[ccp4bb] Richard Kahn

2011-10-11 Thread Rafael Molina 

Dear ccp4 users,

It is with great sadness that I announce that Dr. Richard Kahn, Life 
Sciences Research Director in CNRS at Institute de Biologie Structurale 
Jean-Pierre Ebel (IBS), passed away on October 1, 2011, in Grenoble.


He was a superb crystallographer. He was always very keen to collaborate 
and help on any subject you were involved, non-conventional data 
collections, phasing difficult structures, providing you his new phasing 
strategies and teaching and supervising young crystallographers. In 
addition and specially he was an excellent person and without doubt, 
those who knew Richard will never forget him.


You can send condolences, photos or any message you want to leave to 
jacqueline.cherf...@lebs.cnrs-gif.fr (President of the French 
Crystallography Association). They will be posted in the following web page:
http://www.afc.asso.fr/index.php?option=com_content&view=article&id=121&Itemid=89 



Warm regards

--
---
Rafael Molina, PhD

Structural Biology and Biocomputing Programme

CNIO - Centro Nacional de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3, E-28029 Madrid (España)

www.cnio.es
---



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[ccp4bb] Ice rings...

2011-10-11 Thread Francis E Reyes 
All,


So I have two intense ice rings where there appear to be lattice spots in 
between them. 

I understand that any reflections that lie directly on the ice ring are 
useless, however, how do software programs (HKL2000, d*Trek, mosflm, XDS) deal 
with these intermediate spots? 

It would seem to me that employing a 'resolution cut off' just before the ice 
ring (on the low resolution side) would be improper, as there are spots on the 
high resolution side of the ice. (see enclosed .tiff)


In fact, how do these programs deal with spots lying on ice rings? Are they 
rejected by some algorithm by those programs during integration, or is it up to 
the scaling/merging (by SCALA for example) step to deal with them? 

Thanks!

F
<>

-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

Re: [ccp4bb] Ice rings...

2011-10-11 Thread Bruno KLAHOLZ 
Dear Francis,

the spots will be excluded individually based on the inhomogeneous background, 
so you don't need to apply a resolution cutoff.
However, once you have determined and refined your structure it may be worth 
predicting the intensity of these spots and put them back for map calculation,
this might avoid gaps in your map corresponding to inter-atom distances for 
which data are missing in the resolution range of the ice rings; as long as 
this is done only for a relatively small set of reflections there is not much 
risk of introducing a bias here.

HTH,

Bruno




-Message d'origine-
De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de Francis E 
Reyes
Envoyé : Tuesday, October 11, 2011 5:17 PM
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Ice rings...

All,


So I have two intense ice rings where there appear to be lattice spots in 
between them. 

I understand that any reflections that lie directly on the ice ring are 
useless, however, how do software programs (HKL2000, d*Trek, mosflm, XDS) deal 
with these intermediate spots? 

It would seem to me that employing a 'resolution cut off' just before the ice 
ring (on the low resolution side) would be improper, as there are spots on the 
high resolution side of the ice. (see enclosed .tiff)


In fact, how do these programs deal with spots lying on ice rings? Are they 
rejected by some algorithm by those programs during integration, or is it up to 
the scaling/merging (by SCALA for example) step to deal with them? 

Thanks!

F

###
Dr. Bruno P. Klaholz 
Department of Integrated Structural Biology
Institute of Genetics and of Molecular and Cellular Biology
IGBMC - UMR 7104 - U 964
1, rue Laurent Fries
BP 10142 
67404 ILLKIRCH CEDEX
FRANCE
Tel. from abroad: 0033.388.65.57.55
Tel. inside France: 03.88.65.57.55
Fax from abroad: 0033.388.65.32.76
Fax inside France: 03.88.65.32.76
e-mail: klah...@igbmc.fr
websites:
http://www.igbmc.fr/
http://igbmc.fr/Klaholz

Re: [ccp4bb] Ice rings...

2011-10-11 Thread Edward A. Berry 

If the ice rings are really sharp, they trigger the bad
background rejection in denzo/HKL2000. To reject more spots,
increase the "reject fraction 0.7" parameter to something
greater than .7. This rejection is on a spot by spot basis,
so spots with good background between the rings should not
be affected. During integration, if you are monitoring
the process with Xdisp, you will see the rejected spots
turn red and/or disappear. To verify they are being
rejected by background fraction, try again with
"reject fraction .3" and see if they stay green/yellow.

If the ice ring is broad compared to the integrating box,
it shows up as a high, slanting baseline and the normal
baseline correction procedure is valid, but sigma will
be higher than for a spot on a white background.

Francis E Reyes wrote:

All,


So I have two intense ice rings where there appear to be lattice spots in 
between them.

I understand that any reflections that lie directly on the ice ring are 
useless, however, how do software programs (HKL2000, d*Trek, mosflm, XDS) deal 
with these intermediate spots?

It would seem to me that employing a 'resolution cut off' just before the ice 
ring (on the low resolution side) would be improper, as there are spots on the 
high resolution side of the ice. (see enclosed .tiff)


In fact, how do these programs deal with spots lying on ice rings? Are they 
rejected by some algorithm by those programs during integration, or is it up to 
the scaling/merging (by SCALA for example) step to deal with them?

Thanks!

F





-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

Re: [ccp4bb] Ice rings...

2011-10-11 Thread Dr. Thayumanasamy Somasundaram 

Francis,

I would like to bring your attention to our paper in Acta Cryst D Volume 
66 (6), 741-744 (2010) where we deal with spots under the ice-rings. We 
have been very successful in eliminating the ice-rings and recover the 
data underneath. If you are interested you can request the Python script 
from Michael Chapman at OHSU.



   De-icing: recovery of diffraction intensities in the presence of ice
   rings, Michael S. Chapman and^^Thayumanasamy Somasundaram


If you need help please e-mail me outside the CCP4BB.
**

On 10/11/2011 11:16 AM, Francis E Reyes wrote:

All,


So I have two intense ice rings where there appear to be lattice spots in 
between them.

I understand that any reflections that lie directly on the ice ring are 
useless, however, how do software programs (HKL2000, d*Trek, mosflm, XDS) deal 
with these intermediate spots?

It would seem to me that employing a 'resolution cut off' just before the ice 
ring (on the low resolution side) would be improper, as there are spots on the 
high resolution side of the ice. (see enclosed .tiff)


In fact, how do these programs deal with spots lying on ice rings? Are they 
rejected by some algorithm by those programs during integration, or is it up to 
the scaling/merging (by SCALA for example) step to deal with them?

Thanks!

