Re: [ccp4bb] CCP4 rotation convention
Hi Bernhard
The CCP4/PDBSET/ALMN/AMORE (but NOT X-PLOR ...) convention is:
gamma about z, beta about *fixed* y, alpha about *fixed* z
OR
alpha about z, beta about *rotated* y, gamma about *rotated* z.
... but NOT any other combination of these!!!
In the equation, the component matrices are written down in order from
right to left, pre-multiplying the co-ordinate vectors.
Although the component matrices are in general completely different in
the fixed rotated descriptions, the resultant product matrix is
identical, so they both refer to the *same* convention. So as far as
the convention is concerned it is of no consequence whatsoever which way
you describe it or think about it, as long as you don't confuse these 2
alternatives by having first say gamma, then beta, then alpha about
rotated axes: the component matrices are the same as for the correct
rotated axis case, but because they are multiplied in reverse order it
will give you a completely different and incorrect resultant matrix.
My issue with thinking about or working with rotated axes is just that:
it's well nigh impossible to think about them or work with them! Not
only that, it's a pain just to write them down, e.g. for the matrix
describing the component rotation gamma about the rotated z axis, the
direction of the rotated z axis is a function of both alpha beta, so
the component gamma rotation matrix contains trig functions of all 3
angles! I defy you to write out the complete equation for the rotated
axis case showing all 27 matrix elements (in fact I can't think of a
more pointless exercise!). Contrast that with the fixed axis case where
the component matrices are all functions of a single angle and I can
work them out in 2 secs.
I trust I have convinced you!
Cheers
-- Ian
-Original Message-
From: Bernhard Rupp [mailto:[EMAIL PROTECTED]
Sent: 15 August 2007 07:39
To: Ian Tickle
Subject: RE: [ccp4bb] CCP4 rotation convention
Ian, my question is actually getting simpler in the process,
and all I seek is authoritative answer to:
a) What is the CCP4 convention, if such a convention exists,
b) and what convention does Amore use.
If it is fixed axes, fine. If it is different
depending on the program, also ok. Per Navaza ITCF, we can
all consistently convert the settings - this is not the problem.
(the math is the only thing I can follow. For me this is
an eigenvalue problem (albeit with a few nasty singularities)
so I need no conventions to solve the matrix for the Euler axis
and the principal Euler angle - regardless how the DMC was set up).
I am not sure about the illegality of terms 'new' to indicate
rotating coordinate system. I think it is legit. As you
indicate, the math is clear, the descriptions widely and
wildly divergent.
Thx, BR
-Original Message-
From: Ian Tickle [mailto:[EMAIL PROTECTED]
Sent: Tuesday, August 14, 2007 7:12 AM
To: [EMAIL PROTECTED]
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] CCP4 rotation convention
Bernhard -
In case you're still trying to follow the convoluted arguments in my
previous long answer, here's the short answer (for your summary!):
Replace the word 'new' (twice) in this sentence in Phil's AC
2001 article
with the word 'fixed':
... rotate by gamma around z, then by beta around the new y,
then by alpha
around the new z again..
Then everything is fine we all agree!
Your problems with Y1, Z2 etc in Eleanor's description are
resolved because
the axes never move. In fact it's not clear to me why we
need ZO, Y1 Z2
at all because Z2 = Z0 = Z and Y1 = Y. So the most concise
statement is the
one in my previous email:
R = Rz(a).Ry(b).Rz(g)
... and please don't mention rotated (or 'new' etc) axes in
this context
ever again!
-- Ian
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Rupp
Sent: 13 August 2007 23:07
To: [EMAIL PROTECTED]
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] CCP4 rotation convention
Hmmmthis explanation seems to add another discrepancy - I think
the connection to the physical process is lost - I cannot
rotate first
about something I don't have yet.
Let me try to interpret what E wrote:
I just have to write out matrices:
CCP4 rotation matrix:
[R11 R12 R13] [x]
[R21 R22 R23] [y]
[R31 R32 R33] [z]
where x y z are orthogonal coordinates relative to fixed axes
I suppose from following this means rotating coordinate
system, i.e.
