Re: [ccp4bb] Harold Jeffreys

[James Stroud]

Bah...no Kindle Edition...I guess I'll have to keep reading The Grand Design.

James



On Mar 1, 2011, at 4:40 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote:

> For those who concern themselves with such matters, the 1973 edition of
> Sir Harold Jeffreys' "Scientific Inference" has just been reissued as a
> Cambridge paperback.
> Together with AFW Edwards' "Likelihood" this is good material for the finer
> aspects of
> inference I did only cursory touch in BMC chapter 7.  
> 
> Links and more on
> http://www.ruppweb.org/books/books_and_review_page.htm
> 
> Best, BR
> 
> 1. Edwards AWF (1992) Likelihood - An Account of the Statistical Concept of
> Likelihood and Its Application to Scientific Inference. Baltimore, MD: The
> Johns Hopkins University Press.
> 2. Jeffreys H (1973) Scientific Inference. Cambridge: Cambridge University
> Press.
> 3. Sivia DS (1996) Data Analysis - A Bayesian Tutorial. Oxford, UK: Oxford
> University Press.
> -
> Bernhard Hieronimus Rupp, Hofkristallrat a.D.
> 001 (925) 209-7429
> +43 (676) 571-0536
> b...@ruppweb.org
> hofkristall...@gmail.com
> http://www.ruppweb.org/
> --
> Knowledge: When you know a thing, to know that you know it,
> and when you do not know a thing, to recognize that you 
> do not know it. 
> Conficius.
> --

Re: [ccp4bb] Processing Laue data

[Pius Padayatti]

To all Laue experts up here
How does a Laue data is collected?

Thanks in advance to all
PSP

On Fri, Jan 28, 2011 at 3:43 AM, REX PALMER wrote:

>   What programs are available for processing Laue data to produce an
> intensity data set?
> Are explanatory notes or publications available?
>
> Rex Palmer
> Birkbeck College
>



-- 
Pius S Padayatti

Re: [ccp4bb] Processing Laue data

[Marius Schmidt]

there is a small but brave community that actually
attempted to collect Laue data on proteins with
modern synchrotron sources. They are all centered
around Keith Moffat in Chicago and Michael Wulff
in Grenoble. Maybe you contact these people: 
D. Bourgeois at the ESRF, V. Srajer or Z. Ren at the
APS.

Best
Marius

> What programs are available for processing Laue data to produce an
> intensity data set?
> Are explanatory notes or publications available?
>  
> Rex Palmer
> Birkbeck College
Dr.habil. Marius Schmidt
Asst. Professor
University of Wisconsin-Milwaukee
Department of Physics Room 454
1900 E. Kenwood Blvd.
Milwaukee, WI 53211

phone: +1-414-229-4338
email: m-schm...@uwm.edu
http://users.physik.tu-muenchen.de/marius/

[ccp4bb] Postdoctoral Position in protein crystallography/drug design

[Jenny Martin (IMB) UQ]

A postdoctoral position at research officer/senior research officer  
level is available in the laboratory of Professor Jenny Martin,  
Institute for Molecular Bioscience, University of Queensland,  
Brisbane, Australia.


The position is for one year in the first instance, with the  
possibility of extension out to 3 years.
The successful applicant will join a multidisciplinary team with the  
overall aim of discovering new drugs to tackle antibiotic-resistant  
bacteria.


Information on the project, the facilities available, selection  
criteria and how to apply for the position can be found at:

http://www.seek.com.au/Job/research-officer-senior-research-officer/in/brisbane/18992717

Applications close: Friday March 18, 2011

[ccp4bb] Harold Jeffreys

[Bernhard Rupp (Hofkristallrat a.D.)]

For those who concern themselves with such matters, the 1973 edition of
Sir Harold Jeffreys' "Scientific Inference" has just been reissued as a
Cambridge paperback.
Together with AFW Edwards' "Likelihood" this is good material for the finer
aspects of
inference I did only cursory touch in BMC chapter 7.  

Links and more on
http://www.ruppweb.org/books/books_and_review_page.htm

Best, BR

1. Edwards AWF (1992) Likelihood - An Account of the Statistical Concept of
Likelihood and Its Application to Scientific Inference. Baltimore, MD: The
Johns Hopkins University Press.
2. Jeffreys H (1973) Scientific Inference. Cambridge: Cambridge University
Press.
3. Sivia DS (1996) Data Analysis - A Bayesian Tutorial. Oxford, UK: Oxford
University Press.
-
Bernhard Hieronimus Rupp, Hofkristallrat a.D.
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
--
Knowledge: When you know a thing, to know that you know it,
and when you do not know a thing, to recognize that you 
do not know it. 
Conficius.
--

Re: [ccp4bb] while on the subject of stereo

[Jacob Keller]

> I heard somewhere that the reason chickens (which have eyes on
> the opposite sides of their heads, giving binocular vision a
> different meaning) bob their heads up and down is to get a 3D
> perspective.

Check out egrets when they are fishing--definitely triangulating,
maybe refraction-artifact-cancelling.

JPK

***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
cel: 773.608.9185
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] while on the subject of stereo

[Edward A. Berry]

Jim Pflugrath wrote:


One should be able to see 3D from the depth-cueing and by keeping the view
in motion.



 Don't ever use stereo glasses in a public seminar.


"putting the molecule in motion" is a good way to let the audience see 3D.
I like to make a small animated gif ("rocking gif") which rotates back
and forth through 3 or 5 pictures covering 5-10 degrees of rotaton about Y.

It seems recent versions of powerpoint have dropped support for
animated gif, so if I ever have to upgrade PP beyond office97 or 2000,
I will have to use movies, which I suspect will be significantly larger.

