[ccp4bb] The oldest science

2021-03-31 Thread David Schuller

https://www.haaretz.com/archaeology/.premium-somebody-in-the-kalahari-had-a-crystal-collection-105-000-years-ago-1.9670735


 Somebody in the Kalahari Had a Crystal Collection 105,000 Years Ago


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




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Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

2021-02-17 Thread David Schuller
It was my understanding that you attended medical school. I am surprised 
that there was no instruction pertaining to the ethics of obtaining 
consent for human subject trials.




On 2/17/21 2:09 PM, Jacob Keller wrote:
But does it end better than the current best-seller "Smoldering 
Pandemic Paralyzes Human Race, Fuels Contention, Kills Millions, 
Drives the Rest Mad?"


JPK



On Wed, Feb 17, 2021 at 12:40 PM David Schuller <mailto:schul...@cornell.edu>> wrote:


I read that book. It does not end well.


On 2/17/21 12:33 PM, Jacob Keller wrote:

It would seem to me that it should be possible to generate
versions of the Covid virus that would:

A. be extremely contagious and yet
B. be clinically benign, and
C. confer immunity to the original covid virus.

If, then, this virus could be released, with appropriate "kill
switch" safeguards built in, would this not solve the world's
pandemic problems? Is there any reason, practically, why this
approach would not be feasible?

Maybe we don't really know enough to manipulate A, B, C yet?

Or maybe it's too scary for primetime...nightmare bio-warfare
apocalypse?

Has this sort of thing been done, or does it have a name?

Jacob
-- 


+

Jacob Pearson Keller

Assistant Professor

Department of Pharmacology and Molecular Therapeutics

Uniformed Services University

4301 Jones Bridge Road

Bethesda MD 20814

jacob.kel...@usuhs.edu <mailto:jacob.kel...@usuhs.edu>;
jacobpkel...@gmail.com <mailto:jacobpkel...@gmail.com>

Cell: (301)592-7004

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Jacob Pearson Keller

Assistant Professor

Department of Pharmacology and Molecular Therapeutics

Uniformed Services University

4301 Jones Bridge Road

Bethesda MD 20814

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jacobpkel...@gmail.com <mailto:jacobpkel...@gmail.com>


Cell: (301)592-7004

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   schul...@cornell.edu




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Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

2021-02-17 Thread David Schuller

I read that book. It does not end well.


On 2/17/21 12:33 PM, Jacob Keller wrote:
It would seem to me that it should be possible to generate versions of 
the Covid virus that would:


A. be extremely contagious and yet
B. be clinically benign, and
C. confer immunity to the original covid virus.

If, then, this virus could be released, with appropriate "kill switch" 
safeguards built in, would this not solve the world's pandemic 
problems? Is there any reason, practically, why this approach would 
not be feasible?


Maybe we don't really know enough to manipulate A, B, C yet?

Or maybe it's too scary for primetime...nightmare bio-warfare apocalypse?

Has this sort of thing been done, or does it have a name?

Jacob
--

+

Jacob Pearson Keller

Assistant Professor

Department of Pharmacology and Molecular Therapeutics

Uniformed Services University

4301 Jones Bridge Road

Bethesda MD 20814

jacob.kel...@usuhs.edu ; 
jacobpkel...@gmail.com 


Cell: (301)592-7004

+




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Re: [ccp4bb] Tiny rocks on my CX100 shipping dewar

2020-12-04 Thread David Schuller
We use aquarium gravel for this purpose. It does not have the fine 
dust-like particles that normal construction gravel might.


On 12/4/20 11:42 AM, Nukri Sanishvili wrote:

Hi John,
I think I know what might have happened:
Many of the MX beamlines at the APS use some sort of filler in the 
containers where the LN2 is dumped. If I remember correctly, one of 
the beamlines is using fine gravel for this purpose. Also, it is 
required that before shipping, the dewars are emptied - i.e. don't 
contain liquid. Now, imagine somebody dumping the liquid into the 
grave-filled container without removing the blue cap and without 
holding the dewar in the air - i.e. the top of the dewar with the cap 
on is slightly buried into the gravel. Upon straightening the dewar 
up, the blue cap would scoop up a little bit of the gravel. 
Distribution of the pebbles on your picture is also noteworthy. It 
suggests the side where the pebbles are was the side dipped into the 
gravel.

