Re: [ccp4bb] CCP4 rotation convention

2007-08-15 Thread Ian Tickle
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

2007-08-15 Thread Ian Tickle
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
 
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Re: [ccp4bb] Rejected posting to CCP4BB@JISCMAIL.AC.UK

2007-08-15 Thread Andy Purkiss-Trew
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 
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-- 
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+--+
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|   E-mail   [EMAIL PROTECTED]|
+--+


Re: [ccp4bb] Rejected posting to CCP4BB@JISCMAIL.AC.UK

2007-08-15 Thread Kay Diederichs

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


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Re: [ccp4bb] Rejected posting to CCP4BB@JISCMAIL.AC.UK

2007-08-15 Thread Eleanor Dodson

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

2007-08-15 Thread Ian Tickle
 
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

2007-08-15 Thread Charles Ballard
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

2007-08-15 Thread Oganesyan, Vaheh
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

2007-08-15 Thread Eleanor Dodson

test..


[ccp4bb] Oligomer which lacks conformational cooperativity

2007-08-15 Thread Jacob Keller
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

2007-08-15 Thread Kumar, Abhinav
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?

2007-08-15 Thread Das, Debanu
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

2007-08-15 Thread Yanming Zhang

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

2007-08-15 Thread Juergen Bosch

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