I heard somewhere that the reason chickens (which have eyes on
the opposite sides of their heads, giving binocular vision a
different meaning) bob their heads up and down is to get a 3D
perspective.  Definitely Jan Löwe's "type B" beings.

eab

Re: [ccp4bb] while on the subject of stereo

[Jan Löwe]

Ah! The question of to stereo or not to stereo! There has to be a 
scientific reason why this question is more popular than asking for what 
Linux distro is more fashionable this spring or why an Rmerge of 0.90 in 
the outermost shell is good for you and your structure.


I am offering my two (conflicting) theories (and apologies that both 
seem to imply some problem):


A) people who do use stereo have a problem with their brain because they 
cannot produce three dimensional vision from depth cues alone.


B) people who do not use stereo have a problem with their brain because 
they cannot see properly in three dimensions and rely on depth cues alone.


I personally prefer people with A) when I am their passenger in a car 
since they do not need to rotate by 90° to see how far the braking 
lights of the car in front are away :-)


jan



On 01/03/2011 21:35, Jim Pflugrath wrote:

I will offer my view.

I hate stereo glasses and hate stereo in general.

One should be able to see 3D from the depth-cueing and by keeping the view
in motion.  For fitting, I like to flip the view by 90 degrees.  I know I am
going to move in displayX and displayY, but never in displayZ.  I then
rotate the view around the vertical axis so thatn the old displayZ becomes
displayX.

Furthermore, I don't waste too much time fitting.  I know the software can
fit the map better than me, so I let it do its job.  I only need to get the
coordinates within the radius of convergence of the refinement program.  I
also know that 9 times out of 10, the displayed electron density is probably
suspect, so I believe in stereochemistry more than I believe in the map.

The main trick is to realize that as a human being, you really are not that
good at fitting the map or that it is unnecessary to waste your time since
the software is really so much better than you.  Refinement is quick enough
that you can try various hypotheses as in:  "If I move this here, then
refinement will do the trick" and "Well, that didn't work, so I will move
that over there and see if refinement will do the trick."

As for stereo figures, you should be able to convey what you want to say
from a good figure with depth-cueing, shadows, etc.  Don't ever use stereo
glasses in a public seminar.  Maybe my opinion will change with better
stereo technology.

OK, I know quite a lot of people will disagree with me. :)

Jim

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of David
Roberts
Sent: Tuesday, March 01, 2011 10:29 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] while on the subject of stereo

Hi again,

I'd like to ask a question about the pedagogy of stereo.  That is, using
stereo with students in the classroom.

Do you all find that, after setting up these elaborate stereo devices,
students really use the stereo or do they tend not to?

I am a huge fan of stereo - and frankly here we have quite a few options for
doing stereo - from the active Nvidia systems that people have recently been
discussing to passive zalmans. ...

As I mentioned, I like stereo a lot, but really projecting on a nice bright
lcd monitor also has it's advantages, and with the ease of moving things
using the mouse (or whatever device you use), the overall need for stereo
seems to be decreasing.  I don't know - I just wonder what peoples views are
out there for the actual "need" for stereo.  It's incredibly cool - and I
think is a very powerful way to show things - but I'm wondering if we focus
too much on it because it's cool and not because it's pedagogically
necessary.

Just wondering, no worries.  Thanks

Dave

[ccp4bb] Post-doctoral position in Structural Immunology (T and NK cell synapses) in Stockholm, Sweden

[Adnane Achour]

Dear group members, I would also like to bring this second opening to your 
attention:



ANNOUNCEMENT TITLE: 2 years Post-doctoral position in structural immunology 
with applications in T cell and NK cell receptor recognition of MHC class I and 
class II complexes in Stockholm, Sweden

DEADLINE FOR APPLICATIONS: 25 Mars 2011

TYPE OF POSITION: Post-doc

AFFILIATION INSTITUTION/DEPARTMENT: Center for Infectious Medicine (CIM), 
Department of Medicine, F59 Karolinska University Hospital in Huddinge, 
Karolinska Institutet, 16933 Stockholm.

LOCALIZATION OF THE ACHOUR LABORATORY: Department of Microbiology, Tumor and 
Cell Biology (MTC), Nobelsvägen 13, Karolinska Institute, 171 77 Stockholm.

CONTACT PERSON: Adnane Achour, Department of Microbiology, Tumor and Cell 
Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden. e-mail address: 
adnane.ach...@ki.se, Phone: +46-8-5248 6216, Fax: +46-8-30 42 76, website: 
http://www.medhs.ki.se/cim/



DESCRIPTION/REQUIREMENTS: A post-doctoral position is available for an 
enthusiastic individual for a period of at least two years within the 
laboratory of Assoc. Prof. Adnane Achour at the Center for Infectious Medicine 
(CIM), Karolinska Institutet in Stockholm, Sweden.


The candidate should be a good team-player, with excellent knowledge of X-ray 
crystallography and biochemistry. Insights in TCR/MHC interactions are an 
advantage. but not absolutely necessary She/he will help to co-supervise PhD 
students and will collaborate with other post-doctoral fellows in the group. 
She/he will be responsible for the expression, purification, crystallization 
and structural analysis of proteins that are involved in the structure of the T 
cell and NK cell synapse. The prime targets of this project are T and NK cell 
receptors and a large array of MHC class I and class II alleles as well as 
other co-receptors. Site directed mutagenesis studies will be combined with a 
wide array of biochemical and immunological assays, as well as imaging, in 
order to assess the molecular mechanisms underlying the modulation of T cell 
activation in cancer and infection-related projects. Determination of 
crystallization conditions as well as the determination and interpretation of 
three-dimensional structures of several of these proteins, alone and in 
complex, should be undertaken by the candidate in close collaboration with 
other members of the research group.



The Achour structural biology research group at CIM is well equipped for all 
aspects of modern structural biology, with state-of-the-art laboratories for 
molecular biology, recombinant expression in bacterial and eukaryotic systems, 
biochemistry, biophysics and X-ray crystallography. Excellent synchrotron 
access is available at BESSY and ESRF. Applicants must have a PhD, and 
experience in recombinant expression, protein purification, crystallization and 
X-ray crystallography. Information on our previous work in this field can be 
found by searching PubMed and via the CIM website



APPLICATION PROCEDURE: The application should include a personal motivation 
letter, a CV (including in particular any experience relevant to the position 
announced) as well as the names and contact details of 2 references. The 
applicants should also submit a list of publications and submitted manuscripts.