You might want to discuss this with your beamline host.
Best,
Nukri

On Fri, Dec 4, 2020 at 10:05 AM Tanner, John J. > wrote:


When we opened our CX100 shipping dewar returned from APS via
FedEx this week, we observed what appears to be tiny rocks on the
rim below the foam neck core:

https://www.dropbox.com/s/ky09a1vbm9t0mrl/CX100withrocks.png?dl=0


Has anyone seen this before? Is this perhaps the absorbent
material from the inside of the dewar?

Thanks,

Jack

John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: tanne...@missouri.edu 
https://cafnrfaculty.missouri.edu/tannerlab/

Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A



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Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Quote source inquiry

2020-07-16 Thread David Schuller
There are cases where cell dimensions vary in a very real way. I have a 
system in which the unit cell volume can differ by more than 10%. When I 
first explored this system in the long ago times, before 
cryo-crystallography was a thing, the unit cell dimensions would change 
during data collection. This is one reason I am not eager to jump on the 
"RT is superior" bandwagon.


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



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Re: [ccp4bb] Relaying a remote data collection on using moodle collaborate or Microsoft Teams

2020-07-03 Thread David Schuller
We routinely use NoMachine NX or X2Go to share the desktop for remote 
data collection. And recently I have personally collected data using 
such while simultaneously running a Zoom window for communication. 
Internet speed to my home is about 100 Mbps download, 11 Mbps upload. A 
few notes:


If the remote desktop is full access rather than view-only, there is the 
fun game of fighting for control of the mouse. A voice channel is useful 
for establishing who gets the wheel.


If limited bandwidth and latency are issues, limit use of streaming 
video. Our video windows allow reduction of the frame rate for precisely 
that reason.


In Zoom, and I presume in equivalent applications, you can turn the 
video off and use it for sound sharing only. If the desktop is being 
shared via NX there is no need to share it again with a second app.


The data collection and the Zoom or equivalent do not necessarily need 
to be running on the same machine. Our data collection workstations tend 
not to have cameras and microphones.


I have no experience with Teams nor anything else that is geared to 
Microsoft/Windows.


Cheers,


On 2020-07-03 04:18, Nicholas Keep wrote:
We are going to be doing a data collection for an MRes student at 
Diamond in the next couple of weeks.  These are his first crystals.  
It would be good if he could be involved in watching it.


I was wondering if anyone had tried sharing screen and voice via 
moodle collaborate or Microsoft Teams while doing a data collection?  
Zoom is deprecated by our institution but if anyone had succeeded on 
zoom that would also be interesting.


I am on Virgin media 100 MB broadband which is pretty much achieving 
that (upload is only around 9 MB though).


Alternatively we can try and set him up to connect via nx and watch, 
but that would lose the sound connection unless I have a phone tucked 
under my chin.


We could just record my screen and sound and he could watch later.

Any tips?

Best wishes

Nick





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===
All Things Serve the Beam
===
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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

2020-06-30 Thread David Schuller
By all means, if you still have "disks" you should get rid of them, and 
replace them with some modern storage.




On 2020-06-29 21:17, Edward A. Berry wrote:
Now can we get rid of all the superfluous disks in our RAID? Or at 
least not replace them when they fail?


On 06/29/2020 06:24 PM, Andreas Förster wrote:
I like to think that the reflections I carefully measured at high 
multiplicity are not redundant, which the dictionary on my computer 
defines as "not or no longer needed or useful; superfluous" and the 
American Heritage Dictionary as "exceeding what is necessary or 
natural; superfluous" and "needlessly repetitive; verbose".


Please don't use the term Needless repetitivity in your Table 1.  It 
sends the wrong message.  Multiplicity is good.


All best.


Andreas



On Tue, Jun 30, 2020 at 12:03 AM James Holton > wrote:


    I have found that the use of "redundancy" vs "multiplicity" 
correlates very well with the speaker's favorite processing 
software.  The Denzo/HKL program scalepack outputs "redundancy", 
whereas scala/aimless and other more Europe-centric programs output 
"multiplicity".


    At least it is not as bad as "intensity", which is so ambiguous 
as to be almost useless as a word on its own.


    -James Holton
    MAD Scientist

    On 6/24/2020 10:27 AM, Bernhard Rupp wrote:


    > Oh, and some of us prefer the word 'multiplicity' ;-0

    Hmmm…maybe not. ‘Multiplicity’ in crystallography is context 
sensitive, and not uniquely defined. It can refer to 


 1. the position multiplicity (number of equivalent sites per 
unit cell, aka Wyckoff-Multiplicity), the only (!) cif use of 
multiplicity
 2. the multiplicity of the reflection, which means the 
superposition of reflections with the same /d/  (mostly powder 
diffraction) 

 3. the multiplicity of observations, aka redundancy.

