Re: [ccp4bb] Comparison of Water Positions across PDBs
Hmmm..does that mean that the journals are now the ultimate authority of what stays in the PDB? I find this slightly irritating and worthy of change. Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nat Echols Sent: Dienstag, 5. November 2013 15:09 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs On Tue, Nov 5, 2013 at 12:22 AM, Bernhard Rupp hofkristall...@gmail.com wrote: Given their otherwise almost paranoid sensitivity to ultimate author authority (resulting in things like still having 2hr0 etc in the bank because certain authors go AWOL or ignore major issues) In defense of the PDB, it's not just the authors who went AWOL in that case - it is ultimately the responsibility of the journals to retract clearly fraudulent publications. -Nat
[ccp4bb] Joint CCP4-6.4.0 and ARP/wARP-7.4 Update
Dear CCP4 Users An update for the CCP4-6.4.0 series has just been released. This is the first update for both CCP4 and ARP/wARP in tandem. The ARP/wARP component of this update will be available to those Mac and Linux users who have previously installed both packages via the CCP4 Package manager or from the joint bundle downloaded from CCP4 web-site. A standalone ARP/wARP package including the current update can be downloaded from the EMBL-Hamburg site at www.arp-warp.orghttp://www.arp-warp.org/. The following changes will be applied to the ARP/wARP installation: • The use of non-crystallographic symmetry for protein chain tracing has been enabled (it was accidentally disabled in version 7.4). • The `SAD refinement protocol' (Murshudov et al 2011) has undergone many fixes and now works well. • The routine for ligand identification has been made faster and some small bugs have been fixed. • A few bugs have been fixed in the ARP/wARP installer and shell-specific problems sometimes occurring on Linux should now be cured. • The manual has been updated. The following changes will be applied to the CCP4-6.4.0 installation: • MrBUMP (all): a new option of model re-building after SHELXE; a fix for phaser_sculptor dispatcher. • Xia2 (windows): update to release 0.3.6.3 (fixes ctruncate issue). • aimless (all): bug fixes. • pointless (all): bug fixes. • ViewHKL (all): additional visual control to enhance weak reflections and bug fixes. • truncate (Mac): Fixed harvesting option of old truncate. • Molrep: New interface. • Update (all): Increased maximum waiting time for background update check in ccp4i. Andrey Lebedev -- Scanned by iCritical.
Re: [ccp4bb] Joint CCP4-6.4.0 and ARP/wARP-7.4 Update
Hi,
I just installed the update using ccp4um.
All I get now is:
ccp4i
Def file /software/ccp4-6.4.0/share/ccp4i/etc/unix/configure.def
does not have correct file label configure
Def file /software/ccp4-6.4.0/share/ccp4i/etc/preferences.def.dist
does not have correct file label preferences
Error in startup script: can't read array(MAPVIEWER_DEFAULT): no such element
in array
while executing
set viewercmd $array(MAPVIEWER_DEFAULT)
(procedure set_default_mapviewer line 9)
invoked from within
set_default_mapviewer $arrayname
(preferences arm line 2)
invoked from within
switch -- $taskname {
directories {
catch {update_defdir_menu $arrayname}
} configure {
# We over-write the user TYPEDEF_LIST with...
(procedure InitialisePreferences line 113)
invoked from within
InitialisePreferences preferences preferences
(file /software/ccp4-6.4.0/share/ccp4i/bin/ccp4i.tcl line 128)
invoked from within
source [file join $env(CCP4I_TOP) bin ccp4i.tcl]
(file /software/ccp4-6.4.0/bin/ccp4i line 12)
What went wrong?
Am 06.11.2013 um 13:52 schrieb Andrey Lebedev andrey.lebe...@stfc.ac.uk:
Dear CCP4 Users
An update for the CCP4-6.4.0 series has just been released. This is the first
update for both CCP4 and ARP/wARP in tandem.
The ARP/wARP component of this update will be available to those Mac and
Linux users who have previously installed both packages via the CCP4 Package
manager or from the joint bundle downloaded from CCP4 web-site. A standalone
ARP/wARP package including the current update can be downloaded from the
EMBL-Hamburg site at www.arp-warp.orghttp://www.arp-warp.org/.
The following changes will be applied to the ARP/wARP installation:
• The use of non-crystallographic symmetry for protein chain tracing has been
enabled (it was accidentally disabled in version 7.4).
• The `SAD refinement protocol' (Murshudov et al 2011) has undergone many
fixes and now works well.
• The routine for ligand identification has been made faster and some small
bugs have been fixed.
• A few bugs have been fixed in the ARP/wARP installer and shell-specific
problems sometimes occurring on Linux should now be cured.
• The manual has been updated.
The following changes will be applied to the CCP4-6.4.0 installation:
• MrBUMP (all): a new option of model re-building after SHELXE; a fix for
phaser_sculptor dispatcher.
• Xia2 (windows): update to release 0.3.6.3 (fixes ctruncate issue).
• aimless (all): bug fixes.
• pointless (all): bug fixes.
• ViewHKL (all): additional visual control to enhance weak reflections and
bug fixes.
• truncate (Mac): Fixed harvesting option of old truncate.
• Molrep: New interface.
• Update (all): Increased maximum waiting time for background update check in
ccp4i.
Andrey Lebedev
--
Scanned by iCritical.
Mit freundlichen Grüßen
Joachim Reichelt
Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124
Braunschweig | www.helmholtz-hzi.de
Das HZI ist seit 2007 zertifiziertes Mitglied im audit berufundfamilie
Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe,
Bundesministerium für Bildung und Forschung
Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches Ministerium
für Wissenschaft und Kultur
Geschäftsführung: Prof. Dr. Dirk Heinz; Dr. Michael Strätz
Gesellschaft mit beschränkter Haftung (GmbH)
Sitz der Gesellschaft: Braunschweig
Handelsregister: Amtsgericht Braunschweig, HRB 477
Re: [ccp4bb] Joint CCP4-6.4.0 and ARP/wARP-7.4 Update
Hi Joachim
Thanks for reporting the problem
Please run
sudo /software/ccp4-6.4.0/bin/ccp4um
and uninstall the last update for now.
There should be something wrong with your config files.
I'll trace what it could be and then contact you.
Regards
Andrey
On 6 Nov 2013, at 13:13, Joachim Reichelt wrote:
Hi,
I just installed the update using ccp4um.