Adnane Achour, Associate Professor
fax:+46-8-30 42 76 phone:+46-8-5248 6216

Center for Infectious Medicine;

Department of Medicine,

Karolinska University Hospital Huddinge

Karolinska Institute

141 86 Stockholm, Sweden

url: http://ki.se/cim

url:http://www.medhs.ki.se/cim/medhs_eng.asp?Id=12&tabell=medhs_english

[ccp4bb] Post-doctoral position in Structural Parasitology in Stockholm, Sweden

[Adnane Achour]

Dear group members, I would like to bring the following opening to your 
attention:



ANNOUNCEMENT TITLE: 2 years Post-doctoral position in structural parasitology 
in Stockholm, Sweden

DEADLINE FOR APPLICATIONS: 25 Mars 2011 or until position filled

TYPE OF POSITION: Post-doc

AFFILIATION INSTITUTION/DEPARTMENT: Center for Infectious Medicine (CIM), 
Department of Medicine, F59 Karolinska University Hospital in Huddinge, 
Karolinska Institutet, 16933 Stockholm.

LOCALIZATION OF THE ACHOUR LABORATORY: Department of Microbiology, Tumor and 
Cell Biology (MTC), Nobelsvägen 13, Karolinska Institute, 171 77 Stockholm.

CONTACT PERSON: Adnane Achour, Department of Microbiology, Tumor and Cell 
Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden.

e-mail address: adnane.ach...@ki.se, Phone: +46-8-5248 6216, Fax: +46-8-30 42 
76, website: http://www.medhs.ki.se/cim/



DESCRIPTION/REQUIREMENTS: A post-doctoral position is available for an 
enthusiastic individual for a period of at least two years within the 
laboratory of Assoc. Prof. Adnane Achour at the Center for Infectious Medicine 
(CIM), Karolinska Institutet in Stockholm, Sweden.


The candidate should be a good team-player, with excellent knowledge of X-ray 
crystallography and biochemistry. She/he will be responsible for the 
expression, purification, crystallization and structural analysis of proteins 
that are involved in cytoadherence and sequestration of P. falciparum-infected 
erythrocytes. The prime targets of this project are several domains of the 
PfEMP1 variant antigen. Determination of crystallization conditions as well as 
the determination and interpretation of three-dimensional structures of several 
of these proteins, alone and in complex with ligands, should be undertaken by 
the candidate in close collaboration with other members of the research groups.



The Achour structural biology research group at CIM is well equipped for all 
aspects of modern structural biology, with state-of-the-art laboratories for 
molecular biology, recombinant expression in bacterial and eukaryotic systems, 
biochemistry, biophysics and X-ray crystallography. Excellent synchrotron 
access is available at BESSY and ESRF. Applicants must have a PhD, and 
experience in recombinant expression, protein purification, crystallization and 
X-ray crystallography. Information on our previous work in this field can be 
found by searching PubMed and via the CIM website



APPLICATION PROCEDURE: The application should include a personal motivation 
letter, a CV (including in particular any experience relevant to the position 
announced) as well as the names and contact details of 2 references. The 
applicants should also submit a list of publications and submitted manuscripts.



Adnane Achour, Associate Professor

fax:+46-8-30 42 76 tel;work:+46-8-5248 6216

Center for Infectious Medicine;

Department of Medicine,

Karolinska University Hospital Huddinge

Karolinska Institute

141 86 Stockholm, Sweden

url: http://ki.se/cim

url:http://www.medhs.ki.se/cim/medhs_eng.asp?Id=12&tabell=medhs_english

Re: [ccp4bb] while on the subject of stereo

[Jim Pflugrath]

I will offer my view.

I hate stereo glasses and hate stereo in general.  

One should be able to see 3D from the depth-cueing and by keeping the view
in motion.  For fitting, I like to flip the view by 90 degrees.  I know I am
going to move in displayX and displayY, but never in displayZ.  I then
rotate the view around the vertical axis so thatn the old displayZ becomes
displayX.

Furthermore, I don't waste too much time fitting.  I know the software can
fit the map better than me, so I let it do its job.  I only need to get the
coordinates within the radius of convergence of the refinement program.  I
also know that 9 times out of 10, the displayed electron density is probably
suspect, so I believe in stereochemistry more than I believe in the map.

The main trick is to realize that as a human being, you really are not that
good at fitting the map or that it is unnecessary to waste your time since
the software is really so much better than you.  Refinement is quick enough
that you can try various hypotheses as in:  "If I move this here, then
refinement will do the trick" and "Well, that didn't work, so I will move
that over there and see if refinement will do the trick."

As for stereo figures, you should be able to convey what you want to say
from a good figure with depth-cueing, shadows, etc.  Don't ever use stereo
glasses in a public seminar.  Maybe my opinion will change with better
stereo technology.

OK, I know quite a lot of people will disagree with me. :)

Jim

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of David
Roberts
Sent: Tuesday, March 01, 2011 10:29 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] while on the subject of stereo

Hi again,

I'd like to ask a question about the pedagogy of stereo.  That is, using
stereo with students in the classroom.

Do you all find that, after setting up these elaborate stereo devices,
students really use the stereo or do they tend not to?

I am a huge fan of stereo - and frankly here we have quite a few options for
doing stereo - from the active Nvidia systems that people have recently been
discussing to passive zalmans. ...

As I mentioned, I like stereo a lot, but really projecting on a nice bright
lcd monitor also has it's advantages, and with the ease of moving things
using the mouse (or whatever device you use), the overall need for stereo
seems to be decreasing.  I don't know - I just wonder what peoples views are
out there for the actual "need" for stereo.  It's incredibly cool - and I
think is a very powerful way to show things - but I'm wondering if we focus
too much on it because it's cool and not because it's pedagogically
necessary.