F



-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder







--

Dr. Thayumanasamy Somasundaram [Soma]
Director, X-Ray Crystallography Facility (XRF)  
Off. Ph: (850)644-6448| Lab Ph: (850)645-1333   
Fax:(850)644-7244 | E-mail: tsomasunda...@fsu.edu   

URI: www.sb.fsu.edu/~soma | URI: www.sb.fsu.edu/~xray   
Postal Address--
91, Chieftan Way | KLB 414  
Institute of Molecular Biophysics   
Florida State University
Tallahassee, FL 32306-4380, USA.

Re: [ccp4bb] Ice rings...

2011-10-11 Thread James Stroud 
I've used a technique called "annealing", which amounts to holding an index 
card between the cryo stream and the crystal for a few seconds then removing 
the card quickly.

In my experience, about 70% of the time the diffraction is worse and about 30% 
of the time the ice rings will be gone with slightly improved diffraction, 
allowing recovery of a significant range of data. Most of the time, though, I 
find another crystal that had a better initial freeze, so annealing has never 
been a life saver--but it could be under dire circumstances.

James




On Oct 11, 2011, at 9:30 AM, Dr. Thayumanasamy Somasundaram wrote:

> Francis,
> 
> I would like to bring your attention to our paper in Acta Cryst D Volume 66 
> (6), 741-744 (2010) where we deal with spots under the ice-rings. We have 
> been very successful in eliminating the ice-rings and recover the data 
> underneath. If you are interested you can request the Python script from 
> Michael Chapman at OHSU.
> De-icing: recovery of diffraction intensities in the presence of ice rings, 
> Michael S. Chapman and Thayumanasamy Somasundaram
> 
> 
> If you need help please e-mail me outside the CCP4BB. 
> 
> On 10/11/2011 11:16 AM, Francis E Reyes wrote:
>> 
>> All,
>> 
>> 
>> So I have two intense ice rings where there appear to be lattice spots in 
>> between them. 
>> 
>> I understand that any reflections that lie directly on the ice ring are 
>> useless, however, how do software programs (HKL2000, d*Trek, mosflm, XDS) 
>> deal with these intermediate spots? 
>> 
>> It would seem to me that employing a 'resolution cut off' just before the 
>> ice ring (on the low resolution side) would be improper, as there are spots 
>> on the high resolution side of the ice. (see enclosed .tiff)
>> 
>> 
>> In fact, how do these programs deal with spots lying on ice rings? Are they 
>> rejected by some algorithm by those programs during integration, or is it up 
>> to the scaling/merging (by SCALA for example) step to deal with them? 
>> 
>> Thanks!
>> 
>> F
>> 
>> 
>> 
>> -
>> Francis E. Reyes M.Sc.
>> 215 UCB
>> University of Colorado at Boulder
>> 
>> 
>> 
>> 
>> 
> 
> -- 
> 
> Dr. Thayumanasamy Somasundaram [Soma]
> Director, X-Ray Crystallography Facility (XRF)
> Off. Ph: (850)644-6448  | Lab Ph: (850)645-1333   
> Fax:(850)644-7244   | E-mail: tsomasunda...@fsu.edu   
> 
> URI: www.sb.fsu.edu/~soma | URI: www.sb.fsu.edu/~xray 
> Postal Address--
> 91, Chieftan Way | KLB 414
> Institute of Molecular Biophysics 
> Florida State University  
> Tallahassee, FL 32306-4380, USA.  
>

Re: [ccp4bb] Ice rings... [maps and missing reflections]

2011-10-11 Thread Ed Pozharski 
On Tue, 2011-10-11 at 15:24 +, Bruno KLAHOLZ wrote:
> However, once you have determined and refined your structure it may be
> worth predicting the intensity of these spots and put them back for
> map calculation,

REFMAC does this by default, because

"expected value of unknown structure factors for missing reflections are
better approximated using DFc than with 0 values."

CNS defaults to excluding them.  As for phenix, I am not entirely sure -
it seems that phenix.refine does too (fill_missing_f_obs= False), but if
you use the GUI then the fill in option is turned on.



-- 
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs

Re: [ccp4bb] Ice rings... [maps and missing reflections]

2011-10-11 Thread Nat Echols 
On Tue, Oct 11, 2011 at 10:34 AM, Ed Pozharski wrote:

> CNS defaults to excluding them.  As for phenix, I am not entirely sure -
> it seems that phenix.refine does too (fill_missing_f_obs= False), but if
> you use the GUI then the fill in option is turned on.


In practice, it will be turned on for command-line phenix.refine too if you
don't supply your own custom map definitions - actually it produces both
"filled" and "unfilled" maps, but the former is what most users will see in
Coot.

-Nat

Re: [ccp4bb] Ice rings... [maps and missing reflections]

2011-10-11 Thread Pavel Afonine 
On Tue, Oct 11, 2011 at 10:34 AM, Ed Pozharski wrote:
>
> "expected value of unknown structure factors for missing reflections are
> better approximated using DFc than with 0 values."
>


better, but not always. What about say 80% or so complete dataset? Filling
in 20% of Fcalc (or DFcalc or bin-averaged  or else - it doesn't
matter, since the phase will dominate anyway) will highly bias the map
towards the model. Clearly there are cases where filling in a few missing
reflections significantly improves map interpretability without introducing
any bias.



> As for phenix, I am not entirely sure -
> it seems that phenix.refine does too (fill_missing_f_obs= False), but if
> you use the GUI then the fill in option is turned on.
>

phenix.refine always outputs two 2mFo-DFc maps: one is computed using the
original set of Fobs, and the other one is computed using set of Fobs where
missing reflections filled in with DFc calculated using well determined
atoms only. By default, Coot will open the "filled" one.

Pavel

[ccp4bb] off topic: Adobe demos deblur of photos...

2011-10-11 Thread Francis E Reyes 
http://hoowstuffworks.blogspot.com/2011/10/adobe-demos-amazing-unblur-feature.html

Though I can't really see the image myself... the gasp of the audience is 
telling


With respect to existing density modification programs, I wonder if such 
technology (whatever it is) can ever clear up my messy density maps.


F



-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

Re: [ccp4bb] off topic: Adobe demos deblur of photos...

2011-10-11 Thread Pete Meyer 
I could be wrong, but my understanding is that they're removing motion 
blur from the image - so I don't think it'll be directly applicable to 
density modification.


But I'd be very happy to be wrong on this one.

Pete

Francis E Reyes wrote:

http://hoowstuffworks.blogspot.com/2011/10/adobe-demos-amazing-unblur-feature.html

Though I can't really see the image myself... the gasp of the audience is 
telling


With respect to existing density modification programs, I wonder if such 
technology (whatever it is) can ever clear up my messy density maps.


