
 Dear Tim, but probably I should adres this to Kai Diederichs,
 
 not including the resolution cutoff in COLSPOT and IDXREF is a feature 
 of XDS I do not understand at all. For most cases, it may not matter 
 since only the strong spots are used, but what are the advantages?
 
 In fact there are disadvantages, especially when dealing with poorly 
 diffracting difficult data sets: -when a crystallographer imposes a 
 resolution limit, there are usually good reasons for it.
 -outside the resolution limit, there may be ice rings or contaminating 
 salt spots, which make the autoindexing fail. -when processing 900 
 frame Pilatus data sets, running COLSPOT on the complete detector 
 surface takes significantly longer then running it only on the center 
 region.
 
 Of course, one could fudge a resolution cutoff by translating 
 resolution into pixels and then calculating a TRUSTED_REGION, or 
 manually editing the SPOT.XDS file, but this is a lot of extra and in 
 my view unneccessary work.
 
 I would really consider using the resolution cutoff for COLSPOT as 
 well.
 
 Best, Herman
 
 
 -Original Message- From: CCP4 bulletin board 
 [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent:
 Tuesday, March 19, 2013 11:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject:
 Re: [ccp4bb] Resolution limit of index in XDS
 
 Dear Niu,
 
 indexing relies on strong reflections only, that is (in very
 brieft) why INCLUDE_RESOLUTION_RANGE indeed does not affect the 
 relections collected in COLSPOT which in turn are used by IDXREF.
 You can work around this, however, by making use of TRUSTED_REGION and 
 set it to e.g. 0.7 or 0.6 (you can use adxv to translate resolution 
 into pixel and then calculate the fraction you need to set the second 
 number in TRUSTED_REGION to (or the first if you want to exclude the 
 inner resolution reflections - I remember one data set where this was 
 essential for indexing - DNA was involved
 there)
 
 Best, Tim
 
 On 03/19/2013 08:53 PM, Niu Tou wrote:
 Dear All,
 
 Is there any command can set the resolution limit for index step in 
 XDS? I only found a keyword INCLUDE_RESOLUTION_RANGE, but it looks to 
 be a definition of resolution range after index step as it says:
 
 INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by 
 DEFPIX,INTEGRATE,CORRECT
 
 Thanks! Niu
 
 
 

- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFRSjVtUxlJ7aRr7hoRApZhAJ9RFBs8D9NGjgLY3KOoNHhNtdOWggCgj7U0

Re: [ccp4bb] Resolution limit of index in XDS

2013-03-21 Thread Herman . Schreuder
I was a little provokative. A GUI with a viewer would actually be an excellent 
idea since it allows one to see what one is doing, which would be of great help 
for difficult data sets. Nevertheless, since XDS is part of many automated 
pipelines, the possibility to run XDS offline with a command file should not be 
touched. If IDXREF would take the INCLUDE_RESOLUTION_RANGE into account, I am 
sure this would improve the performance of XDS.

Best regards and thank you for the work you put into XDS!
Herman

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kay 
Diederichs
Sent: Thursday, March 21, 2013 10:02 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Resolution limit of index in XDS

On Thu, 21 Mar 2013 08:28:27 +, herman.schreu...@sanofi.com wrote:

Dear Tim,

It could be that COLSPOT does not rely on experimental setup parameters. 
However, XDS must have reasonably close starting values for distance, direct 
beam position etc., otherwise the autoindexing would fail, so the information 
to calculate an approximate TRUSTED_REGION is available.

TRUSTED_REGION and INCLUDE_RESOLUTION_RANGE are orthogonal concepts; both are 
input by the user and not calculated by the program.


For good data, a limited spot range usually works as well. However, for the 
weakly diffracting bad crystals with ice rings, salt spots, multiple 
diffraction patterns etc., one often needs the full range and often needs 
several tries with different parameters before indexing is successful. Since 
it is only cpu-time, it is the least of my worries and, as you mention, it is 
not bad to be forced to think once in a while instead of just clicking buttons 
in GUI's.