Just wondering, no worries.  Thanks

Dave

Re: [ccp4bb] Problem with refinement and positive electron density

[Judith Reeks]

Dear All,

Thank you for your suggestions. Many of you asked what the occupancies 
were in the region and they were all one, so partial occupancy was not 
the problem.


I was using TLS restraints during the refinement when this problem 
happened. Given the suggestions that TLS may be a problem and that might 
be causing the low B-factors, I went back and re-ran the refinement 
without TLS and the problem disappeared. Then I submitted my latest file 
to the TLSMD server for new restraints and the next round of refinement 
got rid of the problem. The B-factors increased to normal levels (~15 
compared to ~5 before) so it seems to have done the trick.


Thank you to everybody for their help,

Judith Reeks

ja...@st-andrews.ac.uk

School of Chemistry

University of St Andrews


On 01/03/2011 17:28, Mark Robien wrote:

Hmm - kinda interesting

In addition to the sorts of things suggested by Mark van Raaij, older 
versions of Refmac
were prone to have a phenomenon with B factors - once they get over a 
certain level, the algorithm
has a very hard time bring them back down, even when the data suggests 
it.


I've usually seen it with much higher B factors than you seem to have 
here - for example, loops where the B's
are actually 40-60, but previous rounds of refinement have the B 
factors 60-80 or higher.
Judging from the coot screen & the residues you are focusing on, I 
doubt that is the answer (unless you also
have a TLS model, in which case I'd wonder). If you do have TLS - 
well, things get more complicated; for example,

is this the edge of a TLS domain?

Nonetheless, you could try the solution for the problem that I 
describe - which is to reset all the B factors to a (very)
low B factor - maybe even as low as 2.0 (lower?), and then another 
round of refmac - with a sufficient number of
cycles - will re-refine the B (and xyz), thus escaping the region of 
refinement space that has a very weak gradient.


A variant approach that might be appropriate - similarly reset the B 
for the (?small) region of your model that has the problem.


Sadly, it's been awhile since I did any refinement myself - but the 
uppsala suite had some of the nicer tools for resetting B within pdb 
files, without having to do it manually (ugh - not appealing) - or 
writing an adhoc awk script (a very easy alternative, if you're 
familiar enough).


Mark Robien


On 3/1/2011 10:32 AM, Judith Reeks wrote:

Dear All,

I am currently refining a structure using the latest experimental 
version of Refmac (5.6) and there seems to be a problem with my Fo-Fc 
map. There is a region where I have fitted residues to the electron 
density but after refinement there is still positive electron density 
assigned to the region despite the fact that residues fit the 
electron density (see link below for a screenshot). Multiple rounds 
of refinement have yet to get rid of this problem. I have checked the 
PDB file and there does not appear to be any problems with this 
region. Has anybody seen something like this before?


http://i1083.photobucket.com/albums/j382/jreeks/Screenshot2011-03-01at1613402.png

Regards,

Judith Reeks

ja...@st-andrews.ac.uk

School of Chemistry

University of St Andrews

Re: [ccp4bb] Graphics card for Nvidia 3D vision

[David Schuller]

The Viewsonic and Samsung monitors are both 1680x1050 resolution. A new 
crop of monitors came out last year with 1920x1080 resolution.


We have an Acer GD235HZ and a Planar SA2311W, each operating off a 
Quadro 3800 with the optional stereo connector.


Other monitor models compatible with the nVidia 3D Vision are listed here:
http://www.nvidia.com/object/3d-vision-requirements.html

The sync signal to the glasses is infrared, so if you have two systems 
interfering with each other you can try to restrict the spread from the 
transmitter with a paper cone, or by careful placement of equipment, or 
some such.



On 03/01/2011 08:39 AM, Harry M. Greenblatt wrote:

BS"D

Dear Andreas

   We have several examples of Linux working with the Quadro FX3800 
with the optional 3pin connector, and either the Viewsonic 3D display, 
or the Samsung 2233RZ


On Mar 1, 2011, at 11:14 AM, Andreas Eichinger wrote:


Dear colleagues,

We are currently setting up a new 3D workstation with a Samsung 
SyncMaster 2233RZ monitor


--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

[ccp4bb] International PhD Programme at CNIO, Madrid

[Daniel Lietha]

Dear colleague,

We would like to draw your attention to the call for the * International
Ph.D. Programme* at the Spanish National Cancer Research Centre (CNIO) in
Madrid. We would greatly appreciate if you could forward the information
below to potential candidates.



The CNIO offers excellent training and research opportunities in cutting
edge basic and applied cancer research. The centre is equipped with state of
the art facilities for protein expression, crystallisation, X-ray
crystallography and NMR (including crystallisation robots, crystal farms,
X-ray generators etc.). Several structural biology groups offer research
opportunities in various areas of cancer biology.


 The deadline for applications is *March 15th, 2011*. Further information on
the programme and the application procedure can be found at: www.cnio.es/phd

To print a copy of the poster:
http://www.cnio.es/es/cursos/descargas/doctorado/Poster_PhD_2011.pdf


For further information, please contact our Training Manager, Mar Pérez at
p...@cnio.es.


Thank you,


Daniel Lietha
Cell Signalling and Adhesion Group
Structural Biology and Biocomputing Programme
Spanish National Cancer Research Centre (CNIO)
C/ Melchor Fernández Almagro, 3, E-28029
Madrid, Spain
Tel: + (34) 917 328 000 ext. 3090
Email: dlie...@cnio.es

Re: [ccp4bb] Problem with refinement and positive electron density

[Vellieux Frederic]

Judith Reeks wrote:


Dear All,

 

I am currently refining a structure using the latest experimental 
version of Refmac (5.6) and there seems to be a problem with my Fo-Fc 
map. There is a region where I have fitted residues to the electron 
density but after refinement there is still positive electron density 
assigned to the region despite the fact that residues fit the electron 
density (see link below for a screenshot). Multiple rounds of 
refinement have yet to get rid of this problem. I have checked the PDB 
file and there does not appear to be any problems with this region. 
Has anybody seen something like this before?