All I get now is:
ccp4i
Def file /software/ccp4-6.4.0/share/ccp4i/etc/unix/configure.def
does not have correct file label configure
Def file /software/ccp4-6.4.0/share/ccp4i/etc/preferences.def.dist
does not have correct file label preferences
Error in startup script: can't read array(MAPVIEWER_DEFAULT): no such
element in array
while executing
set viewercmd $array(MAPVIEWER_DEFAULT)
(procedure set_default_mapviewer line 9)
invoked from within
set_default_mapviewer $arrayname
(preferences arm line 2)
invoked from within
switch -- $taskname {
directories {
catch {update_defdir_menu $arrayname}
} configure {
# We over-write the user TYPEDEF_LIST with...
(procedure InitialisePreferences line 113)
invoked from within
InitialisePreferences preferences preferences
(file /software/ccp4-6.4.0/share/ccp4i/bin/ccp4i.tcl line 128)
invoked from within
source [file join $env(CCP4I_TOP) bin ccp4i.tcl]
(file /software/ccp4-6.4.0/bin/ccp4i line 12)
What went wrong?
Am 06.11.2013 um 13:52 schrieb Andrey Lebedev andrey.lebe...@stfc.ac.uk:
Dear CCP4 Users
An update for the CCP4-6.4.0 series has just been released. This is the
first update for both CCP4 and ARP/wARP in tandem.
The ARP/wARP component of this update will be available to those Mac and
Linux users who have previously installed both packages via the CCP4 Package
manager or from the joint bundle downloaded from CCP4 web-site. A standalone
ARP/wARP package including the current update can be downloaded from the
EMBL-Hamburg site at www.arp-warp.orghttp://www.arp-warp.org/.
The following changes will be applied to the ARP/wARP installation:
• The use of non-crystallographic symmetry for protein chain tracing has
been enabled (it was accidentally disabled in version 7.4).
• The `SAD refinement protocol' (Murshudov et al 2011) has undergone many
fixes and now works well.
• The routine for ligand identification has been made faster and some small
bugs have been fixed.
• A few bugs have been fixed in the ARP/wARP installer and shell-specific
problems sometimes occurring on Linux should now be cured.
• The manual has been updated.
The following changes will be applied to the CCP4-6.4.0 installation:
• MrBUMP (all): a new option of model re-building after SHELXE; a fix for
phaser_sculptor dispatcher.
• Xia2 (windows): update to release 0.3.6.3 (fixes ctruncate issue).
• aimless (all): bug fixes.
• pointless (all): bug fixes.
• ViewHKL (all): additional visual control to enhance weak reflections and
bug fixes.
• truncate (Mac): Fixed harvesting option of old truncate.
• Molrep: New interface.
• Update (all): Increased maximum waiting time for background update check
in ccp4i.
Andrey Lebedev
--
Scanned by iCritical.
Mit freundlichen Grüßen
Joachim Reichelt
Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124
Braunschweig | www.helmholtz-hzi.de
Das HZI ist seit 2007 zertifiziertes Mitglied im audit berufundfamilie
Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe,
Bundesministerium für Bildung und Forschung
Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches
Ministerium für Wissenschaft und Kultur
Geschäftsführung: Prof. Dr. Dirk Heinz; Dr. Michael Strätz
Gesellschaft mit beschränkter Haftung (GmbH)
Sitz der Gesellschaft: Braunschweig
Handelsregister: Amtsgericht Braunschweig, HRB 477
--
Scanned by iCritical.
Re: [ccp4bb] Joint CCP4-6.4.0 and ARP/wARP-7.4 Update
Dear all
If you had a problem similar to that Joachim and Ingo had (see below), please
run
sudo path/ccp4-6.4.0/bin/ccp4um
where path is the full path to your ccp4-6.4.0 installation,
and uninstall the last update.
Then you can launch ccp4i and install it again as usual.
Thanks!
Andrey
On 6 Nov 2013, at 13:13, Joachim Reichelt wrote:
Hi,
I just installed the update using ccp4um.
All I get now is:
ccp4i
Def file /software/ccp4-6.4.0/share/ccp4i/etc/unix/configure.def
does not have correct file label configure
Def file /software/ccp4-6.4.0/share/ccp4i/etc/preferences.def.dist
does not have correct file label preferences
Error in startup script: can't read array(MAPVIEWER_DEFAULT): no such
element in array
while executing
set viewercmd $array(MAPVIEWER_DEFAULT)
(procedure set_default_mapviewer line 9)
invoked from within
set_default_mapviewer $arrayname
(preferences arm line 2)
invoked from within
switch -- $taskname {
directories {
catch {update_defdir_menu $arrayname}
} configure {
# We over-write the user TYPEDEF_LIST with...
(procedure InitialisePreferences line 113)
invoked from within
InitialisePreferences preferences preferences
(file /software/ccp4-6.4.0/share/ccp4i/bin/ccp4i.tcl line 128)
invoked from within
source [file join $env(CCP4I_TOP) bin ccp4i.tcl]
(file /software/ccp4-6.4.0/bin/ccp4i line 12)
What went wrong?
Am 06.11.2013 um 13:52 schrieb Andrey Lebedev andrey.lebe...@stfc.ac.uk:
Dear CCP4 Users
An update for the CCP4-6.4.0 series has just been released. This is the
first update for both CCP4 and ARP/wARP in tandem.
The ARP/wARP component of this update will be available to those Mac and
Linux users who have previously installed both packages via the CCP4 Package
manager or from the joint bundle downloaded from CCP4 web-site. A standalone
ARP/wARP package including the current update can be downloaded from the
EMBL-Hamburg site at www.arp-warp.orghttp://www.arp-warp.org/.
The following changes will be applied to the ARP/wARP installation:
• The use of non-crystallographic symmetry for protein chain tracing has
been enabled (it was accidentally disabled in version 7.4).
• The `SAD refinement protocol' (Murshudov et al 2011) has undergone many
fixes and now works well.
• The routine for ligand identification has been made faster and some small
bugs have been fixed.
• A few bugs have been fixed in the ARP/wARP installer and shell-specific
problems sometimes occurring on Linux should now be cured.
• The manual has been updated.
The following changes will be applied to the CCP4-6.4.0 installation:
• MrBUMP (all): a new option of model re-building after SHELXE; a fix for
phaser_sculptor dispatcher.
• Xia2 (windows): update to release 0.3.6.3 (fixes ctruncate issue).
• aimless (all): bug fixes.
• pointless (all): bug fixes.
• ViewHKL (all): additional visual control to enhance weak reflections and
bug fixes.
• truncate (Mac): Fixed harvesting option of old truncate.
• Molrep: New interface.
• Update (all): Increased maximum waiting time for background update check
in ccp4i.
Andrey Lebedev
--
Scanned by iCritical.