F



-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

Re: [ccp4bb] off topic: Adobe demos deblur of photos...

2011-10-11 Thread Ethan Merritt 
On Tuesday, October 11, 2011 11:21:41 am Francis E Reyes wrote:
> http://hoowstuffworks.blogspot.com/2011/10/adobe-demos-amazing-unblur-feature.html
> 
> Though I can't really see the image myself... the gasp of the audience is 
> telling
> 
> 
> With respect to existing density modification programs, I wonder if such 
> technology 
> (whatever it is) can ever clear up my messy density maps.

The technology is directly parallel to TLSMD analysis.

It creates a model that includes a prediction of the blurring in the
original image, or in our case the blurring in the map generated by
Fourier transform of the original data.  The difference is that in the
case of a photograph one is interested in the altered image rather than
the underlying model.  In the case of a crystal structure one is interested
in the underlying model rather than the electron density map per se.

I have for a long time used the "motion-blurred photograph" parallel
to explain how TLSMD works.  See for example page 3 of
http://www.ccp4.ac.uk/schools/APS-2009/tutorials/tls/Merritt30th.pdf

Ethan

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742

Re: [ccp4bb] Ice rings... [maps and missing reflections]

2011-10-11 Thread Ed Pozharski 
On Tue, 2011-10-11 at 10:47 -0700, Pavel Afonine wrote:
> better, but not always. What about say 80% or so complete dataset?
> Filling in 20% of Fcalc (or DFcalc or bin-averaged  or else - it
> doesn't matter, since the phase will dominate anyway) will highly bias
> the map towards the model.

DFc, if properly calculated, is the maximum likelihood estimate of the
observed amplitude.  I'd say that 0 is by far the worst possible
estimate, as Fobs are really never exactly zero.  Not sure what the
situation would be when it's better to use Fo=0, perhaps if the model is
grossly incorrect?  But in that case the completeness may be the least
of my worries.

Indeed, phases drive most of the model bias, not amplitudes.  If model
is good and phases are good then the DFc will be a much better estimate
than zero.  If model is bad and phases are bad then filling in missing
reflections will not increase bias too much.  But replacing them with
zeros will introduce extra noise.  In particular, the ice rings may mess
things up and cause ripples.

On a practical side, one can always compare the maps with and without
missing reflections.

-- 
After much deep and profound brain things inside my head, 
I have decided to thank you for bringing peace to our home.
Julian, King of Lemurs

Re: [ccp4bb] Ice rings... [maps and missing reflections]

2011-10-11 Thread Pavel Afonine 
Hi Ed,

On Tue, Oct 11, 2011 at 11:47 AM, Ed Pozharski wrote:

> On Tue, 2011-10-11 at 10:47 -0700, Pavel Afonine wrote:
> > better, but not always. What about say 80% or so complete dataset?
> > Filling in 20% of Fcalc (or DFcalc or bin-averaged  or else - it
> > doesn't matter, since the phase will dominate anyway) will highly bias
> > the map towards the model.
>
> DFc, if properly calculated, is the maximum likelihood estimate of the
> observed amplitude.  I'd say that 0 is by far the worst possible
> estimate, as Fobs are really never exactly zero.  Not sure what the
> situation would be when it's better to use Fo=0, perhaps if the model is
> grossly incorrect?  But in that case the completeness may be the least
> of my worries.
>


Yes, that's all true about what is DFc. In terms of missing-Fobs-filling
it's not too important (as map appearance concerned) which values you take,
DFc,  , etc. I spent a few days playing with this some years ago.



> Indeed, phases drive most of the model bias, not amplitudes.  If model
> is good and phases are good then the DFc will be a much better estimate
> than zero.  If model is bad and phases are bad then filling in missing
> reflections will not increase bias too much.  But replacing them with
> zeros will introduce extra noise.  In particular, the ice rings may mess
> things up and cause ripples.
>

Yep, that was the point - sometimes it is good to do, and sometimes it is
not, and ...


> On a practical side, one can always compare the maps with and without
> missing reflections.
>

... this is why phenix.refine outputs both maps -:)

All the best,
Pavel

Re: [ccp4bb] off topic: Adobe demos deblur of photos...

2011-10-11 Thread Garib N Murshudov 
Position (general motion blur is a special case of it) dependent blurring can 
be applied to denisty improvement but problem is extremely ill posed. While 
deblurring you need to reduce noise amplification. Proper regularisation needs 
to be designed, probem becomes NxN linear equation where N is the number of 
grid points in density which might be a little bit large. However iterative 
method exists in inverse problems field.

regards
Garib



On 11 Oct 2011, at 19:37, Pete Meyer wrote:

> I could be wrong, but my understanding is that they're removing motion blur 
> from the image - so I don't think it'll be directly applicable to density 
> modification.
> 
> But I'd be very happy to be wrong on this one.
> 
> Pete
> 
> Francis E Reyes wrote:
>> http://hoowstuffworks.blogspot.com/2011/10/adobe-demos-amazing-unblur-feature.html
>> Though I can't really see the image myself... the gasp of the audience is 
>> telling
>> With respect to existing density modification programs, I wonder if such 
>> technology (whatever it is) can ever clear up my messy density maps.
>> F
>> -
>> Francis E. Reyes M.Sc.
>> 215 UCB
>> University of Colorado at Boulder

Garib N Murshudov 
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road 
Cambridge 
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk 
Web http://www.mrc-lmb.cam.ac.uk

Re: [ccp4bb] Ice rings... [maps and missing reflections]

2011-10-11 Thread Ed Pozharski 
On Tue, 2011-10-11 at 11:54 -0700, Pavel Afonine wrote:
> Yep, that was the point - sometimes it is good to do, and sometimes it
> is not, and

Do you have a real life example of Fobs=0 being better?  You make it
sound as if it's 50/50 situation.

-- 
"Hurry up before we all come back to our senses!"
   Julian, King of Lemurs

[ccp4bb] Pointless (P41) vs. Phaser (P43)

2011-10-11 Thread Young-Jin Cho 
Hi all,
I recently got diffraction data of 214 AA protein.  When I processed
the data, pointless suggested me a space group as P41. However, when I
ran Phaser with 'all choices of alternate space group', it gave me a
pdb file with P43. Additionally, phenix.xtriage suggested me P422 with
twin laws (h,-k,-l).
Anyway, it seems like P43 is right space group (I tried to process and
refine all possible space groups, and  based on R values P43 is most
reasonable).
At this point, I'd like to know more first why different programs
suggested different space group, and which is the most reliable way to
determine the space group. Also, what is the biggest difference
between these space groups. In practice, which way is the best method
to get a right space group other than trying all possible space groups
as I just did.