 


http://i1083.photobucket.com/albums/j382/jreeks/Screenshot2011-03-01at1613402.png

 


Regards,

 


Judith Reeks

ja...@st-andrews.ac.uk

School of Chemistry

University of St Andrews

Yes, I have encountered such a situation before, where the occupancy was 
not set to 1.0. For some reason the occupancy had been set well below 
one. This is the first thing I would check. I can't remember right now 
why this had happened.


Fred.

Re: [ccp4bb] Problem with refinement and positive electron density

[Mark J van Raaij]

when these kind of things occur to me it always is a silly mistake like:
- occupancies of the new residues set to 0.0
- reading in the old pdb-file when running refmac instead of the new one
- calculating the map with the old refmac output instead of the new output
- reading in and/or displaying the old map in coot instead of the new map
but I guess you checked all this...

Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/content/research/macromolecular/mvraaij/index.php?l=1



On 1 Mar 2011, at 17:32, Judith Reeks wrote:

> Dear All,
>  
> I am currently refining a structure using the latest experimental version of 
> Refmac (5.6) and there seems to be a problem with my Fo-Fc map. There is a 
> region where I have fitted residues to the electron density but after 
> refinement there is still positive electron density assigned to the region 
> despite the fact that residues fit the electron density (see link below for a 
> screenshot). Multiple rounds of refinement have yet to get rid of this 
> problem. I have checked the PDB file and there does not appear to be any 
> problems with this region. Has anybody seen something like this before?
>  
> http://i1083.photobucket.com/albums/j382/jreeks/Screenshot2011-03-01at1613402.png
>  
> Regards,
>  
> Judith Reeks
> ja...@st-andrews.ac.uk
> School of Chemistry
> University of St Andrews

[ccp4bb] Problem with refinement and positive electron density

[Judith Reeks]

Dear All,

I am currently refining a structure using the latest experimental 
version of Refmac (5.6) and there seems to be a problem with my Fo-Fc 
map. There is a region where I have fitted residues to the electron 
density but after refinement there is still positive electron density 
assigned to the region despite the fact that residues fit the electron 
density (see link below for a screenshot). Multiple rounds of refinement 
have yet to get rid of this problem. I have checked the PDB file and 
there does not appear to be any problems with this region. Has anybody 
seen something like this before?


http://i1083.photobucket.com/albums/j382/jreeks/Screenshot2011-03-01at1613402.png

Regards,

Judith Reeks

ja...@st-andrews.ac.uk

School of Chemistry

University of St Andrews

[ccp4bb] while on the subject of stereo

[David Roberts]

Hi again,

I'd like to ask a question about the pedagogy of stereo.  That is, using 
stereo with students in the classroom.


Do you all find that, after setting up these elaborate stereo devices, 
students really use the stereo or do they tend not to?


I am a huge fan of stereo - and frankly here we have quite a few options 
for doing stereo - from the active Nvidia systems that people have 
recently been discussing to passive zalmans.  I went from SGI systems 
and crystaleyes to linux systems using nuvision glasses, and finally 
have settled for Zalman stereo - as I think it is the best thing out 
there.  Zalman is passive - go to the movies and get a free pair of 
glasses (realD glasses work fine), and you don't have to have any video 
card requirements (I haven't tried using it with onboard stereo - I do 
have graphics cards, but I have a feeling onboard stereo wouldn't be bad).


When in a classroom - we project using glasses that work on an emitter 
based system (so it's active stereo - we are thinking of going passive 
in the classroom as well).  When we use stereo in a classroom, we find 
you take just as much time telling students they need to look forward as 
we do talking about active sites.  In some cases, the stereo may be 
distracting.  Many can't get it to work - and when they do I don't know 
how effective it is.


I teach a crystallography class, and for that I have a linux lab setup 
with 6 computers equipped with Zalman stereo (recent, it was active 
nuvision before).  Students have to fit a map and build a MIR structure 
(from scratch totally) using coot.  It's a great experience, but I find 
that I have to constantly get them to put on stereo glasses to get the 
best fit of their model in the map.  They tend to not do it, and so I'm 
trying to see if it's the type of stereo used (as I said, I had a few 
options, and this class actually has their range of devices) or if it's 
just that they can do it good enough without stereo.  They do prefer the 
LCD monitor over a CRT display (and that is a brightness thing I think - 
they are just crisper and newer).  When on the CRT's, they will use 
stereo (active), but when on the LCD displays stereo is not necessarily 
used (they don't seem to need it as much).


As I mentioned, I like stereo a lot, but really projecting on a nice 
bright lcd monitor also has it's advantages, and with the ease of moving 
things using the mouse (or whatever device you use), the overall need 
for stereo seems to be decreasing.  I don't know - I just wonder what 
peoples views are out there for the actual "need" for stereo.  It's 
incredibly cool - and I think is a very powerful way to show things - 
but I'm wondering if we focus too much on it because it's cool and not 
because it's pedagogically necessary.


Just wondering, no worries.  Thanks

Dave

[ccp4bb] ICSG 2011 early registration and abstracts submission open until March 4

[Tom Terwilliger]

Dear Colleagues,
 
We hope that you are planning to attend the International Conference on 
Structural Genomics 2011, which will be held in Toronto, Canada on May 10-14, 
2011.
 
Due to technical difficulties with the registration page, we have extended both 
the early registration and abstract submission deadlines. Abstract submission 
and early bird registration will now end Friday March 4th at 11:59pm EST.
 
Please visit http://www.icsg2011.org  for ICSG 2011 meeting and workshop 
registration details and to submit your abstract.
 
We hope to see you there!
 