    While (a) and (b) are clearly defined, (c) is an arbitrary 
experimental number.


    How from (a) real space symmetry follows (b) in reciprocal space 
(including the epsilon zones, another ‘multiplicity’) is explained 
here 


    https://scripts.iucr.org/cgi-bin/paper?a14080 
 



    and also on page 306 in BMC.

    Too much multiplicity might create duplicity… 

    Cheers, BR

    __ __

    Jon Cooper

    __ __

    On 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)" 
mailto:tom.p...@csiro.au>> wrote:


    I would just like to point out that for those of us who have 
worked too many times with P1 or P21 that even 360 degrees will not 
give you 'super' anomalous differences. 


    I'm not a minimalist when it comes to data- redundancy is a 
good thing to have. 


    cheers, tom 

    __ __

    Tom Peat
    Proteins Group
    Biomedical Program, CSIRO
    343 Royal Parade
    Parkville, VIC, 3052
    +613 9662 7304
    +614 57 539 419
    tom.p...@csiro.au  

    __ __



--


    *From:*CCP4 bulletin board > on behalf of 
0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
 
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
>

    *Sent:* Wednesday, June 24, 2020 1:10 AM
    *To:* CCP4BB@JISCMAIL.AC.UK  
mailto:CCP4BB@JISCMAIL.AC.UK>>
    *Subject:* Re: [ccp4bb] number of frames to get a full 
dataset? 


    

    Someone told me there is a cubic space group where you can 
get away with something like 11 degrees of data. It would be 
interesting if that's correct. These minimum ranges for data 
collection rely on the crystal being pre-oriented, which is 
unheard-of these days, 

Re: [ccp4bb] number of frames to get a full dataset?

2020-06-22 Thread David Schuller
The old saying was degrees, not frames. If your frame width is not 1 
degree, the result will differ accordingly.


One factor is whether the detector is centered or offset, and whether it 
is large enough to get the entire pattern. If the detector is offset, 
you are not getting the full diffraction from that position.


I don't think radiation damage figures into this. It might make it more 
difficult to get N degrees, but it does not change how much diffraction 
is necessary.




On 2020-06-22 18:03, Murpholino Peligro wrote:

Hi.
Quick question...
I have seen *somewhere* that to get a 'full dataset we need to collect 
n frames':

at least 180 frames if symmetry is X
at least 90 frames if symmetry is Y
at least 45 frames if symmetry is Z
Can somebody point where is *somewhere*?

...also...
what other factors can change n... besides symmetry and radiation damage?

Thanks



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Re: [ccp4bb] disinfecting keyboards

2020-04-29 Thread David Schuller
If you are going that route, it would make sense to locate the UV lamps 
in the X-ray hutch, since those already have safety interlocks, etc. The 
X-ray beam itself is too directional to uniformly cover much.



On 2020-04-29 15:48, Eduardo Rodríguez-Román wrote:

Hi Tim,
It may be convenient to install a UV light lamp in the room. Have you 
thought about that?
I do not know if any of the equipment may suffer damage in the medium 
or long term due to the incidence of UV light. You must evaluate this.
UV light is used in different microbiology laboratories around the 
world to sterilize the work area.
Just turn on the UV light about ten min before entering the room, then 
turn off the UV light, and wait another 15 min to enter. When leaving, 
turn on the UV light for 10 min, and then turn off.

The UV light on/off switch should be located outside the room.
Best,
Eduardo.

On Wed, Apr 29, 2020 at 2:53 PM Tim Gruene > wrote:


Dear all,

can you make suggestions for how to disinfect computer keyboards, and
instrument panels?

Our facility is going to reboot next week, with shifts so that people
don't meet. The main interface will be the computer keyboards, as well
as the door of our X-ray diffractometer and the mounting of the
crystals.

The keyboard labels may not like alcohols (and the efficiency of
injecting disinfecting through the USB cable is also under discussion,
so I heard).

One way would be to use individual keyboards, and wearing gloves for
replugging, and to use gloves for mounting crystals.

But maybe there are other ways that won't require gloves?