Euler convention.
represents a rotation of ccordinates by first gamma then beta then
alpha as Phil says:
[R11 R12 R13]
[R21 R22 R23]
[R31 R32 R33]
== [R_alpha_about Z0] {R_beta_about_Y1] [ R_gamma_about_Z2]
in br alternate notation R = RZ0(al)RY1(be)RZ2(ga)
but this means: apply the first physical rotation about z2 (I don't
have z2 yet!),
Re: [ccp4bb] Rejected posting to CCP4BB@JISCMAIL.AC.UK
All - is anyone else getting this response every time they post a message or is it just me? The received header shows [EMAIL PROTECTED] (ms1.kissei.co.jp [210.238.65.82]). -- Ian -Original Message- From: JISCMAIL LISTSERV Server (14.5) [mailto:[EMAIL PROTECTED] Sent: 15 August 2007 10:51 To: Ian Tickle Subject: Rejected posting to CCP4BB@JISCMAIL.AC.UK Your message is being returned to you unprocessed because it appears to have already been distributed to the CCP4BB list. That is, a message with identical text (but possibly with different mail headers) has been posted to the list recently, either by you or by someone else. If you have reason to resend this message to the list (for instance because you have been notified of a hardware failure with loss of data), please alter the text of the message in some way and resend it to the list. Note that altering the Subject: line or adding blank lines at the top or bottom of the message is not sufficient; you should instead add a sentence or two at the top explaining why you are resending the message, so that the other subscribers understand why they are getting two copies of the same message. Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] Rejected posting to CCP4BB@JISCMAIL.AC.UK
Hi Ian and list, I don't know about rejected postings, as I've not made any recently, but I am getting two copies of each posting made and the second has gone through the same server as below: Received: from ms1.kissei.co.jp ([210.238.65.82]) by a12536.general.kissei.co.jp (Lotus Domino Release 6.5.4FP2) with ESMTP id 2007081510253541-2677 ; Wed, 15 Aug 2007 10:25:35 +0900 Received: from ictmailer1.itd.rl.ac.uk (ictmailer1.itd.rl.ac.uk [130.246.192.56]) by ms1.kissei.co.jp (8.11.6/3.7W) with ESMTP id l7F1PYJ20264 for [EMAIL PROTECTED]; Wed, 15 Aug 2007 10:25:34 +0900 Looks like problem with someone's e-mail system to me. Andy On Wed, 2007-08-15 at 11:03 +0100, Ian Tickle wrote: All - is anyone else getting this response every time they post a message or is it just me? The received header shows [EMAIL PROTECTED] (ms1.kissei.co.jp [210.238.65.82]). -- Ian -Original Message- From: JISCMAIL LISTSERV Server (14.5) [mailto:[EMAIL PROTECTED] Sent: 15 August 2007 10:51 To: Ian Tickle Subject: Rejected posting to CCP4BB@JISCMAIL.AC.UK Your message is being returned to you unprocessed because it appears to have already been distributed to the CCP4BB list. That is, a message with identical text (but possibly with different mail headers) has been posted to the list recently, either by you or by someone else. If you have reason to resend this message to the list (for instance because you have been notified of a hardware failure with loss of data), please alter the text of the message in some way and resend it to the list. Note that altering the Subject: line or adding blank lines at the top or bottom of the message is not sufficient; you should instead add a sentence or two at the top explaining why you are resending the message, so that the other subscribers understand why they are getting two copies of the same message. Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674 -- Cat, n.: Lapwarmer with built-in buzzer. +--+ | Andy Purkiss-Trew, School of Crystallography,Birkbeck College,London | | E-mail [EMAIL PROTECTED]| +--+
Re: [ccp4bb] Rejected posting to CCP4BB@JISCMAIL.AC.UK