Nevertheless I plan to release a GUI for xds soon; among other things, this 
enables to visualize and change TRUSTED_REGION and INCLUDE_RESOLUTION_RANGE .

best,

Kay


Best regards,
Herman



-Original Message-
From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de]
Sent: Wednesday, March 20, 2013 11:17 PM
To: Schreuder, Herman RD/DE
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Resolution limit of index in XDS

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Herman,

the short answer might be that at the stage of COLSPOT the term 'resolution' 
has a limited meaning because COLSPOT does not rely on the experimental setup 
like distance and beam direction, so the term 'resolution limit' is 
conceptually not applicable at this stage.

Indexing does often not require the full data set, you can reduce the 
SPOT_RANGE if you are worried about processing time, or by a multi-CPU 
machine.

One of the great advantages of XDS is that it asks you to think at a level 
higher than the average MS-Windows user while processing your data, so the 
effort to figure out the three  numbers to set the TRUSTED_REGION is in line 
with the philosphy of XDS as I understand it.

But you are right, I do not have access to the source of XDS and I am not the 
person to address a request to.

Kind regards,
Tim

On 03/20/2013 10:29 AM, herman.schreu...@sanofi.com wrote:
 Dear Tim, but probably I should adres this to Kai Diederichs,
 
 not including the resolution cutoff in COLSPOT and IDXREF is a 
 feature of XDS I do not understand at all. For most cases, it may not 
 matter since only the strong spots are used, but what are the advantages?
 
 In fact there are disadvantages, especially when dealing with poorly 
 diffracting difficult data sets: -when a crystallographer imposes a 
 resolution limit, there are usually good reasons for it.
 -outside the resolution limit, there may be ice rings or 
 contaminating salt spots, which make the autoindexing fail. -when 
 processing 900 frame Pilatus data sets, running COLSPOT on the 
 complete detector surface takes significantly longer then running it 
 only on the center region.
 
 Of course, one could fudge a resolution cutoff by translating 
 resolution into pixels and then calculating a TRUSTED_REGION, or 
 manually editing the SPOT.XDS file, but this is a lot of extra and in 
 my view unneccessary work.
 
 I would really consider using the resolution cutoff for COLSPOT as 
 well.
 
 Best, Herman
 
 
 -Original Message- From: CCP4 bulletin board 
 [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent:
 Tuesday, March 19, 2013 11:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject:
 Re: [ccp4bb] Resolution limit of index in XDS
 
 Dear Niu,
 
 indexing relies on strong reflections only, that is (in very
 brieft) why INCLUDE_RESOLUTION_RANGE indeed does not affect the 
 relections collected in COLSPOT which in turn are used by IDXREF.
 You can work around this, however, by making use of TRUSTED_REGION 
 and set it to e.g. 0.7 or 0.6 (you can use adxv to translate 
 resolution into pixel and then calculate the fraction you need to set 
 the second number in TRUSTED_REGION to (or the first if you want to 
 exclude the inner resolution reflections - I remember one data set 
 where

Re: [ccp4bb] Resolution limit of index in XDS

2013-03-20 Thread vellieux

Hello,

The way I do it is by manually editing the SPOT.XDS file (generated by 
the COLSPOT step). Spots are arranged by order of decreasing intensity 
in that file. So if you do down the file, select an appropriate 
intensity cutoff and then remove all spots below that value, it will 
have the effect of selecting a resolution cutoff (think of the plot of 
I vs. resolution) but you won't know what cutoff this corresponds to 
unless you do a careful analysis of the resulting SPOT.XDS file.


HTH,

Fred.

On 19/03/13 20:53, Niu Tou wrote:

Dear All,

Is there any command can set the resolution limit for index step in 
XDS? I only found a keyword INCLUDE_RESOLUTION_RANGE, but it looks to 
be a definition of resolution range after index step

as it says:

INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by 
DEFPIX,INTEGRATE,CORRECT


Thanks!
Niu



--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494


Re: [ccp4bb] Resolution limit of index in XDS

2013-03-20 Thread Herman . Schreuder
Dear Tim, but probably I should adres this to Kai Diederichs,

not including the resolution cutoff in COLSPOT and IDXREF is a feature of XDS I 
do not understand at all. For most cases, it may not matter since only the 
strong spots are used, but what are the advantages?