Best regards,
Tim

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Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Biotechnology and Plant Virology Lab
Center for Microbiology and Cell Biology
Instituto Venezolano de Investigaciones Científicas
PO Box 20632, Caracas 1020A, Venezuela.
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Phone: +58 (212) 504 1189/1366/1500 
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Re: [ccp4bb] CCP4 7.1 released

2020-04-23 Thread David Schuller
Coincidentally, Python 2 had its final release just a few days ago. I 
trust python components of CCP4 are all now using Python 3.


https://www.theregister.co.uk/2020/04/21/the_final_python_2_release/

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

--


On 2020-04-23 12:30, Eugene Krissinel wrote:



Dear CCP4 Users,

The CCP4 Core Group is very pleased to announce the release of the 
latest version of the CCP4 Software Suite. Version 7.1 (Skipton) is 
now available from the CCP4 download website 
. The release is available for all 
MS Windows, Linux and Mac OSX platforms.



Is it really necessary to switch to CCP4 7.1 now?

While CCP4 7.0 can be kept on your computers for as long as necessary 
and in parallel to CCP4 7.1 (Mac OSX and Linux only), we encourage all 
our users to switch over at first convenience because:


 1. the release brings new, updated and improved components that make
structure solution with CCP4 yet more efficient and easy
 2. the update line for CCP4 7.0 is now discontinued
 3. support for CCP4 7.0, as well as for all earlier versions of CCP4,
is no longer available


CCP4 7.1 Release Highlights

CCP4 Release 7.1 comes as a complete modernisation of version 7.0, 
which have seen the longest life time ever in CCP4 history, being 
released more than 4 years ago and complemented with 79 updates. 
However, changes in operating systems and advances in computer 
languages, accumulated over this significant time period, have made it 
necessary to introduce technical modifications, such as progressing to 
C++-11, that could not be carried out using the CCP4 update system.



  Main Updates and Improvements

CCP4 7.1 represents the final state of 7.0 update series, complemented 
with newest versions of many important components, for example:



COOT 0.9

/The latest version of Interactive Model Building Software from Dr. 
Paul Emsley, MRC/LMB, Cambridge, with many improvements and new features./


Currently available only for Mac OSX and Linux users. The 
corresponding update for Windows systems will be issued as soon as 
feasible



DIALS 2.1

/Diffraction image processing software from Diamond Light Source Ltd., 
CCP4 and the Lawrence Berkeley National Laboratory. DIALS now includes 
a scaling module and improved multi-crystal symmetry tools./



DUI 2019.12

/A Graphical User Interface for DIALS programs./


XIA2 0.6.0

/Automated diffraction image processing using an expert system./


PHASER 2.8.3

/Maximum likelihood structure solution software from the group of 
Prof. Randy Read, Cambridge./



SHELX

/SHELX Software from Prof. George Sheldrick, University of Goettingen, 
Germany (SHELXE is supported by Dr. Isabel Uson, Barcelona, Spain)/



Buccaneer

/BUCCANEER Software from Dr. Kevin Cowtan, University of York, UK, 
with important fixes and improvements/


and many others. CCP4 continues to provide


ARP/wARP 8.0

/Automated Model Building Software from Dr. Victor Lamzin, EMBL 
Outstation in Hamburg, Germany/ integrated with the CCP4 Core package.


In CCP4 7.1, you will find considerably advanced and improved:


CCP4i2

/CCP4 Graphical Interface with many tasks and report pages revised and 
partly redesigned, numerous bugs fixed and overall stability 
enhanced./ In particular, CCP4i2 now contains the deposition module, 
which allows you to prepare files in mmCIF format, suitable for 
deposition to the PDB in a fairly automated manner.



  New Software

In addition to numerous modifications, advances and updates, CCP4 7.1 
introduces a few brand new components:



GEMMI

/C++/Python application and library for handling coordinate and 
reflection data (from Marcin Wojdyr, Global Phasing Ltd., Cambridge, UK)/


GEMMI is a highly efficient and sophisticated package for manipulating 
coordinate and reflection data in various formats (such as .pdb, 
.mmcif, .mtz). The package is very useful for developing MX-related 
applications in C++ and Python.



MRparse

/Assistant application for making and analysing search models for 
Molecular Replacement (from the group of Prof. Daniel Rigden, 
University of Liverpool, UK)/


MRparse finds suitable structure homologs, aligns and represents them 
graphically for reference and more efficient MR ensembling. Available 
in CCP4i2 interface.



CCP4 Cloud

/A framework for distributed CCP4 Computation/

CCP4 Cloud represents a conceptually new approach to organising and 
maintaining crystallographic projects in CCP4 and running CCP4 tasks. 

Re: [ccp4bb] Methods to improve ligand density of a homodimer?