Ian, yesterday evening I posted Re: [ccp4bb] coot in stereo. I then got an email Rejected posting to CCP4BB@JISCMAIL.AC.UK . The header indicates that it indeed comes from ictmailer1.itd.rl.ac.uk; no other email address but mine is involved. I have no explanation for this as I surely only sent my posting once. Kay Ian Tickle schrieb: All - is anyone else getting this response every time they post a message or is it just me? The received header shows [EMAIL PROTECTED] (ms1.kissei.co.jp [210.238.65.82]). -- Ian -Original Message- From: JISCMAIL LISTSERV Server (14.5) [mailto:[EMAIL PROTECTED] Sent: 15 August 2007 10:51 To: Ian Tickle Subject: Rejected posting to CCP4BB@JISCMAIL.AC.UK Your message is being returned to you unprocessed because it appears to have already been distributed to the CCP4BB list. That is, a message with identical text (but possibly with different mail headers) has been posted to the list recently, either by you or by someone else. If you have reason to resend this message to the list (for instance because you have been notified of a hardware failure with loss of data), please alter the text of the message in some way and resend it to the list. Note that altering the Subject: line or adding blank lines at the top or bottom of the message is not sufficient; you should instead add a sentence or two at the top explaining why you are resending the message, so that the other subscribers understand why they are getting two copies of the same message. Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674 -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz smime.p7s Description: S/MIME Cryptographic Signature
Re: [ccp4bb] Rejected posting to CCP4BB@JISCMAIL.AC.UK
Ditto - I am getting everything in duplicate Eleanor Andy Purkiss-Trew wrote: Hi Ian and list, I don't know about rejected postings, as I've not made any recently, but I am getting two copies of each posting made and the second has gone through the same server as below: Received: from ms1.kissei.co.jp ([210.238.65.82]) by a12536.general.kissei.co.jp (Lotus Domino Release 6.5.4FP2) with ESMTP id 2007081510253541-2677 ; Wed, 15 Aug 2007 10:25:35 +0900 Received: from ictmailer1.itd.rl.ac.uk (ictmailer1.itd.rl.ac.uk [130.246.192.56]) by ms1.kissei.co.jp (8.11.6/3.7W) with ESMTP id l7F1PYJ20264 for [EMAIL PROTECTED]; Wed, 15 Aug 2007 10:25:34 +0900 Looks like problem with someone's e-mail system to me. Andy On Wed, 2007-08-15 at 11:03 +0100, Ian Tickle wrote: All - is anyone else getting this response every time they post a message or is it just me? The received header shows [EMAIL PROTECTED] (ms1.kissei.co.jp [210.238.65.82]). -- Ian -Original Message- From: JISCMAIL LISTSERV Server (14.5) [mailto:[EMAIL PROTECTED] Sent: 15 August 2007 10:51 To: Ian Tickle Subject: Rejected posting to CCP4BB@JISCMAIL.AC.UK Your message is being returned to you unprocessed because it appears to have already been distributed to the CCP4BB list. That is, a message with identical text (but possibly with different mail headers) has been posted to the list recently, either by you or by someone else. If you have reason to resend this message to the list (for instance because you have been notified of a hardware failure with loss of data), please alter the text of the message in some way and resend it to the list. Note that altering the Subject: line or adding blank lines at the top or bottom of the message is not sufficient; you should instead add a sentence or two at the top explaining why you are resending the message, so that the other subscribers understand why they are getting two copies of the same message. Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] CCP4 rotation convention
Bernhard
Sorry, correction, this statement in my last posting is not correct:
... by having first say gamma, then beta, then alpha about
rotated axes: the component matrices are the same as for the correct
rotated axis case, but because they are multiplied in reverse order it
will give you a completely different and incorrect resultant matrix.
The component matrices in the case described are not the same as for the
correct rotated axis case because for say the 2nd rotation about beta
the matrix would be a function of alpha beta in the correct case, but
of beta and gamma in the incorrect case, so the component matrices can't
possibly all be the same - but it will still give you a completely
different and incorrect resultant matrix, so my point is still valid.