In fact there are disadvantages, especially when dealing with poorly 
diffracting difficult data sets:
-when a crystallographer imposes a resolution limit, there are usually good 
reasons for it.
-outside the resolution limit, there may be ice rings or contaminating salt 
spots, which make the autoindexing fail.
-when processing 900 frame Pilatus data sets, running COLSPOT on the complete 
detector surface takes significantly longer then running it only on the center 
region.

Of course, one could fudge a resolution cutoff by translating resolution into 
pixels and then calculating a TRUSTED_REGION, or manually editing the SPOT.XDS 
file, but this is a lot of extra and in my view unneccessary work.

I would really consider using the resolution cutoff for COLSPOT as well.

Best,
Herman
 

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene
Sent: Tuesday, March 19, 2013 11:06 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Resolution limit of index in XDS

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Niu,

indexing relies on strong reflections only, that is (in very brieft) why 
INCLUDE_RESOLUTION_RANGE indeed does not affect the relections collected in 
COLSPOT which in turn are used by IDXREF. You can work around this, however, by 
making use of TRUSTED_REGION and set it to e.g. 0.7 or 0.6 (you can use adxv to 
translate resolution into pixel and then calculate the fraction you need to set 
the second number in TRUSTED_REGION to (or the first if you want to exclude the 
inner resolution reflections - I remember one data set where this was essential 
for indexing - DNA was involved there)

Best,
Tim

On 03/19/2013 08:53 PM, Niu Tou wrote:
 Dear All,
 
 Is there any command can set the resolution limit for index step in 
 XDS? I only found a keyword INCLUDE_RESOLUTION_RANGE, but it looks to 
 be a definition of resolution range after index step as it
 says:
 
 INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by 
 DEFPIX,INTEGRATE,CORRECT
 
 Thanks! Niu
 

- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFRSOFJUxlJ7aRr7hoRAo6TAKC+BePgeODbDyngO7N8vCE4CnjxmQCfS5cP
srShHNz1sDK0EMHSbE3fDwA=
=kAwf
-END PGP SIGNATURE-


Re: [ccp4bb] Resolution limit of index in XDS

2013-03-20 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Herman,

the short answer might be that at the stage of COLSPOT the term
'resolution' has a limited meaning because COLSPOT does not rely on
the experimental setup like distance and beam direction, so the term
'resolution limit' is conceptually not applicable at this stage.

Indexing does often not require the full data set, you can reduce the
SPOT_RANGE if you are worried about processing time, or by a
multi-CPU machine.

One of the great advantages of XDS is that it asks you to think at a
level higher than the average MS-Windows user while processing your
data, so the effort to figure out the three  numbers to set the
TRUSTED_REGION is in line with the philosphy of XDS as I understand it.

But you are right, I do not have access to the source of XDS and I am
not the person to address a request to.

Kind regards,
Tim

On 03/20/2013 10:29 AM, herman.schreu...@sanofi.com wrote:
 Dear Tim, but probably I should adres this to Kai Diederichs,
 
 not including the resolution cutoff in COLSPOT and IDXREF is a
 feature of XDS I do not understand at all. For most cases, it may
 not matter since only the strong spots are used, but what are the
 advantages?
 
 In fact there are disadvantages, especially when dealing with
 poorly diffracting difficult data sets: -when a crystallographer
 imposes a resolution limit, there are usually good reasons for it. 
 -outside the resolution limit, there may be ice rings or
 contaminating salt spots, which make the autoindexing fail. -when
 processing 900 frame Pilatus data sets, running COLSPOT on the
 complete detector surface takes significantly longer then running
 it only on the center region.
 