2020-04-20 Thread David Schuller

It sounds like you are looking for MAPROT.

http://www.ccp4.ac.uk/html/maprot.html


On 2020-04-20 15:23, Kyle Gregory wrote:

Hello all,

I have a homodimer structure in P1 21 1 spacegroup, the dimer is 
likely a crystallographic artefact, where it looks like the monomer is 
rotated by ~ 180 degrees around the Y axis.


I am assessing ligand binding and each of the monomers display density 
at the site but it is not as clear as I would like. A polder map does 
help things but I was wondering if it is feasible, or if there are any 
tools, that can be used to improve density based of the fact there are 
two molecles present. Is there some way to sum (probably the wrong 
word here) the densities at the binding site?


Kind regards,

Kyle



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Re: [ccp4bb] MX data processing with GPUs??

2020-02-19 Thread David Schuller
Thank you for the info. Another of the Threadripper 3xxx series, the 
3990X has 64 cores for 128 threads, so perhaps it is time to raise that 
99*99 limit in XDS.




On 2020-02-19 07:21, Kay Diederichs wrote:

Dear Ana,

it is easy to ask the question (and I've been asked several times), but 
somewhat difficult to answer. To add to Graeme's excellent explanations:

- all developers of MX processing software have seriously considered to 
implement their algorithms on GPUs, and have decided that the effort (which is 
very significant) is not worth it, in terms of benefit for users and developers 
(who should pay them for the effort? - after all, this would not result in a 
highly cited publication!). We are aware of the fact that they are much faster 
than CPUs for specific types of calculations that are most useful for images 
where each pixel is treated in the same way - but these types of (potentially 
highly parallel) calculations do not represent a large fraction of where a MX 
data processing program spends its time, and even worse, the parallel and 
serial parts of the calculation alternate in fast succession (XDS has on the 
order of 10 parallel regions, none of which dominates the CPU time). 
Ultimately, it is the serial fraction of a program that determines its 
potential speed-up, due to Amdahl's law.

- MX data processing programs (at least XDS and DIALS) already exploit 
parallelism by using multiple CPUs at the same time; the current version of XDS 
can in principle use up to 99*99=9801 processors, and 60 machines each running 
60 threads (see below) would process a 360° dataset composed of 0.1° frames 
within seconds, if DELPHI=6.

- the recent Ryzen Threadripper 3XXX series CPUs have a significantly better 
cost/performance ratio than other processor families. A TR 3970X workstation 
can be bought for less than 5000€, and offers 64 threads. Graeme mentions AMD 
Rome; this is the server variant. The data transfer would become the 
bottleneck; to me, a cluster of workstations each equipped with two 10Gb ports 
looks attractive.

Finally, I have the feeling that speed in data collection and processing is 
over-rated. I get the impression that some (many?) people think they should 
collect a data set as quickly as the machine permits. But they may not be aware 
of the fact that the quality of the data is then not optimal. Going 10 times 
slower, and reducing the transmission to 10%, gives a resonable safety margin.

Further questions arise - does every crap crystal have to be put into the beam? 
And does every crap data set have to be processed? Do all of us really want and 
need to collect from thousands of crystals every synchrotron day? Are all of us 
really producing that many crystals? Who is? (you probably realize my lack of 
imagination by now)
I know that people who build and run synchrotron beamlines have a different perspective, 
concerning these questions, than their users. Some common sense, and a lot of discussion, 
would  benefit our community more than resorting to technological "solutions".

best wishes,
Kay

On Wed, 19 Feb 2020 08:08:40 +, Winter, Graeme (DLSLtd,RAL,LSCI) 
 wrote:


Dear Ana,

To follow up on the contributions from others, there are some particular 
annoyances with MX processing which differentiate it from other “big data” or 
imaging problems.

In tomographic reconstruction you have a big block of data which needs to (as a 
simplistic approximation) be transformed by a bunch of trigonometric functions 
to another big block of data. The shape of the calculation is the same 
independent of the data itself, and overall this represents a massively 
parallel computationally expensive problem, which makes it worth the cost of 
getting the data in and out of the GPU (this is not cheap) - even in this case, 
the parallelism of modern CPUs means that this is not a given. These folks are 
usually the ones who are making a lot of noise about how awesome GPU boards 
are, and for their use case this is absolutely true.