You see the kind of confusion that occurs as soon as you start thinking
in terms of rotated axes!
Otherwise I stand by everything I said!
-- Ian
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Ian Tickle
Sent: 15 August 2007 10:47
To: [EMAIL PROTECTED]
Cc: CCP4BB@jiscmail.ac.uk
Subject: RE: [ccp4bb] CCP4 rotation convention
Hi Bernhard
The CCP4/PDBSET/ALMN/AMORE (but NOT X-PLOR ...) convention is:
gamma about z, beta about *fixed* y, alpha about *fixed* z
OR
alpha about z, beta about *rotated* y, gamma about *rotated* z.
... but NOT any other combination of these!!!
In the equation, the component matrices are written down in order from
right to left, pre-multiplying the co-ordinate vectors.
Although the component matrices are in general completely different in
the fixed rotated descriptions, the resultant product matrix is
identical, so they both refer to the *same* convention. So as far as
the convention is concerned it is of no consequence
whatsoever which way
you describe it or think about it, as long as you don't
confuse these 2
alternatives by having first say gamma, then beta, then alpha about
rotated axes: the component matrices are the same as for the correct
rotated axis case, but because they are multiplied in reverse order it
will give you a completely different and incorrect resultant matrix.
My issue with thinking about or working with rotated axes is
just that:
it's well nigh impossible to think about them or work with them! Not
only that, it's a pain just to write them down, e.g. for the matrix
describing the component rotation gamma about the rotated z axis, the
direction of the rotated z axis is a function of both alpha beta, so
the component gamma rotation matrix contains trig functions of all 3
angles! I defy you to write out the complete equation for the rotated
axis case showing all 27 matrix elements (in fact I can't think of a
more pointless exercise!). Contrast that with the fixed axis
case where
the component matrices are all functions of a single angle and I can
work them out in 2 secs.
I trust I have convinced you!
Cheers
-- Ian
-Original Message-
From: Bernhard Rupp [mailto:[EMAIL PROTECTED]
Sent: 15 August 2007 07:39
To: Ian Tickle
Subject: RE: [ccp4bb] CCP4 rotation convention
Ian, my question is actually getting simpler in the process,
and all I seek is authoritative answer to:
a) What is the CCP4 convention, if such a convention exists,
b) and what convention does Amore use.
If it is fixed axes, fine. If it is different
depending on the program, also ok. Per Navaza ITCF, we can
all consistently convert the settings - this is not the problem.
(the math is the only thing I can follow. For me this is
an eigenvalue problem (albeit with a few nasty singularities)
so I need no conventions to solve the matrix for the Euler axis
and the principal Euler angle - regardless how the DMC was set up).
I am not sure about the illegality of terms 'new' to indicate
rotating coordinate system. I think it is legit. As you
indicate, the math is clear, the descriptions widely and
wildly divergent.
Thx, BR
-Original Message-
From: Ian Tickle [mailto:[EMAIL PROTECTED]
Sent: Tuesday, August 14, 2007 7:12 AM
To: [EMAIL PROTECTED]
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] CCP4 rotation convention
Bernhard -
In case you're still trying to follow the convoluted arguments in my
previous long answer, here's the short answer (for your summary!):
Replace the word 'new' (twice) in this sentence in Phil's AC
2001 article
with the word 'fixed':
... rotate by gamma around z, then by beta around the new y,
then by alpha
around the new z again..
Then everything is fine we all agree!