 Of course, one could fudge a resolution cutoff by translating
 resolution into pixels and then calculating a TRUSTED_REGION, or
 manually editing the SPOT.XDS file, but this is a lot of extra and
 in my view unneccessary work.
 
 I would really consider using the resolution cutoff for COLSPOT as
 well.
 
 Best, Herman
 
 
 -Original Message- From: CCP4 bulletin board
 [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent:
 Tuesday, March 19, 2013 11:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject:
 Re: [ccp4bb] Resolution limit of index in XDS
 
 Dear Niu,
 
 indexing relies on strong reflections only, that is (in very
 brieft) why INCLUDE_RESOLUTION_RANGE indeed does not affect the
 relections collected in COLSPOT which in turn are used by IDXREF.
 You can work around this, however, by making use of TRUSTED_REGION
 and set it to e.g. 0.7 or 0.6 (you can use adxv to translate
 resolution into pixel and then calculate the fraction you need to
 set the second number in TRUSTED_REGION to (or the first if you
 want to exclude the inner resolution reflections - I remember one
 data set where this was essential for indexing - DNA was involved
 there)
 
 Best, Tim
 
 On 03/19/2013 08:53 PM, Niu Tou wrote:
 Dear All,
 
 Is there any command can set the resolution limit for index step
 in XDS? I only found a keyword INCLUDE_RESOLUTION_RANGE, but it
 looks to be a definition of resolution range after index step as
 it says:
 
 INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by 
 DEFPIX,INTEGRATE,CORRECT
 
 Thanks! Niu
 
 
 

- -- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFRSjVtUxlJ7aRr7hoRApZhAJ9RFBs8D9NGjgLY3KOoNHhNtdOWggCgj7U0
zY7jEFDYZfl0Umb9E1Bzs1U=
=+HjR
-END PGP SIGNATURE-


Re: [ccp4bb] Resolution limit of index in XDS

2013-03-19 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Niu,

indexing relies on strong reflections only, that is (in very brieft)
why INCLUDE_RESOLUTION_RANGE indeed does not affect the relections
collected in COLSPOT which in turn are used by IDXREF. You can work
around this, however, by making use of TRUSTED_REGION and set it to
e.g. 0.7 or 0.6 (you can use adxv to translate resolution into pixel
and then calculate the fraction you need to set the second number in
TRUSTED_REGION to (or the first if you want to exclude the inner
resolution reflections - I remember one data set where this was
essential for indexing - DNA was involved there)

Best,
Tim

On 03/19/2013 08:53 PM, Niu Tou wrote:
 Dear All,
 
 Is there any command can set the resolution limit for index step in
 XDS? I only found a keyword INCLUDE_RESOLUTION_RANGE, but it looks
 to be a definition of resolution range after index step as it
 says:
 
 INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by 
 DEFPIX,INTEGRATE,CORRECT
 
 Thanks! Niu
 

- -- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFRSOFJUxlJ7aRr7hoRAo6TAKC+BePgeODbDyngO7N8vCE4CnjxmQCfS5cP
srShHNz1sDK0EMHSbE3fDwA=
=kAwf
-END PGP SIGNATURE-


Re: [ccp4bb] resolution limit

2012-07-19 Thread Kay Diederichs
Hi Narayan,

there's nothing wrong with using data with I/sigmaI 2.5, Rsym 224.3 % for 
multiplicity 7.8 and completeness 98.2 %. 

However, when you discarded frames you might have made the data worse - one 
should only reject data if they deviate systematically (e.g. from radiation 
damage). Weak data should not be rejected, and Rmerge is the wrong measure to 
judge about data quality.

best,

Kay

On Wed, 18 Jul 2012 02:41:48 -0700, narayan viswam nvisw...@gmail.com wrote:

Hello CCP4ers,

 In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI 2.5  Rsym
224.3 % for multiplicity 7.8 and completeness 98.2 %. I solved the
structure by MAD  refined it to Rfree 27.3 %. Ths crystal belongs to P622
space group and it is not twinned. The water content is 68%. I loweredthe
 multiplicity to 4.1 by excluding few images but still the Rsym is  200 %
and I/sigmaI  2.0. My rudimentary crystallography knowledge makes me
believe it's quite Ok to use data upto 2.8 A and report the statistics.
Could I request people's views. Thanks very much.
Narayan



Re: [ccp4bb] resolution limit

2012-07-18 Thread Ian Tickle
Hi Narayan

My only comment would be that P622 is a fairly uncommon space group
(currently 43 PDB entries excl homologs), but obviously that doesn't
mean it's wrong - just worth double-checking!  Just out of interest
what's the CC(1/2) statistic for your highest shell?

Personally I specify more bins than the default (e.g. 20 instead of
10) so that the highest resolution bin would be somewhat narrower than
yours.  I would also prefer that the binning is done by equal steps in
d*^3 rather than d*^2 as many programs do since this gives a more even
spread of reflections in the bins and gives an even narrower binning
at the high res end (though it does tend to lump all the low res data
into 1 bin!).

Cheers

-- Ian

On 18 July 2012 10:41, narayan viswam nvisw...@gmail.com wrote:


 Hello CCP4ers,

  In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI 2.5  Rsym
 224.3 % for multiplicity 7.8 and completeness 98.2 %. I solved the structure
 by MAD  refined it to Rfree 27.3 %. Ths crystal belongs to P622 space group
 and it is not twinned. The water content is 68%. I loweredthe  multiplicity
 to 4.1 by excluding few images but still the Rsym is  200 % and I/sigmaI 
 2.0. My rudimentary crystallography knowledge makes me believe it's quite Ok
 to use data upto 2.8 A and report the statistics. Could I request people's
 views. Thanks very much.
 Narayan


Re: [ccp4bb] resolution limit

2012-07-18 Thread Edward A. Berry

narayan viswam wrote:

Hello CCP4ers,
  In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI 2.5  Rsym 
224.3 %
for multiplicity 7.8 and completeness 98.2 %. I solved the structure by MAD  
refined it
to Rfree 27.3 %. Ths crystal belongs to P622 space group and it is not twinned. 
The water
content is 68%. I loweredthe  multiplicity to 4.1 by excluding few images but 
still the
Rsym is  200 % and I/sigmaI  2.0. My rudimentary crystallography knowledge 
makes me
believe it's quite Ok to use data upto 2.8 A and report the statistics. Could I 
request
people's views. Thanks very much.
Narayan


After refinement, what is R-free in the last shell? If it is significantly 
better
than random, say around .4 or less, that could be taken as evidence that there
is data in the last shell.
Also check the error model- Rsym 2 sort of implies the error is greater than
the signal, so I/sigI 2 seems surprising.
eab


Re: [ccp4bb] resolution limit

2012-07-18 Thread Edwin Pozharski


As has been shown recently (and discussed on this board), Rsym is not the
best measure of data quality (if any measure at all):

http://www.sciencemag.org/content/336/6084/1030.abstract


 narayan viswam wrote:
 Hello CCP4ers,
  
In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI 2.5

 Rsym 224.3 %
 for multiplicity 7.8 and
completeness 98.2 %. I solved the structure by
 MAD 
refined it
 to Rfree 27.3 %. Ths crystal belongs to P622
space group and it is not
 twinned. The water

content is 68%. I loweredthe  multiplicity to 4.1 by excluding few
 images but still the
 Rsym is  200 % and
I/sigmaI  2.0. My rudimentary crystallography
 knowledge
makes me
 believe it's quite Ok to use data upto 2.8 A and
report the statistics.
 Could I request

people's views. Thanks very much.
 Narayan
 
 After refinement, what is R-free in the last shell? If it is
significantly
 better
 than random, say around .4 or
less, that could be taken as evidence that
 there
 is
data in the last shell.
 Also check the error model- Rsym 2
sort of implies the error is greater
 than
 the signal,
so I/sigI 2 seems surprising.
 eab
 


--

Edwin Pozharski, PhD
University of Maryland, Baltimore


Re: [ccp4bb] resolution limit

2012-07-18 Thread Edwin Pozharski


http://www.ysbl.york.ac.uk/ccp4bb/2001/msg00383.html



Rsym...what's that?
 