In MX we have a particularly annoying problem, as about half of the 
calculations are nicely parallel (spot finding, peak integration) and are 
memory bandwidth / CPU breadth limited and the other half (indexing, 
refinement, scaling) are not very parallel CPU speed bound, so finding the best 
CPU architecture is hard to start with. In terms of GPU, the data need to 
typically pass through main memory three times - for spot finding you need to 
look at every pixel, and integration typically needs to load full frames to 
extract the profiles and then fit them (the shoebox regions can be cached 
between these, but they still need to pass in and out of the CPU). Since moving 
data in and out of memory is expensive and GPU memory is expensive this is a 
problem. For reference, a typical Eiger 16M data set uncompressed needs about 
half a terabyte of RAM (7,200 * 18 megapixels * 4 bytes) so in memory 
processing presents real challenges. The image analysis 

[ccp4bb] Explore your inner lattice

2019-10-08 Thread David Schuller

https://www.cnet.com/news/diamonception-miners-find-diamond-trapped-inside-another-diamond/


 Diamonception: Miners find diamond trapped inside another diamond


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Re: [ccp4bb] Shelx and debian 10

2019-10-08 Thread David Schuller
There is now another alternative. There are platforms for packaging 
software with necessary libraries. PyMOL for example is available using 
"snap".


https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg46623.html



On 2019-10-08 06:21, George Sheldrick wrote:
As explained in the attached email from Peter Keller, I was 
deliberately preparing the binary Linux SHELX distribution using older 
(2011) system libraries so that the programs would run on older 
systems that many users are still using. Unfortunately this means that 
they do not run on some recent cutting edge distributions including 
Debian 10. This can be fixed with 'vsyscall=emulate' when installing 
the OS but not all users may be allowed to do this. Dynamic binaries 
would be smaller but would require the user to provide the right 
libraries.


If I prepare statically linked binaries (using the latest ifort and 
ubuntu) they appear to run on current systems but may have problems on 
older systems. I may have to offer (e.g. in CCP4 and on the SHELX 
server) two sets of Linux binaries in the future, one for 'vintage' 
systems and one for current systems. Alternatively I could provide 
both statically and dynamically linked versions. What do users think?


Best wishes, George


On 08.10.19 11:04, Peter Keller wrote:

HI Tim,

On Mon, 7 Oct 2019, Tim Gruene wrote:


Date: Mon, 07 Oct 2019 23:04:28 +0200
From: Tim Gruene 
To: Peter Keller 
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Shelx and debian 10




@Peter: are you sure that without 'vsyscall=emulate' linux binaries 
need to be

dynamically linked? I would be very surprised if the linux kernel would
disable statically linked binaries. I rather think that the vanilla 
versions
of shelx c/d/e (from shelx.uni-goettingen.de) are compiled with an 
obsolete

compiler / obsolete compiler options.


You're right, I wrote my reply to Bernhard too rapidly, and conflated 
two separate issues. Debian 10 still supports static binaries of 
course, but in its default configuration (without vsyscall=emulate), 
those static binaries must be linked with a version of glibc that 
doesn't require vsyscalls. OTOH, dynamic binaries don't suffer from 
this problem, because they can use vDSO provided by the running 
(rather than the build) system.


I think that part of the problem is that traditionally when we want 
to build portable linux binaries, we tend to build on the oldest 
distribution that we want to support, relying on backwards 
compatibility to provide the portability that we are after. We often 
build statically, because it is a robust way of including all the 
required libraries and is less fiddly and error-prone than providing 
them as dynamic libraries. There is also no danger of breakage caused 
by rogue values of LD_LIBRARY_PATH (which users shouldn't be setting 
of course, but we have no way of stopping them). The drawback of this 
approach is that when backwards compatibility is broken, there is no 
application-level fix.


These kinds of problems are rare, but when they do happen the onus is 
on those of us who distribute binary applications to find solutions. 
Some sysadmins may have good reasons for being reluctant to change 
kernel parameters to get third-party applications to work.


Regards,
Peter.




On Monday, October 7, 2019 5:53:44 PM CEST Peter Keller wrote:

Dear Bernhard,

We had this issue drawn to our attention last year by an early adopter
of Debian 10 while it was still in testing. I thought that it was a 
bug,

and submitted a report accordingly here:
. I was told
that it is not a bug, but a feature ;-)

If you are able, you could try setting the kernel parameter
vsyscall=emulate. In the longer term, SHELXC/D/E will have to be 
rebuilt
to support systems where the vsyscall has been disabled. This means 
they
have to be dynamic executables that include the following in the 
output

of 'ldd':

% ldd /bin/bash
 linux-vdso.so.1 (0x7fff50952000)
 

All current distros use vDSO, so this shouldn't cause portability
problems by itself, but handling dynamic executables can be trickier
than static ones.