Your problems with Y1, Z2 etc in Eleanor's description are
resolved because
the axes never move. In fact it's not clear to me why we
need ZO, Y1 Z2
at all because Z2 = Z0 = Z and Y1 = Y. So the most concise
statement is the
one in my previous email:
Re: [ccp4bb] Rejected posting to CCP4BB@JISCMAIL.AC.UK
Check, thanks for the heads up. I have removed the eiichi_tsuiji address from the list, which I guess was bouncing e-mails (miss configured spam filtering perhaps). Interestingly, this was not one of the 51 addresses being monitored. We are running with automatic removal to try and reduce problems (which works overtime at this time of year). Subscribers will be automatically deleted from the list when delivery errors have been reported for a period of 4 days or more, or when 100 delivery errors have been received, whichever occurs first. Monitoring will cease after 5 days without any reported errors. Charles ps Eleanor, I think you are actually registered from two addresses. On 15 Aug 2007, at 11:24, Kay Diederichs wrote: Ian, yesterday evening I posted Re: [ccp4bb] coot in stereo. I then got an email Rejected posting to CCP4BB@JISCMAIL.AC.UK . The header indicates that it indeed comes from ictmailer1.itd.rl.ac.uk; no other email address but mine is involved. I have no explanation for this as I surely only sent my posting once. Kay Ian Tickle schrieb: All - is anyone else getting this response every time they post a message or is it just me? The received header shows [EMAIL PROTECTED] (ms1.kissei.co.jp [210.238.65.82]). -- Ian -Original Message- From: JISCMAIL LISTSERV Server (14.5) [mailto:[EMAIL PROTECTED] Sent: 15 August 2007 10:51 To: Ian Tickle Subject: Rejected posting to CCP4BB@JISCMAIL.AC.UK Your message is being returned to you unprocessed because it appears to have already been distributed to the CCP4BB list. That is, a message with identical text (but possibly with different mail headers) has been posted to the list recently, either by you or by someone else. If you have reason to resend this message to the list (for instance because you have been notified of a hardware failure with loss of data), please alter the text of the message in some way and resend it to the list. Note that altering the Subject: line or adding blank lines at the top or bottom of the message is not sufficient; you should instead add a sentence or two at the top explaining why you are resending the message, so that the other subscribers understand why they are getting two copies of the same message. Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] therapeutics.com and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674 -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
Re: [ccp4bb] coot in stereo
Similar thing was happening on the dual Xeon 2.8 GHz machines in O as well. But it was 2-5 sec long in time. Vaheh Oganesyan -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of Kay Diederichs Sent: Tuesday, August 14, 2007 3:54 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] coot in stereo Paul D. Cook schrieb: Hello, I'm running stereocoot on linux (centos) machines with nvidia video cards and stereographics emitters and glasses. The setup seems to work fine most of the time, but the stereo will invert every now and then (the right eye is shown the left image and vice versa). This seems to happen especially after a computation such as realspace refine is performed. The stereo will usually spontaneously correct itself, but sometimes I have to minimize the window and restore it. This is occuring on three machines with the above configuration. Swapping emitters and glasses seems to do nothing. Has anyone had such a problem? Thanks, Paul D. Cook Paul, I've seen this problem too, on AMD dual-processor machines with powersaving enabled. I could not find a version of the NVIDIA driver that did not show the problem. I believe that the switch in CPU frequency disturbs the synchronization. So you might want to experiment with e.g. service cpuspeed stop (as root) and see what happens. If it does help, you can switch powersaving off permanently (chkconfig cpuspeed off). Unfortunately powersaving depends on proper interaction of kernel, hardware and usermode software. Intel CPUs are quite different from AMD ones in that respect. HTH, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
[ccp4bb] test
test..