Mit freundlichen Grüßen
Joachim Reichelt
Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124
Braunschweig | www.helmholtz-hzi.de
Das HZI ist seit 2007 zertifiziertes Mitglied im audit berufundfamilie
Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe,
Bundesministerium für Bildung und Forschung
Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches
Ministerium für Wissenschaft und Kultur
Geschäftsführung: Prof. Dr. Dirk Heinz; Dr. Michael Strätz
Gesellschaft mit beschränkter Haftung (GmbH)
Sitz der Gesellschaft: Braunschweig
Handelsregister: Amtsgericht Braunschweig, HRB 477
--
Scanned by iCritical.
Re: [ccp4bb] Joint CCP4-6.4.0 and ARP/wARP-7.4 Update
Dear all
A comment to my last e-mail
If your ccp4 installation is not write-protected,
do not use sudo, just run
ccp4um
Regards
Andrey
On 6 Nov 2013, at 14:49, Lebedev, Andrey (STFC,RAL,SC) wrote:
Dear all
If you had a problem similar to that Joachim and Ingo had (see below), please
run
sudo path/ccp4-6.4.0/bin/ccp4um
where path is the full path to your ccp4-6.4.0 installation,
and uninstall the last update.
Then you can launch ccp4i and install it again as usual.
Thanks!
Andrey
On 6 Nov 2013, at 13:13, Joachim Reichelt wrote:
Hi,
I just installed the update using ccp4um.
All I get now is:
ccp4i
Def file /software/ccp4-6.4.0/share/ccp4i/etc/unix/configure.def
does not have correct file label configure
Def file /software/ccp4-6.4.0/share/ccp4i/etc/preferences.def.dist
does not have correct file label preferences
Error in startup script: can't read array(MAPVIEWER_DEFAULT): no such
element in array
while executing
set viewercmd $array(MAPVIEWER_DEFAULT)
(procedure set_default_mapviewer line 9)
invoked from within
set_default_mapviewer $arrayname
(preferences arm line 2)
invoked from within
switch -- $taskname {
directories {
catch {update_defdir_menu $arrayname}
} configure {
# We over-write the user TYPEDEF_LIST with...
(procedure InitialisePreferences line 113)
invoked from within
InitialisePreferences preferences preferences
(file /software/ccp4-6.4.0/share/ccp4i/bin/ccp4i.tcl line 128)
invoked from within
source [file join $env(CCP4I_TOP) bin ccp4i.tcl]
(file /software/ccp4-6.4.0/bin/ccp4i line 12)
What went wrong?
Am 06.11.2013 um 13:52 schrieb Andrey Lebedev andrey.lebe...@stfc.ac.uk:
Dear CCP4 Users
An update for the CCP4-6.4.0 series has just been released. This is the
first update for both CCP4 and ARP/wARP in tandem.
The ARP/wARP component of this update will be available to those Mac and
Linux users who have previously installed both packages via the CCP4
Package manager or from the joint bundle downloaded from CCP4 web-site. A
standalone ARP/wARP package including the current update can be downloaded
from the EMBL-Hamburg site at www.arp-warp.orghttp://www.arp-warp.org/.
The following changes will be applied to the ARP/wARP installation:
• The use of non-crystallographic symmetry for protein chain tracing has
been enabled (it was accidentally disabled in version 7.4).
• The `SAD refinement protocol' (Murshudov et al 2011) has undergone many
fixes and now works well.
• The routine for ligand identification has been made faster and some small
bugs have been fixed.
• A few bugs have been fixed in the ARP/wARP installer and shell-specific
problems sometimes occurring on Linux should now be cured.
• The manual has been updated.
The following changes will be applied to the CCP4-6.4.0 installation:
• MrBUMP (all): a new option of model re-building after SHELXE; a fix for
phaser_sculptor dispatcher.
• Xia2 (windows): update to release 0.3.6.3 (fixes ctruncate issue).
• aimless (all): bug fixes.
• pointless (all): bug fixes.
• ViewHKL (all): additional visual control to enhance weak reflections and
bug fixes.
• truncate (Mac): Fixed harvesting option of old truncate.
• Molrep: New interface.
• Update (all): Increased maximum waiting time for background update check
in ccp4i.
Andrey Lebedev
--
Scanned by iCritical.
Mit freundlichen Grüßen
Joachim Reichelt
Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124
Braunschweig | www.helmholtz-hzi.de
Das HZI ist seit 2007 zertifiziertes Mitglied im audit berufundfamilie
Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe,
Bundesministerium für Bildung und Forschung
Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches
Ministerium für Wissenschaft und Kultur
Geschäftsführung: Prof. Dr. Dirk Heinz; Dr. Michael Strätz
Gesellschaft mit beschränkter Haftung (GmbH)
Sitz der Gesellschaft: Braunschweig
Handelsregister: Amtsgericht Braunschweig, HRB 477
--
Scanned by iCritical.
Re: [ccp4bb] Joint CCP4-6.4.0 and ARP/wARP-7.4 Update
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Andrey, since you mention the manual: is there a way to retrieve the manual pages for the ccp4 programs? I often use 'man pointless' et al. to check syntax etc and I miss the man pages in 6.4.0. Even the source does not seem to contain them any more. Best, Tim On 11/06/2013 01:52 PM, Andrey Lebedev wrote: Dear CCP4 Users An update for the CCP4-6.4.0 series has just been released. This is the first update for both CCP4 and ARP/wARP in tandem. The ARP/wARP component of this update will be available to those Mac and Linux users who have previously installed both packages via the CCP4 Package manager or from the joint bundle downloaded from CCP4 web-site. A standalone ARP/wARP package including the current update can be downloaded from the EMBL-Hamburg site at www.arp-warp.orghttp://www.arp-warp.org/. The following changes will be applied to the ARP/wARP installation: • The use of non-crystallographic symmetry for protein chain tracing has been enabled (it was accidentally disabled in version 7.4). • The `SAD refinement protocol' (Murshudov et al 2011) has undergone many fixes and now works well. • The routine for ligand identification has been made faster and some small bugs have been fixed. • A few bugs have been fixed in the ARP/wARP installer and shell-specific problems sometimes occurring on Linux should now be cured. • The manual has been updated. The following changes will be applied to the CCP4-6.4.0 installation: • MrBUMP (all): a new option of model re-building after SHELXE; a fix for phaser_sculptor dispatcher. • Xia2 (windows): update to release 0.3.6.3 (fixes ctruncate issue). • aimless (all): bug fixes. • pointless (all): bug fixes. • ViewHKL (all): additional visual control to enhance weak reflections and bug fixes. • truncate (Mac): Fixed harvesting option of old truncate. • Molrep: New interface. • Update (all): Increased maximum waiting time for background update check in ccp4i. Andrey Lebedev - -- - -- 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 Icedove - http://www.enigmail.net/ iD8DBQFSeloAUxlJ7aRr7hoRAkmxAKCU6dqpZAjaUH0nWYnlsmAuaZ392QCeP74S ir8+bKdHF+t2eaPUfCAolnU= =ixyQ -END PGP SIGNATURE-
[ccp4bb] Off Topic: Formulatrix NT8 nanoliter-volume dispenser
Hi there: Has anyone got experience using the Formulatrix NT8 as a 'crystallization robot'? Other options being considered are Art Robbins Phoenix TTP Labtech's Mosquito, both of which I have used in the past. Any feedback on NT8 will be highly appreciated. Thanks and Regards, Dileep