Thanks in advance,

Young-Jin

Re: [ccp4bb] Ice rings... [maps and missing reflections]

2011-10-11 Thread Pavel Afonine 
Do you have a real life example of Fobs=0 being better?



Hopefully, there will be a paper some time soon discussing all this - we
work on this right now.



> You make it
> sound as if it's 50/50 situation.
>


No (sorry if what I wrote sounded that misleading).

Pavel

Re: [ccp4bb] Pointless (P41) vs. Phaser (P43)

2011-10-11 Thread Frederic VELLIEUX 
P4(1) and P4(3) are enantiomorphic space groups. The only difference is the 
helix (one way, or another). No difference in the diffraction pattern. Hence a 
program (or a 
crystallographer) cannot distinguish the 2 based on the diffraction pattern.

Once you start phasing, e.g. by molecular replacement, there is one solution 
for one enantiomer and far worse statistics for the other enantiomer. This 
solves it.

And I'd like to point out that it is always a good idea to keep in mind the 
alternative space groups even if you think you are solving the structure but 
haven't solved it 
completely yet.

Fred.

> Message du 11/10/11 21:02
> De : "Young-Jin Cho" 
> A : CCP4BB@JISCMAIL.AC.UK
> Copie à : 
> Objet : [ccp4bb] Pointless (P41) vs. Phaser (P43)
> 
> Hi all,
> I recently got diffraction data of 214 AA protein. When I processed
> the data, pointless suggested me a space group as P41. However, when I
> ran Phaser with 'all choices of alternate space group', it gave me a
> pdb file with P43. Additionally, phenix.xtriage suggested me P422 with
> twin laws (h,-k,-l).
> Anyway, it seems like P43 is right space group (I tried to process and
> refine all possible space groups, and based on R values P43 is most
> reasonable).
> At this point, I'd like to know more first why different programs
> suggested different space group, and which is the most reliable way to
> determine the space group. Also, what is the biggest difference
> between these space groups. In practice, which way is the best method
> to get a right space group other than trying all possible space groups
> as I just did.
> 
> Thanks in advance,
> 
> Young-Jin
>

Re: [ccp4bb] Ice rings... [maps and missing reflections]

2011-10-11 Thread Randy Read 
If the model is really bad and sigmaA is estimated properly, then sigmaA will 
be close to zero so that D (sigmaA times a scale factor) will be close to zero. 
 So in the limit of a completely useless model, the two methods of map 
calculation converge.

Regards,

Randy Read

On 11 Oct 2011, at 19:47, Ed Pozharski wrote:

> On Tue, 2011-10-11 at 10:47 -0700, Pavel Afonine wrote:
>> better, but not always. What about say 80% or so complete dataset?
>> Filling in 20% of Fcalc (or DFcalc or bin-averaged  or else - it
>> doesn't matter, since the phase will dominate anyway) will highly bias
>> the map towards the model.
> 
> DFc, if properly calculated, is the maximum likelihood estimate of the
> observed amplitude.  I'd say that 0 is by far the worst possible
> estimate, as Fobs are really never exactly zero.  Not sure what the
> situation would be when it's better to use Fo=0, perhaps if the model is
> grossly incorrect?  But in that case the completeness may be the least
> of my worries.
> 
> Indeed, phases drive most of the model bias, not amplitudes.  If model
> is good and phases are good then the DFc will be a much better estimate
> than zero.  If model is bad and phases are bad then filling in missing
> reflections will not increase bias too much.  But replacing them with
> zeros will introduce extra noise.  In particular, the ice rings may mess
> things up and cause ripples.
> 
> On a practical side, one can always compare the maps with and without
> missing reflections.
> 
> -- 
> After much deep and profound brain things inside my head, 
> I have decided to thank you for bringing peace to our home.
>Julian, King of Lemurs

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 44 1223 336500
Wellcome Trust/MRC Building   Fax: + 44 1223 336827
Hills RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk

Re: [ccp4bb] Ice rings... [maps and missing reflections]

2011-10-11 Thread Garib N Murshudov 
In the limit yes. however limit is when we do not have solution, i.e. when 
model errors are very large.  In the limit map coefficients will be 0 even for 
2mFo-DFc maps. In refinement we have some model. At the moment we have choice 
between 0 and DFc. 0 is not the best estimate as Ed rightly points out. We 
replace (I am sorry for self promotion, nevertheless: Murshudov et al, 1997) 
"absent" reflection with DFc, but it introduces bias. Bias becomes stronger as 
the number of "absent" reflections become larger. We need better way of 
estimating "unobserved" reflections. In statistics there are few appraoches. 
None of them is full proof, all of them are computationally expensive. One of 
the techniques is called multiple imputation. It may give better refinement 
behaviour and less biased map. Another one is integration over all errors (too 
many parameters for numerical integration, and there is no closed form formula) 
of model as well as experimental data. This would give less biased map with 
more pronounced signal.

Regards
Garib


On 11 Oct 2011, at 20:15, Randy Read wrote:

> If the model is really bad and sigmaA is estimated properly, then sigmaA will 
> be close to zero so that D (sigmaA times a scale factor) will be close to 
> zero.  So in the limit of a completely useless model, the two methods of map 
> calculation converge.
> 
> Regards,
> 
> Randy Read
> 
> On 11 Oct 2011, at 19:47, Ed Pozharski wrote:
> 
>> On Tue, 2011-10-11 at 10:47 -0700, Pavel Afonine wrote:
>>> better, but not always. What about say 80% or so complete dataset?
>>> Filling in 20% of Fcalc (or DFcalc or bin-averaged  or else - it
>>> doesn't matter, since the phase will dominate anyway) will highly bias
>>> the map towards the model.
>> 
>> DFc, if properly calculated, is the maximum likelihood estimate of the
>> observed amplitude.  I'd say that 0 is by far the worst possible
>> estimate, as Fobs are really never exactly zero.  Not sure what the
>> situation would be when it's better to use Fo=0, perhaps if the model is
>> grossly incorrect?  But in that case the completeness may be the least
>> of my worries.
>> 
>> Indeed, phases drive most of the model bias, not amplitudes.  If model
>> is good and phases are good then the DFc will be a much better estimate
>> than zero.  If model is bad and phases are bad then filling in missing
>> reflections will not increase bias too much.  But replacing them with
>> zeros will introduce extra noise.  In particular, the ice rings may mess
>> things up and cause ripples.
>> 
>> On a practical side, one can always compare the maps with and without
>> missing reflections.
>> 
>> -- 
>> After much deep and profound brain things inside my head, 
>> I have decided to thank you for bringing peace to our home.
>>   Julian, King of Lemurs
> 
> --
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research  Tel: + 44 1223 336500
> Wellcome Trust/MRC Building   Fax: + 44 1223 336827
> Hills RoadE-mail: rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk

Garib N Murshudov 
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road 
Cambridge 
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk 
Web http://www.mrc-lmb.cam.ac.uk

Re: [ccp4bb] Ice rings... [maps and missing reflections]

2011-10-11 Thread Ethan Merritt 
On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
> In the limit yes. however limit is when we do not have solution, i.e. when 
> model errors are very large.  In the limit map coefficients will be 0 even 
> for 2mFo-DFc maps. In refinement we have some model. At the moment we have 
> choice between 0 and DFc. 0 is not the best estimate as Ed rightly points 
> out. We replace (I am sorry for self promotion, nevertheless: Murshudov et 
> al, 1997) "absent" reflection with DFc, but it introduces bias. Bias becomes 
> stronger as the number of "absent" reflections become larger. We need better 
> way of estimating "unobserved" reflections. In statistics there are few 
> appraoches. None of them is full proof, all of them are computationally 
> expensive. One of the techniques is called multiple imputation.

I don't quite follow how one would generate multiple imputations in this case.

Would this be equivalent to generating a map from (Nobs - N) refls, then
filling in F_estimate for those N refls by back-transforming the map?
Sort of like phase extension, except generating new Fs rather than new phases?

Ethan



> It may give better refinement behaviour and less biased map. Another one is 
> integration over all errors (too many parameters for numerical integration, 
> and there is no closed form formula) of model as well as experimental data. 
> This would give less biased map with more pronounced signal.
> 
> Regards
> Garib
> 
> 
> On 11 Oct 2011, at 20:15, Randy Read wrote:
> 
> > If the model is really bad and sigmaA is estimated properly, then sigmaA 
> > will be close to zero so that D (sigmaA times a scale factor) will be close 
> > to zero.  So in the limit of a completely useless model, the two methods of 
> > map calculation converge.
> > 
> > Regards,
> > 
> > Randy Read
> > 
> > On 11 Oct 2011, at 19:47, Ed Pozharski wrote:
> > 
> >> On Tue, 2011-10-11 at 10:47 -0700, Pavel Afonine wrote:
> >>> better, but not always. What about say 80% or so complete dataset?
> >>> Filling in 20% of Fcalc (or DFcalc or bin-averaged  or else - it
> >>> doesn't matter, since the phase will dominate anyway) will highly bias
> >>> the map towards the model.
> >> 
> >> DFc, if properly calculated, is the maximum likelihood estimate of the
> >> observed amplitude.  I'd say that 0 is by far the worst possible
> >> estimate, as Fobs are really never exactly zero.  Not sure what the
> >> situation would be when it's better to use Fo=0, perhaps if the model is
> >> grossly incorrect?  But in that case the completeness may be the least
> >> of my worries.
> >> 
> >> Indeed, phases drive most of the model bias, not amplitudes.  If model
> >> is good and phases are good then the DFc will be a much better estimate
> >> than zero.  If model is bad and phases are bad then filling in missing
> >> reflections will not increase bias too much.  But replacing them with
> >> zeros will introduce extra noise.  In particular, the ice rings may mess
> >> things up and cause ripples.
> >> 
> >> On a practical side, one can always compare the maps with and without
> >> missing reflections.
> >> 
> > 
> > --
> > Randy J. Read
> > Department of Haematology, University of Cambridge
> > Cambridge Institute for Medical Research  Tel: + 44 1223 336500
> > Wellcome Trust/MRC Building   Fax: + 44 1223 336827
> > Hills RoadE-mail: rj...@cam.ac.uk
> > Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk
> 
> Garib N Murshudov 
> Structural Studies Division
> MRC Laboratory of Molecular Biology
> Hills Road 
> Cambridge 
> CB2 0QH UK
> Email: ga...@mrc-lmb.cam.ac.uk 
> Web http://www.mrc-lmb.cam.ac.uk
> 
> 
> 
> 

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742

Re: [ccp4bb] Ice rings... [maps and missing reflections]

2011-10-11 Thread Dale Tronrud 
On 10/11/11 12:58, Ethan Merritt wrote:
> On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
>> In the limit yes. however limit is when we do not have solution, i.e. when 
>> model errors are very large.  In the limit map coefficients will be 0 even 
>> for 2mFo-DFc maps. In refinement we have some model. At the moment we have 
>> choice between 0 and DFc. 0 is not the best estimate as Ed rightly points 
>> out. We replace (I am sorry for self promotion, nevertheless: Murshudov et 
>> al, 1997) "absent" reflection with DFc, but it introduces bias. Bias becomes 
>> stronger as the number of "absent" reflections become larger. We need better 
>> way of estimating "unobserved" reflections. In statistics there are few 
>> appraoches. None of them is full proof, all of them are computationally 
>> expensive. One of the techniques is called multiple imputation.
> 
> I don't quite follow how one would generate multiple imputations in this case.
> 
> Would this be equivalent to generating a map from (Nobs - N) refls, then
> filling in F_estimate for those N refls by back-transforming the map?
> Sort of like phase extension, except generating new Fs rather than new phases?
> 
>   Ethan

   Unless you do some density modification you'll just get back zeros for
the reflections you didn't enter.

Dale
> 
> 
> 
>> It may give better refinement behaviour and less biased map. Another one is 
>> integration over all errors (too many parameters for numerical integration, 
>> and there is no closed form formula) of model as well as experimental data. 
>> This would give less biased map with more pronounced signal.
>>
>> Regards
>> Garib
>>
>>
>> On 11 Oct 2011, at 20:15, Randy Read wrote:
>>
>>> If the model is really bad and sigmaA is estimated properly, then sigmaA 
>>> will be close to zero so that D (sigmaA times a scale factor) will be close 
>>> to zero.  So in the limit of a completely useless model, the two methods of 
>>> map calculation converge.
>>>
>>> Regards,
>>>
>>> Randy Read
>>>
>>> On 11 Oct 2011, at 19:47, Ed Pozharski wrote:
>>>
 On Tue, 2011-10-11 at 10:47 -0700, Pavel Afonine wrote:
> better, but not always. What about say 80% or so complete dataset?
> Filling in 20% of Fcalc (or DFcalc or bin-averaged  or else - it
> doesn't matter, since the phase will dominate anyway) will highly bias
> the map towards the model.

 DFc, if properly calculated, is the maximum likelihood estimate of the
 observed amplitude.  I'd say that 0 is by far the worst possible
 estimate, as Fobs are really never exactly zero.  Not sure what the
 situation would be when it's better to use Fo=0, perhaps if the model is
 grossly incorrect?  But in that case the completeness may be the least
 of my worries.