 JPK
 
 On Wed,
Jul 18, 2012 at 9:12 AM, Edwin Pozharski

epozh...@umaryland.eduwrote:
 
 As has been
shown recently (and discussed on this board), Rsym is not

the
 best measure of data quality (if any measure at all):


http://www.sciencemag.org/content/336/6084/1030.abstract



  narayan viswam wrote:
  Hello CCP4ers,
  In my data, the
highest reolution shell 2.8-3.0 A has I/sigmaI 2.5 

 Rsym 224.3 %
  for multiplicity 7.8 and
completeness 98.2 %. I solved the structure
 by

 MAD  refined it
  to Rfree 27.3 %. Ths
crystal belongs to P622 space group and it is
 not
  twinned. The water
  content is
68%. I loweredthe multiplicity to 4.1 by excluding few

 images but still the
  Rsym is  200 %
and I/sigmaI  2.0. My rudimentary crystallography

 knowledge makes me
  believe it's quite Ok
to use data upto 2.8 A and report the
 statistics.
  Could I request
  people's views.
Thanks very much.
  Narayan
 
  After refinement, what is R-free in the last shell? If it
is
 significantly
  better

 than random, say around .4 or less, that could be taken as
evidence
 that
  there
  is
data in the last shell.
  Also check the error model-
Rsym 2 sort of implies the error is
 greater
  than
  the signal, so I/sigI 2 seems
surprising.
  eab
 


 --
 Edwin Pozharski, PhD
 University of Maryland, Baltimore
 
 
 
 
 --

***
 Jacob Pearson
Keller
 Northwestern University
 Medical Scientist
Training Program
 email: j-kell...@northwestern.edu

***
 


--

Edwin Pozharski, PhD
University of Maryland, Baltimore


Re: [ccp4bb] resolution limit

2012-07-18 Thread Jacob Keller
I was [too] obliquely alluding to this thread...

http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg27056.html

JPK



On Wed, Jul 18, 2012 at 12:32 PM, Edwin Pozharski epozh...@umaryland.eduwrote:

 http://www.ysbl.york.ac.uk/ccp4bb/2001/msg00383.html



  Rsym...what's that?
 
  JPK
 
  On Wed, Jul 18, 2012 at 9:12 AM, Edwin Pozharski
  epozh...@umaryland.eduwrote:
 
  As has been shown recently (and discussed on this board), Rsym is not
  the
  best measure of data quality (if any measure at all):
 
  http://www.sciencemag.org/content/336/6084/1030.abstract
 
 
 
   narayan viswam wrote:
   Hello CCP4ers,
   In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI 2.5 
   Rsym 224.3 %
   for multiplicity 7.8 and completeness 98.2 %. I solved the structure
  by
   MAD  refined it
   to Rfree 27.3 %. Ths crystal belongs to P622 space group and it is
  not
   twinned. The water
   content is 68%. I loweredthe multiplicity to 4.1 by excluding few
   images but still the
   Rsym is  200 % and I/sigmaI  2.0. My rudimentary crystallography
   knowledge makes me
   believe it's quite Ok to use data upto 2.8 A and report the
  statistics.
   Could I request
   people's views. Thanks very much.
   Narayan
  
   After refinement, what is R-free in the last shell? If it is
  significantly
   better
   than random, say around .4 or less, that could be taken as evidence
  that
   there
   is data in the last shell.
   Also check the error model- Rsym 2 sort of implies the error is
  greater
   than
   the signal, so I/sigI 2 seems surprising.
   eab
  
 
 
  --
  Edwin Pozharski, PhD
  University of Maryland, Baltimore
 
 
 
 
  --
  ***
  Jacob Pearson Keller
  Northwestern University
  Medical Scientist Training Program
  email: j-kell...@northwestern.edu
  ***
 