For a little more background, see 

Finally, you have my commiserations: although this change has been a
long time coming, it hasn't attracted a lot of attention. It was bound
to catch users of static executables by surprise.

Regards,

Peter.

On 07/10/2019 16:05, Bernhard Rupp wrote:

Hi Fellows,

we updated to Debian 10 on the local workshop computers, and 
reinstalled


Coot and ccp4. All fine.

Problem: Shelxc/d/e/  does not run, and

the call exits immediately sans any message.

This holds for the binaries included in ccp4 as well as for those 
from

the SHELX site.

The executables from CCP4 and SHELX site – same file size, probably
same - run fine under Debian 9.

I suspect a library problem.

Does some kind soul have CDE binaries for Debian 10 to share?

Many thx 

Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

2019-07-22 Thread David Schuller

On 7/22/19 3:40 AM, Bärbel Blaum wrote:


"As I said, the lead author may not actually be the crystallographer here"

Bärbel

No need to wonder, that info should be in the PDB file header. The 
author of the coordinates is not necessarily the same as the author of 
the primary reference.



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Re: [ccp4bb] [COOT] guile: error while loading shared libraries: libguile.so.17: cannot open shared object file: No such file or direct

2019-05-23 Thread David Schuller

From a Scientific Linux 7 system:


#> yum --enablerepo=epel --enablerepo=elrepo whatprovides "*/libguile.so.17"
...
epel/x86_64/filelists_db |  11 MB 00:01
compat-guile18-1.8.8-14.el7.x86_64 : A GNU implementation of Scheme for
   : application extensibility
Repo    : epel
Matched from:
Filename    : /usr/lib64/libguile.so.17


===

If you are managing a RHEL7 system I presume you know about the epel 
(Extra Packages for Enterprise Linux) repository.





On 5/23/19 12:49 PM, Darin Lory wrote:

cootGurus,

on RHEL 7 error:

  guile: error while loading shared libraries: libguile.so.17: cannot open 
shared object file: No such file or directory

When I run coot on RHEL 7 I get this error.

Is there a yum install for libguile?

Kindly advise,

Darin



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Re: [ccp4bb] crystals mounted in microRT capillaries

2019-05-17 Thread David Schuller
How far are you sending them? If they go by aircraft, they may 
experience unexpected pressure differentials and temperature extremes.


On 5/17/19 2:20 AM, Michael Colaneri wrote:

Dear all,

how can one mail crystals mounted in loops using the microRT 
capillaries of Mitegen?


Thank you.

Mike Colaneri



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Re: [ccp4bb] PyMOL now packaged as a snap on Linux

2019-05-16 Thread David Schuller
It seems to work on Fedora 30 and on Scientific Linux 7 (which means it 
should also work on RHEL7 and Centos 7)


Thank you.



On 5/16/19 10:47 AM, Darren Hart wrote:

Some more info:

https://snapcraft.io/pymol-oss

It seems to work exactly as expected.

Darren


On 16/05/2019 16:05, Folmer Fredslund wrote:

Hi Darren,

That's brilliant!

I'll give it a spin and see how it works.

Best regards
Folmer


tor. 16. maj 2019 13.02 skrev Darren Hart >:


Since yesterday, PyMOL (open source version v2.3) has been
packaged as a
distro-independent "snap" that can be installed easily on linux
platforms - no more cloning from gitlab and compiling after
installing
the dependencies.

On Ubuntu, install from software centre or:

sudo snap install pymol-oss

Many distros have the snap architecture already installed. If
not, you
just need to install snapd in the regular way first (e.g. on Debian:
sudo apt install snapd).

Hope this is useful for some folks.

Best regards,

Darren



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[ccp4bb] 3D

2019-03-11 Thread David Schuller

https://www.engadget.com/2019/03/11/nvidia-ends-3d-vision-support/


 NVIDIA will stop supporting 3D glasses in April


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Re: [ccp4bb] Clear Linux

2019-02-07 Thread David Schuller
I would be wary of an OS developed and promoted by a hardware 
manufacturer (Intel). The Phoronix benchmarks you linked were conducted 
on an Intel Xeon chip. I wonder how Clear OS performs with AMD chips, 
which are featuring very attractive performance and price recently.




On 2/7/19 10:38 AM, Karthik Paithankar wrote:

Dear Program devs and enthusiasts,

After seeing James' email (on dismal CPU performance), I was searching
for various ideas and found the so-called "Clear Linux Project". Seems
" function multi-version patch" leads to significant improvements.
Though I could install the precompiled binary of CCP4 and phenix
without any issues but there are no improvements to runtime as FMV
needs 'patching' and compiling.