[ccp4bb] Oligomer which lacks conformational cooperativity
Sorry about this not being exactly CCP4 related, but I think it is still of general interest to the structural biology community: I am dealing with a membrane protein which seems, on the surface, to present a contradiction: We know from western blots and other data that this protein forms oligomers vehemently, which are all but impervious to monomerization under the most ruthless conditions--we cannot completely monomerize it. We have tried DTT, EDT, BME, all concentrations of SDS, PFO, temperature, and salt, and in various combinations (further suggestions are welcome.) Suffice it to say, this thing is a bona fide vicious oligomer. Here is the paradox: the functional data, on the surface, seem to imply that the protein acts independently, as if a monomer, without being influenced by its (tight) oligomeric partners, even though we think the functional mechanism is a conformational change. Is such a thing observed in the biochemical world? Are there any homo-oligomeric proteins out there, membrane-bound or otherwise, which exhibit conformational changes, and yet the protomers do not influence each other? If so, if the oligomerization has no functional significance, and the subunits do not exhibit crosstalk, what on earth is the reason for their oligomerization? All hypotheses and especially references would be greatly appreciated, Jacob Keller *** Jacob Keller Northwestern University 6541 N. Francisco #3 Chicago IL 60645 (847)467-4049 [EMAIL PROTECTED] ***
Re: [ccp4bb] Dry structures
Hi, Here is a result (attached) of analyzing over 2000 Structural Genomics structures. At ~2 A resolution, you would roughly expect 1 water for every two residues. Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Sabini, Elisabetta Sent: Wednesday, August 15, 2007 10:35 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Dry structures Dear all, what does it mean when a structure doesn't have many water molecules? I have a 2.3A data set, 2 molecules in the AU (260 residues each), space group C2221 - I haven't finished my water search but I don't seem to have more than 20-30 obvious/good water molecules. The Rfac/Rfree are 22/30%, the protein is modeled and the ligands are in. I collected the data at APS SERCAT ID-22. Did I have a dry crystal (!!) or did the beamline dried it up?! How many water molecules should I expect at this resolution? Also, what does it mean when a strong peak in the Fobs-Fc doesn't have the corresponding 2Fobs-Fc map covering it even at very low sigma? Thank you! Eli :o) PS: I have attached the statistics for the data set from XDS -- Elisabetta Sabini, Ph.D. Research Assistant Professor University of Illinois at Chicago Department of Biochemistry and Molecular Genetics Molecular Biology Research Building, Rm. 1108 900 South Ashland Avenue Chicago, IL 60607 U.S.A. Tel: (312) 996-6299 Fax: (312) 355-4535 E-mail: [EMAIL PROTECTED] attachment: waters.png
Re: [ccp4bb] model DNA-binding crystals?
Hi Frank, The N-terminal catalytic fragment/polymerase domain of the MuLV Reverse Transcriptase is easy to express (large yield of soluble protein in E. coli expression, ~270 aa), purify (3 steps) and crystallize (overnight to couple of days with microseeding) with short stretches of DNA (8-16 bp) of different sequences to produce well diffracting protein-DNA complex crystals (1.5-2.5A) where the DNA structure is not influenced by lattice packing interactions as there are no direct crystal contacts between the DNA molecules. This particular system has been used to study the structures of some interesting DNA sequences as well as used in a kind of host-guest approach to study binding of DNA drugs to DNA. You can refer to the following references and the references therein: Cote M.L., Georgiadis M.M. Structure of a pseudo-16mer DNA with stacked guanines and two G-A mispairs complexed with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase. Acta Crystallogr. D Biol. Crystallogr. 2001;57:1238-1250 Goodwin, K. D., Long, E. C., and Georgiadis, M. M. (2005) A host-guest approach for determining drug-DNA interactions: An example using netropsin, Nucleic Acids Res. 33, 4106-4116. Regards, Debanu. -- Debanu Das, JCSG, SSRL. -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Frank von Delft Sent: Wednesday, August 15, 2007 11:14 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] model DNA-binding crystals? Hi, anyone know of a lysozyme-equivalents for protein-DNA complexes? i.e. a protein that a) is easy to obtain (preferably purchase) b) binds some bit of DNA well c) crystallizes easily as protein-DNA complex Cheers phx