 --
 Edwin Pozharski, PhD
 University of Maryland, Baltimore




-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***


Re: [ccp4bb] resolution limit stuck in Refmac5

2010-11-01 Thread Roberto Steiner

Hi Jon
On 30 Oct 2010, at 00:46, Tom Huxford wrote:


Hi all,

I'm working with good quality relatively complete x-ray diffraction
data collected to a resolution limit 2.6 Å from a crystal of a protein
with a small molecule ligand bound.  I ran MR from 10-4 Å and then did
maximum likelihood rigid body refinement in Refmac5 against data from
50-3.5 Å.  Now I would like to run restrained refinement from 50-3 Å.
The reason for doing this is that, in order to minimize the divergence
between R-cryst and R-free during refinement my advisor who, by the
way, is forwarding this e-mail for me (and editing it so please don't
bash him too mercilessly) suggested I first build in the ligand and
newly positioned polypeptide loops and refine against data at a lower
resolution limit before opening it up to all the available data.


I personally would not first build in the ligand and refine against  
low res data...

Assuming the ligand is what you're after, I would:
(a) leave the ligand out of the time being
(b) refine the model using all data
(c) build the ligand in
(d) refine the model using all data

I'm not clear why doing restrained refinement using limited data first  
should help..



Apparently this has worked well for him in the past (and it has!).   
The

problem is that I'm to the point where I'd like to extend the
resolution down to 3 Å during restrained refinement but even if I set
the range from 50-3 Å in the ccp4i window refinement only happens from
50-3.5 Å.  If I take a step back and do the rigid body refinement from
50-3 Å and then carry out restrained refinement from 50-3 Å it works
fine.  Why would the limits imposed by rigid body refinement cause the
subsequent restrained refinement to be stuck at the rigid body
refinement's resolution limits?


Are you using the original reflection file?

Best
Roberto



Thanks for any thoughts,

Jon Fleming
Graduate Student
Structural Biochemistry Laboratory (Huxford Lab)
Department of Chemistry  Biochemistry
San Diego State University


---
Dr. Roberto Steiner
Randall Division of Cell and Molecular Biophysics
New Hunt's House
King's College London
Guy's Campus
London, SE1 1UL
Phone +44 (0)20-7848-8216
Fax   +44 (0)20-7848-6435
e-mail roberto.stei...@kcl.ac.uk


Re: [ccp4bb] resolution limit stuck in Refmac5

2010-10-29 Thread Nat Echols
On Fri, Oct 29, 2010 at 5:46 PM, Tom Huxford thuxf...@sciences.sdsu.eduwrote:

 I'm working with good quality relatively complete x-ray diffraction data
 collected to a resolution limit 2.6 Å from a crystal of a protein with a
 small molecule ligand bound.  I ran MR from 10-4 Å and then did maximum
 likelihood rigid body refinement in Refmac5 against data from 50-3.5 Å.  Now
 I would like to run restrained refinement from 50-3 Å.  The reason for doing
 this is that, in order to minimize the divergence between R-cryst and R-free
 during refinement my advisor who, by the way, is forwarding this e-mail for
 me (and editing it so please don't bash him too mercilessly) suggested I
 first build in the ligand and newly positioned polypeptide loops and refine
 against data at a lower resolution limit before opening it up to all the
 available data.  Apparently this has worked well for him in the past (and it
 has!).  The problem is that I'm to the point where I'd like to extend the
 resolution down to 3 Å during restrained refinement but even if I set the
 range from 50-3 Å in the ccp4i window refinement only happens from 50-3.5
 Å.  If I take a step back and do the rigid body refinement from 50-3 Å and
 then carry out restrained refinement from 50-3 Å it works fine.  Why would
 the limits imposed by rigid body refinement cause the subsequent restrained
 refinement to be stuck at the rigid body refinement's resolution limits?


Did you refine against the file output by Refmac after rigid-body
refinement, instead of using the original reflections?

-Nat