Best regards,
 
Cheryl Arrowsmith
ICSG 2011 Organizer
 
Ted Baker
Stephen Burley
Dino Moras
Joel Sussman
Shigeyuki Yokoyama
Tom Terwilliger
ISGO Executive Committee

Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072 email: terwilli...@lanl.gov
Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: 
http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

Re: [ccp4bb] Examples of images from various detectors

[James Holton]

Well, my personal "museum of image file formats" is here:

http://bl831.als.lbl.gov/example_data_sets/

Which I have organized by light source since although the "file format" 
is technically the same for a given detector model, the meaning of the 
contents of the header (such as the beam center) varies from place to 
place.  So, technically, there are probably as many "file formats" as 
there are beamlines in the world (~100).  My goal here is to try and 
establish a collection of "easy" datasets in each format so that a 
random end user or software developer can be confident that they are 
processing a given image type correctly (like getting the sign of 
anomalous pairs right!). You may notice that my collection is far from 
complete, but you are welcome to copy what you need, and contributions 
are welcome!


-James Holton
MAD Scientist

On 3/1/2011 5:22 AM, Ashley Buckle wrote:

Dear All

I am looking for example files of most common detector formats eg from 
the mosflm doc (below).  I have some of the most common ones we use 
routinely eg Mar, ADSC and R-Axis but if anyone has by chance compiled 
an archive of example files, or can point me in the right direction 
that would be great!


cheers
Ashley

• Mar Research (18cm (SMALLMAR), 30cm or 34.5 cm plate (MAR));
• Mar Research CCD detectors (both 135 and 165 mm) as well as the Mar 
Mosaic detector (MARCCD);

• ADSC Quantum 4, Q210 and Q315 CCD detectors (ADSC);
• Mac Science Dip2000 (DIP2000), 2020 (DIP2020), 2030 (DIP2030) or 
2040 (DIP2040) (horizontal or vertical rotation axis);

• R-Axis II (RAXIS) (horizontal or vertical rotation axis),
• R-Axis IV (RAXIS4 or RAXISIV) (Horizontal or vertical rotation axis),
• R-Axis V (RAXIS5 or RAXISV),
• Rigaku Jupiter, Saturn, Mercury CCD detectors,
• ESRF Image intensifier CCD (ESRF CCD),
• Molecular dynamics (offline) (MD),
• FUJI scanners (offline) (FUJI BAS2000 or FUJI BA100),
• Ed Westbrook or Oxford Instruments 3x3 CCD detector (SBC1),
• Brandeis 2x2 CCD detector (B4) (ADSC),
• ESRF Large Image Plate Scanner (LIPS),
• There is limited support for the Oxford Sapphire CCD and Bruker 
SMART and Proteum detectors.



Associate Professor Ashley M Buckle
NHMRC Senior Research Fellow
The Department of Biochemistry and Molecular Biology,
Faculty of Medicine
Building 77
Monash University, Clayton, Vic 3800
Australia

http://www.med.monash.edu.au/biochem/staff/abuckle.html
iChat: ashley.buc...@me.com 
skype: ashley.buckle
Tel: (613) 9902 9313 (office)
Fax : (613) 9902 9500
mobile: 0430 913031

Re: [ccp4bb] Graphics card for Nvidia 3D vision

[Alexander . Schiffer]

Dear Harry,
 
as you mention two screens: have you ever tried to use two 3D screens?
We currently have that setup but are not too happy with it. So I wonder
if its a general problem or very specific to our setup.
 
Best regards,
 
Alexander
 
 




From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Harry M. Greenblatt
Sent: Tuesday, March 01, 2011 2:40 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Graphics card for Nvidia 3D vision


BS"D 

Dear Andreas

   We have several examples of Linux working with the Quadro
FX3800 with the optional 3pin connector, and either the Viewsonic 3D
display, or the Samsung 2233RZ.  We find the Samsung to have  better
image quality.  As noted by others, in Europe you must specifically ask
for the 3pin cable, since this is not bundled with the glasses, as it
was (still is??) in North America.  We use the consumer grade product,
since we have no need for long range viewing.

As Carsten noted you can also use two screens, and we have one
working example of this (Viewsonic 3D, and LG normal).


Harry


On Mar 1, 2011, at 11:14 AM, Andreas Eichinger wrote:


Dear colleagues,

We are currently setting up a new 3D workstation with a
Samsung SyncMaster 2233RZ monitor and a Nvidia 3D vision glasses kit on
a Redhat Enterprise Linux box. According to Nvidia, a Quadro FX 4800,
Quadro FX 4600 or Quadro FX 3700 graphics card can be used for 3D on
Linux if it is connected via a 3-pin mini-DIN stereo connector. Has
somebody experience with such a setup?

Any help is kindly appreciated. Thanks in advance.

Andreas Eichinger




-

Harry M. Greenblatt

Associate Staff Scientist

Dept of Structural Biology
harry.greenbl...@weizmann.ac.il

Weizmann Institute of SciencePhone:  972-8-934-3625

Rehovot, 76100   Facsimile:   972-8-934-4159

Israel 

[ccp4bb] Opportunity in 2D Crystallography of Membrane proteins

[Schertler Gebhard]

We are looking for a PhD student in cryo electron microscopy. Our laboratory 
(http://lbr.web.psi.ch/) is working with a number of membrane proteins and in 
particular G protein coupled receptors. The goal is to prepare stabilized 
membrane proteins in a highly functional form and reconstitute them with lipids 
into two-dimensional crystals for 2D crystallography strategies. The candidate 
will work in a very experienced group at the Paul Scherrer Institute in 
Switzerland and we have exceptional facilities supporting the preparative work 
and the crystallographic measurements. The project is part of the preparation 
for the Swiss X-ray Free Electron Laser (SwissFEL). The candidate is expected 
to have a Master degree in Chemistry, Biochemistry or related fields. 

Please send a letter of interest and a CV directly to Dr Ching-Ju Tsai 
(ching-ju.t...@psi.ch).