 Indeed, phases drive most of the model bias, not amplitudes.  If model
 is good and phases are good then the DFc will be a much better estimate
 than zero.  If model is bad and phases are bad then filling in missing
 reflections will not increase bias too much.  But replacing them with
 zeros will introduce extra noise.  In particular, the ice rings may mess
 things up and cause ripples.

 On a practical side, one can always compare the maps with and without
 missing reflections.

>>>
>>> --
>>> Randy J. Read
>>> Department of Haematology, University of Cambridge
>>> Cambridge Institute for Medical Research  Tel: + 44 1223 336500
>>> Wellcome Trust/MRC Building   Fax: + 44 1223 336827
>>> Hills RoadE-mail: rj...@cam.ac.uk
>>> Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk
>>
>> Garib N Murshudov 
>> Structural Studies Division
>> MRC Laboratory of Molecular Biology
>> Hills Road 
>> Cambridge 
>> CB2 0QH UK
>> Email: ga...@mrc-lmb.cam.ac.uk 
>> Web http://www.mrc-lmb.cam.ac.uk
>>
>>
>>
>>
>

[ccp4bb] Industrial Research Associate Position

2011-10-11 Thread Bussiere, Dirksen 
We are looking for a research associate to join our group.  If you have any 
questions, please contact me.

-Dirk

Dirksen E. Bussiere, Ph.D., MBA
Director, Structural Chemistry
Novartis Institutes for BioMedical Research
4560 Horton Street, M/S 4.6
Emeryville, CA. 94608  USA
dirksen.bussi...@novartis.com

Scientific Associate I/II, Structural Chemistry
Req. No. 87432BR
NIBR - Novartis
Emeryville, CA

About Novartis Institute of Biomedical Research
At Novartis Institutes for BioMedical Research (“NIBR”), the global research 
organization of Novartis, we are committed to discovering innovative medicines 
to cure disease and improve human health. By hiring the best academic, biotech, 
and pharmaceutical trained scientists, we have fostered and atmosphere for drug 
discovery where innovation is rewarded. It is ultimately the talent of the 
individual that determines our success, while our state-of-the-art technologies 
and resources enable these ideas to be realized.

NIBR has sites in Cambridge, Massachusetts; Emeryville, CA; Basel, Switzerland; 
Horsham, UK; and Shanghai, China. Our Emeryville location focuses on early drug 
discovery efforts for the Oncology Disease Area and offers a variety of 
positions in Biology, Chemistry, and functions such as Technology, Patents, 
Research Sciences and other areas that support our scientific resources.

About Structural Chemistry:
The NIBR Emeryville Structural Chemistry group is responsible for actively 
pursuing the structures of macromolecular drug targets either as apo-proteins 
or in complex with lead compounds to help guide structure-based drug design, 
and actively participates in the drug discovery process. The group also 
provides biophysics and solutions studies support for drug discovery projects.

Position Description:
The qualified candidate will use his/her scientific expertise to aid in 
structure-based drug design efforts.   Specifically, this individual will 
determine high-resolution, three-dimensional structures of macromolecular drug 
targets (typically proteins), including crystallization and structure solution 
of medically important structures and target-ligand complexes. Additionally, 
this individual will interact with computational chemists and medicinal 
chemists to design new scaffolds and improve lead compounds.

Qualifications:
Qualified candidates will have a BS/MS in Biochemistry, Chemistry, or Molecular 
Biophysics with at least 4 years of relevant work experience in protein 
biochemistry, protein crystallization, and crystallographic methods, 
pharmaceutical industry experience is a plus. Strong computational and 
molecular modeling skills, experience in solution studies (calorimetry, NMR, 
etc.) and/or experience in structure-based drug design is preferred, as is 
experience with membrane protein biochemistry and/or crystallization. 
Candidates should have excellent verbal and written communication skills and 
the ability to work in large, multidisciplinary project teams.

To apply for this position, please visit:

http://novartis.avature.net/jobs#ViewJob/94

Re: [ccp4bb] Ice rings... [maps and missing reflections]

2011-10-11 Thread Garib N Murshudov 
Best way would be to generate from probability distributions derived after 
refinement, but it has a problem that you need to integrate over all errors. 
Another, simpler way would be generate using Wilson distribution multiple times 
and do refinement multiple times and average results. I have not done any tests 
but on paper it looks like a sensible procedure.

regards
Garib



On 11 Oct 2011, at 20:58, Ethan Merritt wrote:

> On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
>> In the limit yes. however limit is when we do not have solution, i.e. when 
>> model errors are very large.  In the limit map coefficients will be 0 even 
>> for 2mFo-DFc maps. In refinement we have some model. At the moment we have 
>> choice between 0 and DFc. 0 is not the best estimate as Ed rightly points 
>> out. We replace (I am sorry for self promotion, nevertheless: Murshudov et 
>> al, 1997) "absent" reflection with DFc, but it introduces bias. Bias becomes 
>> stronger as the number of "absent" reflections become larger. We need better 
>> way of estimating "unobserved" reflections. In statistics there are few 
>> appraoches. None of them is full proof, all of them are computationally 
>> expensive. One of the techniques is called multiple imputation.
> 
> I don't quite follow how one would generate multiple imputations in this case.
> 
> Would this be equivalent to generating a map from (Nobs - N) refls, then
> filling in F_estimate for those N refls by back-transforming the map?
> Sort of like phase extension, except generating new Fs rather than new phases?
> 
>   Ethan
> 
> 
> 
>> It may give better refinement behaviour and less biased map. Another one is 
>> integration over all errors (too many parameters for numerical integration, 
>> and there is no closed form formula) of model as well as experimental data. 
>> This would give less biased map with more pronounced signal.
>> 
>> Regards
>> Garib
>> 
>> 
>> On 11 Oct 2011, at 20:15, Randy Read wrote:
>> 
>>> If the model is really bad and sigmaA is estimated properly, then sigmaA 
>>> will be close to zero so that D (sigmaA times a scale factor) will be close 
>>> to zero.  So in the limit of a completely useless model, the two methods of 
>>> map calculation converge.
>>> 
>>> Regards,
>>> 
>>> Randy Read
>>> 
>>> On 11 Oct 2011, at 19:47, Ed Pozharski wrote:
>>> 
 On Tue, 2011-10-11 at 10:47 -0700, Pavel Afonine wrote:
> better, but not always. What about say 80% or so complete dataset?
> Filling in 20% of Fcalc (or DFcalc or bin-averaged  or else - it
> doesn't matter, since the phase will dominate anyway) will highly bias
> the map towards the model.
 