[ccp4bb] uncertainites associated with intensities from twinned crystals
Dear ccp4 users a question about the recovering of true intensities from merohedral twinned crystal. Providing alpha and the twin operator one should be able to recover the intensities from the formulas: I(h1) = (1-α)Iobs(h1)-αIobs(h2)/(1-2α) I(h2) = -αIobs(h1)+(1+α)Iobs(h2)/(1-2α) as stated in many papers and books*. However I was wondering about the uncertainties associated to these measurements, I mean: for all physical observable an uncertainty should be given. Hence, what is the uncertainty associated to a perfect merohedrally twinned crystal (alpha=0.5)? It is clear that in this case we drop in a singular value of the above formulas. Please, let me know your hints or your concerns on the matter. Probably there is something that it is not so clear to me. Thanks in advance Fulvio ref. **(C. Giacovazzo, H. L. Monaco, G. Artioli, D. Viterbo, M. Milaneso, G. Ferraris, G. Gilli, P. Gilli, G. Zanotti and M. Catti. Fundamentals of Crystallography, 3rd edition. IUCr Texts on Crystallography No. 15, IUCr/Oxford University Press, 2011; Chandra, N., Acharya, K. R., Moody, P. C. (1999). /Acta Cryst./ *D*55. 1750-1758) -- Fulvio Saccoccia, PhD Dept. of Biochemical Sciences A. Rossi Fanelli Sapienza University of Rome Tel. +39 0649910556
Re: [ccp4bb] Comparison of Water Positions across PDBs
On Wed, Nov 6, 2013 at 12:39 AM, Bernhard Rupp hofkristall...@gmail.comwrote: Hmmm….does that mean that the journals are now the ultimate authority of what stays in the PDB? I find this slightly irritating and worthy of change. http://www.wwpdb.org/UAB.html It is the current wwPDB (Worldwide PDB) policy that entries can be made obsolete following a request from the people responsible for publishing it (be it the principal author or journal editors). I'm not sure I understand why things should be any different; the PDB is not advertising itself as anything other than an archival service, unlike the journals which are supposed to be our primary mechanism of quality control. -Nat
[ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals
Dear Fulvio, you cannot detwin perfectly twinned data with this formula. The term (1-2α) becomes zero, so you are dividing by zero. With good refinement programs (ShelX, Refmac), refinement is done against twinned data, which is better than to detwin the data with the formula you mention. As I understand it, to get map coefficients, the calculated contribution of the twin domain (Fcalc’s) is substracted from Fobs (with the appropriate weighting factors), so what you see in coot is detwinned electron density. In practical terms, the only thing you have to do is to specify the TWIN keyword in Refmac. Best regards, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Fulvio Saccoccia Gesendet: Mittwoch, 6. November 2013 16:58 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] uncertainites associated with intensities from twinned crystals Dear ccp4 users a question about the recovering of true intensities from merohedral twinned crystal. Providing alpha and the twin operator one should be able to recover the intensities from the formulas: I(h1) = (1-α)Iobs(h1)-αIobs(h2)/(1-2α) I(h2) = -αIobs(h1)+(1+α)Iobs(h2)/(1-2α) as stated in many papers and books*. However I was wondering about the uncertainties associated to these measurements, I mean: for all physical observable an uncertainty should be given. Hence, what is the uncertainty associated to a perfect merohedrally twinned crystal (alpha=0.5)? It is clear that in this case we drop in a singular value of the above formulas. Please, let me know your hints or your concerns on the matter. Probably there is something that it is not so clear to me. Thanks in advance Fulvio ref. **(C. Giacovazzo, H. L. Monaco, G. Artioli, D. Viterbo, M. Milaneso, G. Ferraris, G. Gilli, P. Gilli, G. Zanotti and M. Catti. Fundamentals of Crystallography, 3rd edition. IUCr Texts on Crystallography No. 15, IUCr/Oxford University Press, 2011; Chandra, N., Acharya, K. R., Moody, P. C. (1999). Acta Cryst. D55. 1750-1758) -- Fulvio Saccoccia, PhD Dept. of Biochemical Sciences A. Rossi Fanelli Sapienza University of Rome Tel. +39 0649910556
Re: [ccp4bb] Comparison of Water Positions across PDBs
I've remained silent as this thread evolved into a discussion of how the PDB deals with water names and numbers. But Nat's comment about the PDB not advertising itself as anything other than an archival service finally prodded me into saying something. Something I've slowly come to realize is that the PDB, while it started as an archive, has developed into a working database. That's why they (the PDB workers/organizers/managers) have gotten into this mode where they change things from the original deposited files. I learned several years ago that the PDB is willing to change the atom names in a ligand from those previously used in the published literature. This was done in the name of consistency and essentially made the PDB files into database entries, rather than archival files since the atom names no longer matched the atom names used in the papers. Given the difficulties I had in discussing this with the annotaters, I've come to realize that as soon as I hit the submit button on a PDB submission, I've lost control over what will appear in the distributed file. In a way, it's been liberating to reach that point. It reduces my sense of responsibility for the contents of the file. Ron On Wed, 6 Nov 2013, Nat Echols wrote: On Wed, Nov 6, 2013 at 12:39 AM, Bernhard Rupp hofkristall...@gmail.com wrote: Hmmm….does that mean that the journals are now the ultimate authority of what stays in the PDB? I find this slightly irritating and worthy of change. http://www.wwpdb.org/UAB.html It is the current wwPDB (Worldwide PDB) policy that entries can be made obsolete following a request from the people responsible for publishing it (be it the principal author or journal editors). I'm not sure I understand why things should be any different; the PDB is not advertising itself as anything other than an archival service, unlike the journals which are supposed to be our primary mechanism of quality control. -Nat
[ccp4bb] R: [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals
Thank you for reply. My question mostly concern a theoretical aspect rather than practical one. To be not misunderstood, what is the mathematical model that one should apply to be able to deal with twinned intensities with their errors? I mean, I+_what? I ask this In order to state some general consideration on the accuracy about the recovery the true intensities on varying of alpha. Thanks Fulvio Fulvio Saccoccia PhD Dept. of Biochemical Sciences Sapienza University of Rome 5, Piazzale A. Moro 00185 phone +39 0649910556 Messaggio Originale Da: herman.schreu...@sanofi.com Inviato: 06/11/2013, 17:25 A: CCP4BB@JISCMAIL.AC.UK Oggetto: [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals Dear Fulvio, you cannot detwin perfectly twinned data with this formula. The term (1-2α) becomes zero, so you are dividing by zero. With good refinement programs (ShelX, Refmac), refinement is done against twinned data, which is better than to detwin the data with the formula you mention. As I understand it, to get map coefficients, the calculated contribution of the twin domain (Fcalc’s) is substracted from Fobs (with the appropriate weighting factors), so what you see in coot is detwinned electron density. In practical terms, the only thing you have to do is to specify the TWIN keyword in Refmac. Best regards, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Fulvio Saccoccia Gesendet: Mittwoch, 6. November 2013 16:58 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] uncertainites associated with intensities from twinned crystals Dear ccp4 users a question about the recovering of true intensities from merohedral twinned crystal. Providing alpha and the twin operator one should be able to recover the intensities from the formulas: I(h1) = (1-α)Iobs(h1)-αIobs(h2)/(1-2α) I(h2) = -αIobs(h1)+(1+α)Iobs(h2)/(1-2α) as stated in many papers and books*. However I was wondering about the uncertainties associated to these measurements, I mean: for all physical observable an uncertainty should be given. Hence, what is the uncertainty associated to a perfect merohedrally twinned crystal (alpha=0.5)? It is clear that in this case we drop in a singular value of the above formulas. Please, let me know your hints or your concerns on the matter. Probably there is something that it is not so clear to me. Thanks in advance Fulvio ref. **(C. Giacovazzo, H. L. Monaco, G. Artioli, D. Viterbo, M. Milaneso, G. Ferraris, G. Gilli, P. Gilli, G. Zanotti and M. Catti. Fundamentals of Crystallography, 3rd edition. IUCr Texts on Crystallography No. 15, IUCr/Oxford University Press, 2011; Chandra, N., Acharya, K. R., Moody, P. C. (1999). Acta Cryst. D55. 1750-1758) -- Fulvio Saccoccia, PhD Dept. of Biochemical Sciences A. Rossi Fanelli Sapienza University of Rome Tel. +39 0649910556
[ccp4bb] Error using Coot supplied with CCP4
Dear CCP4 / Coot community, I am trying to use LIDIA from Coot 0.7.2 - as supplied with CCP4-6.4.0 - to look at a protein / ligand complex. However, when trying to launch LIDIA from the Extensions menu of Coot - I get the following error. I guess this suggests some form of fortran compile error? Any help would be gratefully received. Antony. (write-pdb-file 12 coot-ccp4/tmp-residue-for-prodrg.pdb) arg_list ['XYZIN', 'coot-ccp4/tmp-residue-for-prodrg.pdb', 'MOLOUT', 'coot-ccp4/.coot-to-lbg-mol', 'XYZOUT', 'coot-ccp4/.coot-to-lbg-pdb', 'LIBOUT', 'coot-ccp4/.coot-to-lbg-lib'] forrtl: severe (180): SIGBUS, bus error occurred Image PCRoutineLineSource cprodrg000113FC Unknown Unknown Unknown cprodrg000111AC Unknown Unknown Unknown cprodrg00011164 Unknown Unknown Unknown # BFONT COLOR=#FF!--SUMMARY_BEGIN-- # html !-- CCP4 HTML LOGFILE -- # hr # !--SUMMARY_END--/FONT/B # BFONT COLOR=#FF!--SUMMARY_BEGIN-- --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512
Re: [ccp4bb] Off Topic: Formulatrix NT8 nanoliter-volume dispenser
Hi Dileep, We have been a user of the NT8 robot going on a year now, and we're quite happy with it. The initial versions of the machine had a few problems, but engineers over at Formulatrix have worked out a majority of the bugs and the current version of the machine functions quite well. We use it mostly for sitting drop tray setups and for LCP crystallization - haven't attempted any hanging drop setups, but should work fine. My favorite feature of this machine is the humidity controlled chamber. You can set the humidity level within the chamber, and sensors keep the percent humidity within the user-specified range. It makes evaporation problems with LCP setups I've experienced in the past virtually non-existent. Customer service at Formulatrix has also been very quick to reply if anything ever does go wrong with the machine. Hope this helps. Cheers, Jim On Wed, Nov 6, 2013 at 6:53 AM, Dileep V vasudevandil...@gmail.com wrote: Hi there: Has anyone got experience using the Formulatrix NT8 as a 'crystallization robot'? Other options being considered are Art Robbins Phoenix TTP Labtech's Mosquito, both of which I have used in the past. Any feedback on NT8 will be highly appreciated. Thanks and Regards, Dileep -- Jim Fairman, Ph D. Crystal Core Leader I Emerald BioStructures http://www.emeraldbiostructures.com/ Tel: 206-780-8914 Cell: 240-479-6575 E-mail: fairman@gmail.com jfair...@embios.com
[ccp4bb] switching space group
Hi, I have a structure which should have space group P212121, but it has been processed to P21212. It can not be solved and refined. Right now I do not have HKL2000, but I need change the space group to P212121. Is there a way for me to do this using CCP4? Thank you, Maggie
Re: [ccp4bb] switching space group
Hi Maggie echo symm P212121 | mtzutils HKLIN in.mtz HKLOUT out.mtz should do the trick. Cheers -- Ian On 6 November 2013 18:13, MAGGIE dongmeij...@gmail.com wrote: Hi, I have a structure which should have space group P212121, but it has been processed to P21212. It can not be solved and refined. Right now I do not have HKL2000, but I need change the space group to P212121. Is there a way for me to do this using CCP4? Thank you, Maggie
Re: [ccp4bb] switching space group
Hi Maggie, you can re-process your data using XDS and can provide the desired space group in the XDS.INP file. It won't take much time. Vikrant Vikrant Upadhyay Postdoctoral associate Dr. Crina Nimigean's lab, A-1050 Department of Anesthesiology Weill Cornell Medical College 525 East 68th Street New York, NY 10065 On Nov 6, 2013, at 1:13 PM, MAGGIE dongmeij...@gmail.com wrote: Hi, I have a structure which should have space group P212121, but it has been processed to P21212. It can not be solved and refined. Right now I do not have HKL2000, but I need change the space group to P212121. Is there a way for me to do this using CCP4? Thank you, Maggie
Re: [ccp4bb] switching space group
If you're only changing the 2-fold axis along c to a 2-fold screw axis, you don't need to go back to the raw image files and reprocess them! Just tweak the header of the .sca file and carry on (and take notes on what you did). From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Vikrant Upadhyay [vikrant192...@gmail.com] Sent: Wednesday, November 06, 2013 5:13 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] switching space group Hi Maggie, you can re-process your data using XDS and can provide the desired space group in the XDS.INP file. It won't take much time. Vikrant Vikrant Upadhyay Postdoctoral associate Dr. Crina Nimigean's lab, A-1050 Department of Anesthesiology Weill Cornell Medical College 525 East 68th Street New York, NY 10065 On Nov 6, 2013, at 1:13 PM, MAGGIE dongmeij...@gmail.commailto:dongmeij...@gmail.com wrote: Hi, I have a structure which should have space group P212121, but it has been processed to P21212. It can not be solved and refined. Right now I do not have HKL2000, but I need change the space group to P212121. Is there a way for me to do this using CCP4? Thank you, Maggie