[ccp4bb] Structure help
Hi , Please help me on this structure: Data 1.8A: cell 84.892 84.892 172.580 90 90 90 with tetrahedral index Space group: P43212 or P43, Final refinement Rfree indicates P43 is better so most likely P43(also the systematic absence indicate P43 is it) Matthew coeffient indicates: P43 3mol/a.u(2.58,52%) 2mol/a.u(3.87, 68%) MR: Both Molerep and Phaser find out 2mol/au initially. Refinement reaches Rfree 30% , R 27% finally. WE think, comparing with 1.8 resolution, The R and Rfree are too high. Also considering the 1.8A resolution, there should be 3 molecules in total. So we engaged into the effort to find out the 3rd molecule. Phased MR by MOLREP did find out the 3rd, so did Phaser(fix two, find out the 3rd). Both solutions gave relatively poorer statistics but packing is perfect. The 3rd molecule, solved by phased MR of MOLREP and PHaser respectively, can not superpose showing slightly different orientations, but position is similar. Refinement indicates PHased MOLREP MR gives lower Rfree. Using totally 3 molecule, When I restrain or constrain NCS during refinement(used TLS),R free goes way up (R~30, Rfree 36%). If I refine without NCS,R factors slip right away to 27/30 but this strange thing happens: two copies of the original solution refines very well - low B factors,very good looking map. The 3rd copy, however, B factors are high and the map is bad, no good density match with the model.And the 3rd molecule did no help to Rfree or R. Story ends with my questions: 1,It seems the 3rd copy non-exist or globally disordered, under this circumstance, can I say 'because of the 3rd molecule is globally disordered so Rfree and R stay high (2mol/a.u with Rfree 30% R 27%, 1.8A data)? 2,Anything I should worry about in the process finding out the 3rd? 3,Are there suggestions to further lower down Rfree (the reasonable Rfree should be around 22%)? THANKS Yanming
Re: [ccp4bb] Structure help
Hi Yanming, when you use your two correctly placed molecules have you tried to calculate a composite omit map using CNS. I assume your crystal lattice does not look very well packed when you only have two molecules per asu ? That would be a good indication that your third molecule is truly there if the packing would make sense. Even if you only have two molecules, you should try to run DM using twofold NCS that would still increase your signal to noise by a factor of 1.4. I would for example start a DM run from e.g. 2.5 A and extend to 1.8 A in perhaps 200 cycles for a first quick look without improving your mask derived from one molecule. Then check with Coot in the difference density map if there is a hint for your third molecule. Good luck, Juergen Yanming Zhang wrote: Hi , Please help me on this structure: Data 1.8A: cell 84.892 84.892 172.580 90 90 90 with tetrahedral index Space group: P43212 or P43, Final refinement Rfree indicates P43 is better so most likely P43(also the systematic absence indicate P43 is it) Matthew coeffient indicates: P43 3mol/a.u(2.58,52%) 2mol/a.u(3.87, 68%) MR: Both Molerep and Phaser find out 2mol/au initially. Refinement reaches Rfree 30% , R 27% finally. WE think, comparing with 1.8 resolution, The R and Rfree are too high. Also considering the 1.8A resolution, there should be 3 molecules in total. So we engaged into the effort to find out the 3rd molecule. Phased MR by MOLREP did find out the 3rd, so did Phaser(fix two, find out the 3rd). Both solutions gave relatively poorer statistics but packing is perfect. The 3rd molecule, solved by phased MR of MOLREP and PHaser respectively, can not superpose showing slightly different orientations, but position is similar. Refinement indicates PHased MOLREP MR gives lower Rfree. Using totally 3 molecule, When I restrain or constrain NCS during refinement(used TLS),R free goes way up (R~30, Rfree 36%). If I refine without NCS,R factors slip right away to 27/30 but this strange thing happens: two copies of the original solution refines very well - low B factors,very good looking map. The 3rd copy, however, B factors are high and the map is bad, no good density match with the model.And the 3rd molecule did no help to Rfree or R. Story ends with my questions: 1,It seems the 3rd copy non-exist or globally disordered, under this circumstance, can I say 'because of the 3rd molecule is globally disordered so Rfree and R stay high (2mol/a.u with Rfree 30% R 27%, 1.8A data)? 2,Anything I should worry about in the process finding out the 3rd? 3,Are there suggestions to further lower down Rfree (the reasonable Rfree should be around 22%)? THANKS Yanming -- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002