 DFc, if properly calculated, is the maximum likelihood estimate of the
 observed amplitude.  I'd say that 0 is by far the worst possible
 estimate, as Fobs are really never exactly zero.  Not sure what the
 situation would be when it's better to use Fo=0, perhaps if the model is
 grossly incorrect?  But in that case the completeness may be the least
 of my worries.
 
 Indeed, phases drive most of the model bias, not amplitudes.  If model
 is good and phases are good then the DFc will be a much better estimate
 than zero.  If model is bad and phases are bad then filling in missing
 reflections will not increase bias too much.  But replacing them with
 zeros will introduce extra noise.  In particular, the ice rings may mess
 things up and cause ripples.
 
 On a practical side, one can always compare the maps with and without
 missing reflections.
 
>>> 
>>> --
>>> Randy J. Read
>>> Department of Haematology, University of Cambridge
>>> Cambridge Institute for Medical Research  Tel: + 44 1223 336500
>>> Wellcome Trust/MRC Building   Fax: + 44 1223 336827
>>> Hills RoadE-mail: rj...@cam.ac.uk
>>> Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk
>> 
>> Garib N Murshudov 
>> Structural Studies Division
>> MRC Laboratory of Molecular Biology
>> Hills Road 
>> Cambridge 
>> CB2 0QH UK
>> Email: ga...@mrc-lmb.cam.ac.uk 
>> Web http://www.mrc-lmb.cam.ac.uk
>> 
>> 
>> 
>> 
> 
> -- 
> Ethan A Merritt
> Biomolecular Structure Center,  K-428 Health Sciences Bldg
> University of Washington, Seattle 98195-7742

Garib N Murshudov 
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road 
Cambridge 
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk 
Web http://www.mrc-lmb.cam.ac.uk

Re: [ccp4bb] Ice rings... [maps and missing reflections]

2011-10-11 Thread Ethan Merritt 
> On 10/11/11 12:58, Ethan Merritt wrote:
> > On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
> >> In the limit yes. however limit is when we do not have solution, i.e. when 
> >> model errors are very large.  In the limit map coefficients will be 0 even 
> >> for 2mFo-DFc maps. In refinement we have some model. At the moment we have 
> >> choice between 0 and DFc. 0 is not the best estimate as Ed rightly points 
> >> out. We replace (I am sorry for self promotion, nevertheless: Murshudov et 
> >> al, 1997) "absent" reflection with DFc, but it introduces bias. Bias 
> >> becomes stronger as the number of "absent" reflections become larger. We 
> >> need better way of estimating "unobserved" reflections. In statistics 
> >> there are few appraoches. None of them is full proof, all of them are 
> >> computationally expensive. One of the techniques is called multiple 
> >> imputation.
> > 
> > I don't quite follow how one would generate multiple imputations in this 
> > case.
> > 
> > Would this be equivalent to generating a map from (Nobs - N) refls, then
> > filling in F_estimate for those N refls by back-transforming the map?
> > Sort of like phase extension, except generating new Fs rather than new 
> > phases?
> > 
> > Ethan

Dale Tronrud wrote>
> 
>Unless you do some density modification you'll just get back zeros for
> the reflections you didn't enter.

Sure.  And different DM procedures would give you different imputations,
or at least that was my vague idea.

Garib N Murshudov wrote>
> Best way would be to generate from probability distributions derived after 
> refinement, but it has a problem that you need to integrate over all errors. 
> Another, simpler way would be generate using Wilson distribution multiple 
> times and do refinement multiple times and average results. I have not done 
> any tests but on paper it looks like a sensible procedure.

OK.  That makes sense.

Ethan

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742

[ccp4bb] change of origin for reflections or map

2011-10-11 Thread Klaas Decanniere 
Hi,

I have two solutions from the ShelX C/D/E pipeline I would like to compare
(different datasets, same protein). They seem to have different origins.
Space group is I222, with a choice of 8 origins.
How can I find and apply the correct shift to have the phase sets on a
common origin?
The information on http://www.ccp4.ac.uk/html/alternate_origins.html and
http://www.ccp4.ac.uk/html/non-centro_origins.html  explain it very well,
but thy don't point to the tools to use.
Is it a matter of reindex and trying all 8 possibilities?

thanks for your help,

Klaas Decanniere

Re: [ccp4bb] change of origin for reflections or map

2011-10-11 Thread George M. Sheldrick 
There are 4 possible origins in I222. There is a simple but inelegant way to
check. Run the SHELXE job for the second dataset four times, first with no MOVE 
instruction, then with one of the following MOVE instructions inserted between 
UNIT and the first atom in the *_fa.res file from SHELXD:

MOVE 0.5 0 0
MOVE 0 0.5 0
MOVE 0.5 0.5 0

one of these should give you phases with the same origin as your first dataset,
so if you display both maps from the .phs files in COOT they will superimpose.

George

On Tue, Oct 11, 2011 at 11:29:14PM +0200, Klaas Decanniere wrote:
> 
> 
> Hi,
> 
> I have two solutions from the ShelX C/D/E pipeline I would like to compare
> (different datasets, same protein). They seem to have different origins.
> Space group is I222, with a choice of 8 origins.
> How can I find and apply the correct shift to have the phase sets on a common
> origin?
> The information on http://www.ccp4.ac.uk/html/alternate_origins.html and 
> http:/
> /www.ccp4.ac.uk/html/non-centro_origins.html  explain it very well, but thy
> don't point to the tools to use.
> Is it a matter of reindex and trying all 8 possibilities?
> 
> thanks for your help,
> 
> Klaas Decanniere

-- 
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry, 
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

[ccp4bb] Postdoctoral position - membrane protein structure determination

2011-10-11 Thread Dr. M. Joanne Lemieux 
Applications are invited for a postdoctoral position to work on the
development of high throughput techniques for membrane protein structure
determination in collaboration with the Canadian Light Source researches
Drs. P. Grochulski and M. Fodje. The Canadian Macromolecular Crystallography
Facility (http://cmcf.lightsource.ca/), where the fellow will work part of
the time is located in Saskatoon a short drive away. Lemieux lab is involved
in the structure determination of membrane protein targets including
Rhomboid membrane embedded enzymes. These proteases are critical in cell
signaling pathways and have been linked to human disorders such as
hereditary blindness and breast cancer. We seek an enthusiastic
candidate *experienced
in macromolecular crystallography.* Experience with membrane protein
biochemistry would be an asset. In addition, the successful candidate should
be well-versed in one or more of the following areas: molecular biology,
protein purification, crystallization, membrane protein & lipid biochemistry
or automation.