Re: [ccp4bb] switching space group
I liked Ian Tickle's 1-line ccp4 script for changing the space group with mtzutils. I believe CAD can do this also. In any case, there's no need to reprocess. Some reflections present in the current data will be systematically absent in the new space group, but presumably they will be eliminated in the process. Phoebe A. Rice wrote: If you're only changing the 2-fold axis along c to a 2-fold screw axis, you don't need to go back to the raw image files and reprocess them! Just tweak the header of the .sca file and carry on (and take notes on what you did). -- *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Vikrant Upadhyay [vikrant192...@gmail.com] *Sent:* Wednesday, November 06, 2013 5:13 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] switching space group Hi Maggie, you can re-process your data using XDS and can provide the desired space group in the XDS.INP file. It won't take much time. Vikrant Vikrant Upadhyay Postdoctoral associate Dr. Crina Nimigean's lab, A-1050 Department of Anesthesiology Weill Cornell Medical College 525 East 68th Street New York, NY 10065 On Nov 6, 2013, at 1:13 PM, MAGGIE dongmeij...@gmail.com mailto:dongmeij...@gmail.com wrote: Hi, I have a structure which should have space group P212121, but it has been processed to P21212. It can not be solved and refined. Right now I do not have HKL2000, but I need change the space group to P212121. Is there a way for me to do this using CCP4? Thank you, Maggie
Re: [ccp4bb] R: [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Fulvio, with simple error propagation, the error would be sigma(I(h1)) = (1-α)sigma(Iobs(h1))-α*sigma(Iobs(h2))/(1-2α) would it not? Although especially for theoretical aspects you should be concerned about division by zero. Best, Tim On 11/06/2013 05:54 PM, Fulvio Saccoccia wrote: Thank you for reply. My question mostly concern a theoretical aspect rather than practical one. To be not misunderstood, what is the mathematical model that one should apply to be able to deal with twinned intensities with their errors? I mean, I+_what? I ask this In order to state some general consideration on the accuracy about the recovery the true intensities on varying of alpha. Thanks Fulvio Fulvio Saccoccia PhD Dept. of Biochemical Sciences Sapienza University of Rome 5, Piazzale A. Moro 00185 phone +39 0649910556 Messaggio Originale Da: herman.schreu...@sanofi.com Inviato: 06/11/2013, 17:25 A: CCP4BB@JISCMAIL.AC.UK Oggetto: [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals Dear Fulvio, you cannot detwin perfectly twinned data with this formula. The term (1-2α) becomes zero, so you are dividing by zero. With good refinement programs (ShelX, Refmac), refinement is done against twinned data, which is better than to detwin the data with the formula you mention. As I understand it, to get map coefficients, the calculated contribution of the twin domain (Fcalc’s) is substracted from Fobs (with the appropriate weighting factors), so what you see in coot is detwinned electron density. In practical terms, the only thing you have to do is to specify the TWIN keyword in Refmac. Best regards, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Fulvio Saccoccia Gesendet: Mittwoch, 6. November 2013 16:58 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] uncertainites associated with intensities from twinned crystals Dear ccp4 users a question about the recovering of true intensities from merohedral twinned crystal. Providing alpha and the twin operator one should be able to recover the intensities from the formulas: I(h1) = (1-α)Iobs(h1)-αIobs(h2)/(1-2α) I(h2) = -αIobs(h1)+(1+α)Iobs(h2)/(1-2α) as stated in many papers and books*. However I was wondering about the uncertainties associated to these measurements, I mean: for all physical observable an uncertainty should be given. Hence, what is the uncertainty associated to a perfect merohedrally twinned crystal (alpha=0.5)? It is clear that in this case we drop in a singular value of the above formulas. Please, let me know your hints or your concerns on the matter. Probably there is something that it is not so clear to me. Thanks in advance Fulvio ref. **(C. Giacovazzo, H. L. Monaco, G. Artioli, D. Viterbo, M. Milaneso, G. Ferraris, G. Gilli, P. Gilli, G. Zanotti and M. Catti. Fundamentals of Crystallography, 3rd edition. IUCr Texts on Crystallography No. 15, IUCr/Oxford University Press, 2011; Chandra, N., Acharya, K. R., Moody, P. C. (1999). Acta Cryst. D55. 1750-1758) -- Fulvio Saccoccia, PhD Dept. of Biochemical Sciences A. Rossi Fanelli Sapienza University of Rome Tel. +39 0649910556 - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSewyuUxlJ7aRr7hoRAnP/AJ9biIGWJsHnbcQ4IaG5fusZTN0iOgCfR6bu 3po97EKDH98F881dH3CgD2M= =2QkU -END PGP SIGNATURE-
Re: [ccp4bb] switching space group
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Maggie, in addition to what others explained, data integration does not depend on the space group. It only depends on the Laue group, and P21212 and P212121 belong to the same Laue group. You would see no difference at all in reprocessing, and in this case Ian's suggestion is sufficient. When I am not sure whether or not changing the space group make any real difference to the data I like using pointless to set it right, or even run phaser if I do have a PDB-file. Cheers, Tim On 11/06/2013 07:13 PM, MAGGIE wrote: Hi, I have a structure which should have space group P212121, but it has been processed to P21212. It can not be solved and refined. Right now I do not have HKL2000, but I need change the space group to P212121. Is there a way for me to do this using CCP4? Thank you, Maggie - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSew/8UxlJ7aRr7hoRAsgsAKDCRrGiLW+jvKfFy3rDdnjYOWIMpgCfXSUd 6gYf1SJYB3SwS5QerUcVaIo= =rQCR -END PGP SIGNATURE-
Re: [ccp4bb] convert orientation matrix format
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Almudena, depending on your application there might be a different approach from what I suggested before: you could use my 'spots4cellnow' (http://shelx.uni-ac.gwdg.de/~tg/research/programs/conv/spots4cellnow/) to convert the SPOTS.XDS into reciprocal coordinates (it only applies the maths from W. Kabsch, Acta Crystallogr. D66 (2010), pp 133-144). The output can be read by cell_now which you have access to if you have access to saint / apex. cell_now writes a p4p file including the orientation matrix. This should be a work-around if the transformation does not fit. Best, Tim On 11/05/2013 02:29 PM, Almudena Ponce Salvatierra wrote: Hi everyone, I would like to know how to change matrix format from the one I get out of XDS to the one that comes out of SAINTS. Or the other way around. My question is: is the beam along the same axis in both matrices? as well as the rotation axis and the third axis? How can I convert one into the other one? Thank you very much in advance. Best wishes, Almudena. - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSexI0UxlJ7aRr7hoRAqKiAKDu1ONYykRkAU0ZGZsqCAWJQR8NZACg8uvV EZl/PdpZ4YrlXi4rcD5tqCM= =G2Yg -END PGP SIGNATURE-