Recent publications from the Schertler Laboratory:

Standfuss J, Edwards PC, D'Antona A, Fransen M, Xie G., Oprian DD, & Schertler 
GF. The structural basis of agonist induced activation in constitutively active 
rhodopsin. Nature. 2011; in press.

 

Warne T, Moukhametzianov R, Baker JG, Nehmé R, Edwards PC, Leslie AG, Schertler 
GF, Tate CG. The structural basis for agonist and partial agonist action on a 
β(1)-adrenergic receptor. Nature. 2011; 469(7329):241-4.

 

Prof. Gebhard F.X. Schertler

Head of Biology and Chemistry

Paul Scherrer Institut

Laboratory of Biomolecular Research, BMR

OFLC 109

CH-5232 Villigen PSI

gebhard.schert...@psi.ch

phone +41 (0)56 310 4265

http://bio.web.psi.ch/  

 

 

Re: [ccp4bb] Graphics card for Nvidia 3D vision

[Harry M. Greenblatt]

BS"D

Dear Andreas

   We have several examples of Linux working with the Quadro FX3800  
with the optional 3pin connector, and either the Viewsonic 3D  
display, or the Samsung 2233RZ.  We find the Samsung to have  better  
image quality.  As noted by others, in Europe you must specifically  
ask for the 3pin cable, since this is not bundled with the glasses,  
as it was (still is??) in North America.  We use the consumer grade  
product, since we have no need for long range viewing.


As Carsten noted you can also use two screens, and we have one  
working example of this (Viewsonic 3D, and LG normal).



Harry


On Mar 1, 2011, at 11:14 AM, Andreas Eichinger wrote:


Dear colleagues,

We are currently setting up a new 3D workstation with a Samsung  
SyncMaster 2233RZ monitor and a Nvidia 3D vision glasses kit on a  
Redhat Enterprise Linux box. According to Nvidia, a Quadro FX 4800,  
Quadro FX 4600 or Quadro FX 3700 graphics card can be used for 3D  
on Linux if it is connected via a 3-pin mini-DIN stereo connector.  
Has somebody experience with such a setup?


Any help is kindly appreciated. Thanks in advance.

Andreas Eichinger


 
-

Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology   harry.greenbl...@weizmann.ac.il
Weizmann Institute of SciencePhone:  972-8-934-3625
Rehovot, 76100   Facsimile:   972-8-934-4159
Israel

[ccp4bb] Examples of images from various detectors

[Ashley Buckle]

Dear All

I am looking for example files of most common detector formats eg from the 
mosflm doc (below).  I have some of the most common ones we use routinely eg 
Mar, ADSC and R-Axis but if anyone has by chance compiled an archive of example 
files, or can point me in the right direction that would be great!

cheers
Ashley

• Mar Research (18cm (SMALLMAR), 30cm or 34.5 cm plate (MAR));
• Mar Research CCD detectors (both 135 and 165 mm) as well as the Mar 
Mosaic detector (MARCCD);
• ADSC Quantum 4, Q210 and Q315 CCD detectors (ADSC);
• Mac Science Dip2000 (DIP2000), 2020 (DIP2020), 2030 (DIP2030) or 2040 
(DIP2040) (horizontal or vertical rotation axis);
• R-Axis II (RAXIS) (horizontal or vertical rotation axis),
• R-Axis IV (RAXIS4 or RAXISIV) (Horizontal or vertical rotation axis),
• R-Axis V (RAXIS5 or RAXISV),
• Rigaku Jupiter, Saturn, Mercury CCD detectors,
• ESRF Image intensifier CCD (ESRF CCD),
• Molecular dynamics (offline) (MD),
• FUJI scanners (offline) (FUJI BAS2000 or FUJI BA100),
• Ed Westbrook or Oxford Instruments 3x3 CCD detector (SBC1),
• Brandeis 2x2 CCD detector (B4) (ADSC),
• ESRF Large Image Plate Scanner (LIPS),
• There is limited support for the Oxford Sapphire CCD and Bruker SMART 
and Proteum detectors.


Associate Professor Ashley M Buckle
NHMRC Senior Research Fellow
The Department of Biochemistry and Molecular Biology,
Faculty of Medicine
Building 77
Monash University, Clayton, Vic 3800
Australia

http://www.med.monash.edu.au/biochem/staff/abuckle.html
iChat: ashley.buc...@me.com
skype: ashley.buckle
Tel: (613) 9902 9313 (office)
Fax : (613) 9902 9500
mobile: 0430 913031

Re: [ccp4bb] Graphics card for Nvidia 3D vision

[Schubert, Carsten [PRDUS]]

Andreas,

I can only second what Chris was saying. We have the same setup (FX3800
with separate riser for stereo connection) used in all of our machines
and it works very well. In terms of monitor I would recommend to spend a
bit more money and go with an Alienware or Asus 3D LCD, both are running
at 1920x1080, vs. 1680x1050. There may be newer ones out there with the
same capabilities, but you need to make sure the driver supports the
newer monitors. Initially the ASUS monitors were not supported in the
195.xx.xx series of drivers, but it worked after updating to the latest
drivers. I personally prefer the Alienware since it has a matte finish,
but the quality on both is excellent. 

As for the kit, I ran into the issue were the 3D vision kit was bundled
with the Asus monitors and they were missing the stereo cables, I
suppose they were bundled for the European market. NVIDIA support was
unwilling to send me the missing cables even though we are using quite a
bit of their hardware, so much for customer support... So beware when
you are buying the cheaper bundles. The Nvidia website has a list of the
Kits, which include the stereo cable. Also another thing to watch out
for is not to confuse the newer 3D Vision Pro line with the older
consumer grade line. The Pro line emitter work on RF vs. the older grade
emitters work on IR. As far as I know they are not compatible.