This is an opportunity to join a lab experienced in the expression and
crystallization of membrane proteins (See *PNAS *(2007) 104(3):750-4,
and *Science,
*(2003)*. *301:616-620). Our department provides interaction with numerous
crystallographers. In addition, the membrane protein research group provides
a dedicated forum for membrane protein research at the University of Alberta
(http://www.mprg.med.ualberta.ca/index.php).The University of Alberta,
located in Edmonton, Alberta (Canada), is home to a large and interactive
community of biomedical scientists http://www.med.ualberta.ca/; support and
facilities for structural biology are excellent.

Edmonton, having a population of over 1 million, offers a
cosmopolitan environment with world class performing arts, sports, culinary
and recreational opportunities.  In addition, the city’s proximity to the
Rocky Mountains including the towns of Jasper and Banff is an additional
bonus.

Salary is commensurate with training and experience at the CIHR standard
rates. A medical and dental benefit package is included with salary. The
University of Alberta hires on the basis of merit. We are committed to the
principle of equity in employment. We welcome diversity and encourage
applications from all qualified women and men, including persons with
disabilities, members of visible minorities, and Aboriginal persons. The
records arising from this competition will be managed in accordance with
provisions of the Alberta Freedom of Information and Protection of Privacy
Act (FOIPP).



Please direct CV's or inquiries to Dr. M. Joanne Lemieux at the following
email address: joanne.lemi...@ualberta.ca .


-- 

**
M. Joanne Lemieux, Ph.D.
Assistant Professor,
Canada Research Chair in Membrane Protein
Structure and Function; AIHS Scholar
Department of Biochemistry,
Faculty of Medicine & Dentistry,
University of Alberta
Medical Sciences Bldg.
Office 4-53
Lab4-51
University of Alberta
Edmonton AB, T6G 2H7

office phone: 780-492-3586
lab phone:780-492-3465
fax: 780-492-0886

Lab web page:
http://www.biochem.ualberta.ca/faculty_detail.php?id=39#
 http://www2.biochem.ualberta.ca/LemieuxLab

Membrane protein disease research group:
http://www.mprg.med.ualberta.ca/index.php


CONFIDENTIALITY WARNING
This communication is intended for the use of the recipient to which it is
addressed, and may contain confidential, personal, and/or privileged
information. Please contact me immediately if you are not the intended
recipient of this communication, and do not copy, distribute, or take action
relying on it. Any communication received in error, or subsequent reply,
should be deleted or destroyed.

Re: [ccp4bb] change of origin for reflections or map

2011-10-11 Thread James Holton 
I wrote a little jiffy program for doing things like this:

http://bl831.als.lbl.gov/~jamesh/pickup/origins.com

you run it like this:
origins.com rigthorigin.pdb wrongorigin.pdb I222 correlate

This will shift "wrongorigin.pdb" by each of what I think are the
"allowed origin shifts", calculate an electron density map using
SFALL, and compare that map to the one made from "rightorigin.pdb".
The shift that gives the best correlation coefficient will then be
applied to "wrongorigin.pdb" and output as "neworigin.pdb".  There are
plenty of faster ways to do this, such as phenix.emma, but I still
like to use this script when I feel like being puerile (which is
often).

Now, the list of origins (at the bottom of the script) is something I
derived empirically by generating random atoms in a random cell and
applying random fractional shifts, searching for cases where the
structure factors are the same as the no-shift case.  Again, I did it
this way to avoid thinking about it.  My list has 8 different allowed
shifts for I222, but I assume this is because the 0,0,1/2 shift is
part of a symmetry operator.  I guess it is a matter of semantics as
to wether or not that is an "allowed shift"?

-James Holton
MAD Scientist

On Tue, Oct 11, 2011 at 2:58 PM, George M. Sheldrick
 wrote:
> There are 4 possible origins in I222. There is a simple but inelegant way to
> check. Run the SHELXE job for the second dataset four times, first with no 
> MOVE
> instruction, then with one of the following MOVE instructions inserted between
> UNIT and the first atom in the *_fa.res file from SHELXD:
>
> MOVE 0.5 0 0
> MOVE 0 0.5 0
> MOVE 0.5 0.5 0
>
> one of these should give you phases with the same origin as your first 
> dataset,
> so if you display both maps from the .phs files in COOT they will superimpose.
>
> George
>
> On Tue, Oct 11, 2011 at 11:29:14PM +0200, Klaas Decanniere wrote:
>>
>>
>> Hi,
>>
>> I have two solutions from the ShelX C/D/E pipeline I would like to compare
>> (different datasets, same protein). They seem to have different origins.
>> Space group is I222, with a choice of 8 origins.
>> How can I find and apply the correct shift to have the phase sets on a common
>> origin?
>> The information on http://www.ccp4.ac.uk/html/alternate_origins.html and 
>> http:/
>> /www.ccp4.ac.uk/html/non-centro_origins.html  explain it very well, but thy
>> don't point to the tools to use.
>> Is it a matter of reindex and trying all 8 possibilities?
>>
>> thanks for your help,
>>
>> Klaas Decanniere
>
> --
> Prof. George M. Sheldrick FRS
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Re: [ccp4bb] what is this called?

2011-10-11 Thread James Holton 
I think this is called "P21", with the additional annoyance that you
need to pick your Rfree set in P212121 and then symmetry-expand it.
Otherwise, your NCS operators will constrain your "free" reflections
to have the same intensity as their "NCS mates".  I'm sure you didn't
make that mistake, but a lot of other people have.

I suppose you could still call this "NCS", for "nearly
crystallographic symmetry".  But I think the general term
"pseudosymmetry" is what I would use in a paper.

I have seen one case (1FYK) where the protein followed the cannonical
crystallographic symmetry and the DNA was disordered along the screw
of the double helix.  Since O.L. was having a hard time interpreting
the DNA density, he re-grew the crystals with a new oligo containing a
single iodinated base to try and clear up the register, only to find
that the iodine difference map lit up _every_ base in the DNA ladder,
forming a beautiful double helix, with one atom!  That is: all the
"base pairs" in the density was actually composed of an equal portion
of all the bases in the oligo.

Not exactly the situation you are in, but definitely a case where one
part of the ASU had different "symmetry" than another.

-James Holton
MAD Scientist

On Mon, Oct 10, 2011 at 2:41 PM, Jon Schuermann  wrote:
> I am sure this has happened many many times before but I cannot find a
> reference. I have a protein/DNA complex structure where the protein has
> P212121 symmetry, but the DNA only has P21 symmetry. I know its
> pseudosymmetry caused by the NCS. Has anyone seen this with protein/DNA or
> have a reference I can add to my paper?
>
> Thanks so much,
>   Jon
>
> --
> Jonathan P. Schuermann, Ph. D.
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