Re: [ccp4bb] Comparison of Water Positions across PDBs
Dear all, there is a tool to identify invariant water molecules in homologous protein structures and the tool can be accessed via http://cluster.physics.iisc.ernet.in/3dss/ best, Sekar Thanks Bernhard you have helpfully distinguished between the two processes - there is certainly a movement of waters to symmetry replacements closer to a chain - and that gets documented in Remark 525 of the PDB file returned to authors - although then it is stripped out, I think, before the entry is released. But generally a renumbering is applied to all the waters - these are not actually moved but are re-ordered. And of course the number count of them may change - in order to accommodate any waters that are swapped in or out of the chain during the symmetry operation. Currently I don't think authors are given access to an audit of what is happening - they can of course check their favourite waters by a superimposition. Still have to say best way to avoid errors would be to check symmetry and re-order at the end of refinement, pre-deposition. All the best Martyn From: Bernhard Rupp hofkristall...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, 4 November 2013, 14:50 Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs As far as confusion as a result of PDB renumbering is concerned: It was useful to run the old REM525 standalone program (I think I got it from PDBe/Kim Hendrick) at the end of solvent building. It does what the PDB did with water renumbering when creating the REMARK 525 (probably based on ccp4 contact with additions). Is there an updated standalone PDB tool available one can use these days to avoid at least that issue? Thx, BR From:CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of MARTYN SYMMONS Sent: Montag, 4. November 2013 15:17 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs Thank you for that, Rachel Even though the tone of your comment does not suggest that you want to carry on a dialogue about this, I thought I would reply in any case - since dialogue is what this forum is supposed to be about. Thing is, I was sort of looking for an explanation of why the rule was adopted that waters were to be renumbered from N to C terminus. If this is not functioning to put the waters in register across a set of related structures then it seems somewhat arbitrary. And other schemes might be suggested to be better for the usability and interpretation of the structural data. In some cases there are only a few waters but in many structures the wwPDB partners renumber hundreds. And this process makes it difficult for authors to check the final deposited structure against the output of their refinement. I have to say that I agree with other contributors to this thread. It would be much better to let the refinement program authors agree on a default water numbering scheme. And then maintain that through deposition. I thought of six possible schemes before breakfast... one of my favourites was to order by B-factor - which might appeal to crystallographers. Another was to give priority to those in the coordination sphere of any metal ions - these actually get priority in the PDB as they are included in the LINKS records above the coordinates. These coordinated waters are often refined together with the metals and so it would make sense to move them closer to their friendly ion. And of course one other clearly suitable option would be to leave the waters in the authors' preferred order - chosen with help from their refinement suite. This is what happens during deposition with the residues of the polymers - (provided the authors chainids are suitably chosen). Following your link the rule for polymers is that: 'If the coordinate residue numbers, as provided by the author, are unique and sequential within a particular chain ID, the residues will not be renumbered.' I'm presuming that if the authors have a preferred suitable set of water numbers then that would be maintained similarly? Perhaps that is what is happening in the cases I notice that do not follow wwPDB rules? On Friday I was looking at TIRAP structures and in 3ub2 the protein construct starts at residue 78 and its final residue is 221 - but the associated DTT is labelled back at residue 1 in the same chain. Then the first ten out of eleven waters are residues 2 to 11 but then oddly the eleventh water is residue 222. Is there a difference in this C-terminal water compared with the N-terminal ones? I imagined it was perhaps maintained to fit in with the associated publication - or maybe started out life modelled as a metal ion - unfortunately I can find no mention of it in the paper. But, regardless of this distracting feature, surely this entry does not conform to the expected numbering scheme you mentioned as
Re: [ccp4bb] R: [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals; Sorry for HTML.
Fulvio, Tim,
error propagation is correct, but wrongly applied in Tim's example.
s_f= \sqrt{ \left(\frac{\partial f}{\partial {x} }\right)^2 s_x^2 +
\left(\frac{\partial f}{\partial {y} }\right)^2 s_y^2 +
\left(\frac{\partial f}{\partial {z} }\right)^2 s_z^2 + ...} (see
http://en.wikipedia.org/wiki/Propagation_of_uncertainty#Simplification)
The uncertainty in a derived magnitude is always larger than any
individual uncertainty, so no subtraction, anytime. Furthermore, in
Tim's example you could end up with negative sigmas..
HTH,
Jens
On Thu, 2013-11-07 at 04:44 +0100, Tim Gruene wrote:
Dear Fulvio,
with simple error propagation, the error would be
sigma(I(h1)) = (1-α)sigma(Iobs(h1))-α*sigma(Iobs(h2))/(1-2α)
would it not?
Although especially for theoretical aspects you should be concerned
about division by zero.
Best,
Tim
On 11/06/2013 05:54 PM, Fulvio Saccoccia wrote:
Thank you for reply. My question mostly concern a theoretical
aspect rather than practical one. To be not misunderstood, what is
the mathematical model that one should apply to be able to deal
with twinned intensities with their errors? I mean, I+_what? I ask
this In order to state some general consideration on the accuracy
about the recovery the true intensities on varying of alpha. Thanks
Fulvio
Fulvio Saccoccia PhD Dept. of Biochemical Sciences Sapienza
University of Rome 5, Piazzale A. Moro 00185 phone +39 0649910556
Messaggio Originale Da: herman.schreu...@sanofi.com
Inviato: 06/11/2013, 17:25 A: CCP4BB@JISCMAIL.AC.UK Oggetto:
[ccp4bb] AW: [ccp4bb] uncertainites associated with intensities
from twinned crystals
Dear Fulvio, you cannot detwin perfectly twinned data with this
formula. The term (1-2α) becomes zero, so you are dividing by zero.
With good refinement programs (ShelX, Refmac), refinement is done
against twinned data, which is better than to detwin the data with
the formula you mention.