You can even run stereo in dual-monitor mode. That's how I reuse old
LCDs. One LCD for stereo, the other adds more real-estate. Haven't found
a reliable way to get this to work from the get-go though. I suppose
it's is a problem with our outdated X-server, but can be overcome with
the nvidia-settings tool.

HTH

Carsten


> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Chris Richardson
> Sent: Tuesday, March 01, 2011 5:27 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Graphics card for Nvidia 3D vision
> 
> >>> Andreas Eichinger  03/01/11 9:24 AM >>>
> 
> > We are currently setting up a new 3D workstation with a Samsung
> > SyncMaster 2233RZ monitor and a Nvidia 3D vision glasses kit on a
> > Redhat Enterprise Linux box. According to Nvidia, a Quadro FX 4800,
> > Quadro FX 4600 or Quadro FX 3700 graphics card can be used for 3D on
> > Linux if it is connected via a 3-pin mini-DIN stereo connector. Has
> > somebody experience with such a setup?
> 
> The FX 3800 will also work, but it doesn't have a mini-DIN connector.
> You can buy a separate riser fitted with the connector, which mounts
in
> a spare slot next to the card and connects to it by a cable.  This is
> made by PNY, part number 900-50762--000.  In our experience, an FX
> 3800 and separate riser is a lot cheaper than a card with a built-in
> DIN connector.
> 
> When you buy the 3D Vision glasses kit, check that it contains the
> mini-DIN to emitter cable.  At one stage this was included in kits for
> the US market, but not in kits for Europe.  This may have changed.
> 
> We use the same monitor with an FX 3800 and 3D vision glasses kit on a
> couple of machines and are very impressed with the quality of the
> stereo.  The glasses are a lot nicer than the old models, and it's
nice
> being able to recharge them by USB rather than constantly swapping
> batteries because someone left the arms open and the glasses active
> overnight.
> 
> Regards,
> 
> Chris
> 
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable
> Company Limited by Guarantee, Registered in England under Company No.
> 534147 with its Registered Office at 123 Old Brompton Road, London SW7
> 3RP.
> 
> This e-mail message is confidential and for use by the addressee only.
> If the message is received by anyone other than the addressee, please
> return the message to the sender by replying to it and then delete the
> message from your computer and network.

Re: [ccp4bb] Graphics card for Nvidia 3D vision

[Chris Richardson]

>>> Andreas Eichinger  03/01/11 9:24 AM >>>

> We are currently setting up a new 3D workstation with a Samsung  
> SyncMaster 2233RZ monitor and a Nvidia 3D vision glasses kit on a  
> Redhat Enterprise Linux box. According to Nvidia, a Quadro FX 4800,  
> Quadro FX 4600 or Quadro FX 3700 graphics card can be used for 3D on  
> Linux if it is connected via a 3-pin mini-DIN stereo connector. Has  
> somebody experience with such a setup?

The FX 3800 will also work, but it doesn't have a mini-DIN connector.  You can 
buy a separate riser fitted with the connector, which mounts in a spare slot 
next to the card and connects to it by a cable.  This is made by PNY, part 
number 900-50762--000.  In our experience, an FX 3800 and separate riser is 
a lot cheaper than a card with a built-in DIN connector.

When you buy the 3D Vision glasses kit, check that it contains the mini-DIN to 
emitter cable.  At one stage this was included in kits for the US market, but 
not in kits for Europe.  This may have changed.

We use the same monitor with an FX 3800 and 3D vision glasses kit on a couple 
of machines and are very impressed with the quality of the stereo.  The glasses 
are a lot nicer than the old models, and it's nice being able to recharge them 
by USB rather than constantly swapping batteries because someone left the arms 
open and the glasses active overnight.

Regards,

Chris

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
message is received by anyone other than the addressee, please return the 
message to the sender by replying to it and then delete the message from your 
computer and network.

[ccp4bb] problem running tutorial data in phenix autosol

[Seema Nath]

dear all,
 i was trying to run the sad tutorial data in phenix autosol. the 
p9 sad worked really well in the fast mode building almost the entire 
structure, but the se17 sad data does not give good results. it shows an fom of 
34.6 and r factor of 33.2 in P41 spacegroup. autobuild built only a part of the 
model which was no where to the deposited structure pdb 1qqe. i would be very 
grateful to know the exact way to run the sec17-sad data in autosol and the 
post processes.
 
seema nath

Re: [ccp4bb] Graphics card for Nvidia 3D vision

[Pedro M. Matias]

Yes, we recently installed such a system and it works very well.

Minor drawback: the 3D Vision system interferes with the older 3D 
stereo (NuVision) system - we have 4 stereo workstations in the same 
room, 3 old and one new.
We don't know yet whether there are interference problems between 
machines with 3D Vision in the same room.


Regards,

Pedro Matias

At 09:14 01-03-2011, Andreas Eichinger wrote:

Dear colleagues,

We are currently setting up a new 3D workstation with a Samsung
SyncMaster 2233RZ monitor and a Nvidia 3D vision glasses kit on a
Redhat Enterprise Linux box. According to Nvidia, a Quadro FX 4800,
Quadro FX 4600 or Quadro FX 3700 graphics card can be used for 3D on
Linux if it is connected via a 3-pin mini-DIN stereo connector. Has
somebody experience with such a setup?

Any help is kindly appreciated. Thanks in advance.

Andreas Eichinger


Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal

[ccp4bb] Graphics card for Nvidia 3D vision

[Andreas Eichinger]

Dear colleagues,

We are currently setting up a new 3D workstation with a Samsung  
SyncMaster 2233RZ monitor and a Nvidia 3D vision glasses kit on a  
Redhat Enterprise Linux box. According to Nvidia, a Quadro FX 4800,  
Quadro FX 4600 or Quadro FX 3700 graphics card can be used for 3D on  
Linux if it is connected via a 3-pin mini-DIN stereo connector. Has  
somebody experience with such a setup?


Any help is kindly appreciated. Thanks in advance.

Andreas Eichinger