As I understand it, to get map coefficients, the calculated
contribution of the twin domain (Fcalc’s) is substracted from Fobs
(with the appropriate weighting factors), so what you see in coot
is detwinned electron density. In practical terms, the only thing
you have to do is to specify the TWIN keyword in Refmac.
Best regards, Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag
von Fulvio Saccoccia Gesendet: Mittwoch, 6. November 2013 16:58 An:
CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] uncertainites associated
with intensities from twinned crystals
Dear ccp4 users
a question about the recovering of true intensities from merohedral
twinned crystal. Providing alpha and the twin operator one should
be able to recover the intensities from the formulas:
I(h1) = (1-α)Iobs(h1)-αIobs(h2)/(1-2α)
I(h2) = -αIobs(h1)+(1+α)Iobs(h2)/(1-2α)
as stated in many papers and books*.
However I was wondering about the uncertainties associated to these
measurements, I mean: for all physical observable an uncertainty
should be given.
Hence, what is the uncertainty associated to a perfect merohedrally
twinned crystal (alpha=0.5)? It is clear that in this case we drop
in a singular value of the above formulas.
Please, let me know your hints or your concerns on the matter.
Probably there is something that it is not so clear to me.
Thanks in advance
Fulvio
ref. **(C. Giacovazzo, H. L. Monaco, G. Artioli, D. Viterbo, M.
Milaneso, G. Ferraris, G. Gilli, P. Gilli, G. Zanotti and M. Catti.
Fundamentals of Crystallography, 3rd edition. IUCr Texts on
Crystallography No. 15, IUCr/Oxford University Press, 2011;
Chandra, N., Acharya, K. R., Moody, P. C. (1999). Acta Cryst. D55.
1750-1758)
--
Fulvio Saccoccia, PhD
Dept. of Biochemical Sciences A. Rossi Fanelli
Sapienza University of Rome
Tel. +39 0649910556
Re: [ccp4bb] [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals; Sorry for HTML.
Tassos,
I'm no expert either, and there are caveats for using this formula on
correlated magnitudes. But I would assume that the intensities of twin
related reflections should be independent from each other (that's my
understanding of the sigmoid cumulative intensity distribution of
twins). Thus, I think the simple Gaussian error propagation should be
applicable to uncertainty estimates in detwinned intensities.
Cheers,
Jens
On Thu, 2013-11-07 at 08:09 +0100, Anastassis Perrakis wrote:
Dear Jens,
That formula for error propagation is correct for independent
measurements.
Does this assumption stand true for Intensities in twinning? I am no
expert, but I would think not.
Tassos
On 7 Nov 2013, at 7:53, Jens Kaiser wrote:
Fulvio, Tim,
error propagation is correct, but wrongly applied in Tim's
example.
s_f= \sqrt{ \left(\frac{\partial f}{\partial {x} }\right)^2 s_x^2 +
\left(\frac{\partial f}{\partial {y} }\right)^2 s_y^2 +
\left(\frac{\partial f}{\partial {z} }\right)^2 s_z^2 + ...} (see
http://en.wikipedia.org/wiki/Propagation_of_uncertainty#Simplification)
The uncertainty in a derived magnitude is always larger than any
individual uncertainty, so no subtraction, anytime. Furthermore, in
Tim's example you could end up with negative sigmas..
HTH,
Jens
On Thu, 2013-11-07 at 04:44 +0100, Tim Gruene wrote:
Dear Fulvio,
with simple error propagation, the error would be
sigma(I(h1)) = (1-α)sigma(Iobs(h1))-α*sigma(Iobs(h2))/(1-2α)
would it not?
Although especially for theoretical aspects you should be concerned
about division by zero.
Best,
Tim
On 11/06/2013 05:54 PM, Fulvio Saccoccia wrote:
Thank you for reply. My question mostly concern a theoretical
aspect rather than practical one. To be not misunderstood, what is
the mathematical model that one should apply to be able to deal
with twinned intensities with their errors? I mean, I+_what? I ask
this In order to state some general consideration on the accuracy
about the recovery the true intensities on varying of alpha. Thanks
Fulvio
Fulvio Saccoccia PhD Dept. of Biochemical Sciences Sapienza
University of Rome 5, Piazzale A. Moro 00185 phone +39 0649910556
Messaggio Originale Da: herman.schreu...@sanofi.com
Inviato: 06/11/2013, 17:25 A: CCP4BB@JISCMAIL.AC.UK Oggetto:
[ccp4bb] AW: [ccp4bb] uncertainites associated with intensities
from twinned crystals
Dear Fulvio, you cannot detwin perfectly twinned data with this
formula. The term (1-2α) becomes zero, so you are dividing by zero.
With good refinement programs (ShelX, Refmac), refinement is done
against twinned data, which is better than to detwin the data with
the formula you mention.
As I understand it, to get map coefficients, the calculated
contribution of the twin domain (Fcalc’s) is substracted from Fobs
(with the appropriate weighting factors), so what you see in coot
is detwinned electron density. In practical terms, the only thing
you have to do is to specify the TWIN keyword in Refmac.
Best regards, Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag
von Fulvio Saccoccia Gesendet: Mittwoch, 6. November 2013 16:58 An:
CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] uncertainites associated
with intensities from twinned crystals
Dear ccp4 users
a question about the recovering of true intensities from merohedral
twinned crystal. Providing alpha and the twin operator one should
be able to recover the intensities from the formulas:
I(h1) = (1-α)Iobs(h1)-αIobs(h2)/(1-2α)
I(h2) = -αIobs(h1)+(1+α)Iobs(h2)/(1-2α)
as stated in many papers and books*.
However I was wondering about the uncertainties associated to these
measurements, I mean: for all physical observable an uncertainty
should be given.
Hence, what is the uncertainty associated to a perfect merohedrally
twinned crystal (alpha=0.5)? It is clear that in this case we drop
in a singular value of the above formulas.
Please, let me know your hints or your concerns on the matter.
Probably there is something that it is not so clear to me.
Thanks in advance
Fulvio
ref. **(C. Giacovazzo, H. L. Monaco, G. Artioli, D. Viterbo, M.
Milaneso, G. Ferraris, G. Gilli, P. Gilli, G. Zanotti and M. Catti.
Fundamentals of Crystallography, 3rd edition. IUCr Texts on
Crystallography No. 15, IUCr/Oxford University Press, 2011;
Chandra, N., Acharya, K. R., Moody, P. C. (1999). Acta Cryst. D55.
1750-1758)
--
Fulvio Saccoccia, PhD
Dept. of Biochemical Sciences A. Rossi Fanelli
Sapienza University of Rome
Tel. +39 0649910556