Could DIALS, CCP4 or Phenix programmers see if this is
useful/possible? Has anyone tried it?

https://clearlinux.org/documentation/clear-linux/tutorials/fmv
https://www.phoronix.com/scan.php?page=article=clear-faster-blas=1

Best regards,
Karthik Paithankar



On 30/11/2018, James Holton < > wrote:

I have a dissenting opinion about computers "moving on a bit".  At least
when it comes to most crystallography software.

Back in the late 20th century I defined some benchmarks for common
crystallographic programs with the aim of deciding which hardware to
buy.  By about 2003 the champion of my refmac benchmark
(https://bl831.als.lbl.gov/~jamesh/benchmarks/index.html#refmac) was the
new (at the time) AMD "Opteron" at 1.4 GHz.  That ran in 74 seconds.

Last year, I bought a rather expensive 4-socket Intel Xeon E7-8870 v3
(turbos to 3.0 GHz), which is the current champion of my XDS benchmark.
The same old refmac benchmark on this new machine, however, runs in 68.6
seconds.  Only a smidge faster than that old Opteron (which I threw away
years ago).



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Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

2018-12-20 Thread David Schuller

I can see two possible paths here:

1) Make the card work with an emitter

or 2) Switch to a monitor with a built-in emitter

Datasheet on the graphics card:


"3D Stereo support with Stereo Connector1
...
1 VGA/DVI/HDMI/stereo support via adapter/connector/bracket"

The task then is to identify the correct bracket to work with this card, 
and find a source for purchase.

Something like this:

https://www.bhphotovideo.com/c/product/652465-REG/PNY_Technologies_900_50762__000_Stereo_Bracket_for_Quadro.html
"PNY Technoligies Stereo Bracket for Quadro FX 3800"
> Is this part also compatible with the Quadro P4000? I do not know.

http://www8.hp.com/h20195/v2/GetPDF.aspx/c04658472.pdf
"NVidia 3D Stereo Bracket...
Supports NVIDIA Quadro® K4000, K5000, K6000, K4200, K5200,
M4000, M5000, M6000, P4000, P5000, P6000 graphics cards"

> Seems promising.

-
Here is a web page listing compatible monitors. You can filter for those 
with "built-in emitter"


https://www.nvidia.com/object/3d-vision-displays.html





On 12/20/18 3:45 PM, Adarsh Kumar wrote:

Hello everyone

We have just purchased a Dell workstation for crystallography data analysis. We 
were trying to use Nvidia 3D vision 2 glasses with it, but failed to do so. 
Please help me out with this one. Some relevant information is as follows:
OS: Ubuntu 16.04 LTS
Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket)
Monitor: Asus VG248QE

Thanks and regards
Adarsh Kumar
Suo Lab
Florida State University College of Medicine



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Re: [ccp4bb] Fedora 29 breaks CCP4

2018-11-01 Thread David Schuller
Does this depend on which desktop is used? We have been using the MATE 
desktop rather than the default Gnome.



On 10/31/18 10:21 PM, Andrey Lebedev wrote:

Dear CCP4 users,

The recently released Fedora 29 breaks all the CCP4 graphical
components (interfaces and update manager).

This is because backward incompatibility of the fontconfig library and
possibly other libraries in Fedora 29.

The CCP4 core group working on this issue.

Meanwhile, please refrain from installing Fedora29 or upgrading
earlier Fedora version.

Regards,
Andrey



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[ccp4bb] Sulphate or phosphate?

2018-07-31 Thread David Schuller
How can one distinguish between a sulphate or phosphate in an electron 
density map? Both are present in the mother liquor, and resolution is in 
the range of 1.75 - 2.25 A



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[ccp4bb] Might be of interest to this group

2018-02-09 Thread David Schuller

http://www.cell.com/current-biology/fulltext/S0960-9822(18)30014-9


 A Novel Form of Stereo Vision in the Praying Mantis

Vivek Nityananda,Ghaith Tarawneh, Sid 
Henriksen,Diana Umeton,Adam Simmons, Jenny C.A. Read


DOI: https://doi.org/10.1016/j.cub.2018.01.012

Current Biology

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Re: [ccp4bb] Super protein wire model bender

2018-01-09 Thread David Schuller
I think those used to be sold by the Charles Supper Co. Check out their 
cat# 7145


http://www.charles-supper.com/en/page/product.cfm?idProduct=33



On 01/09/18 03:34, syed ibrahim wrote:

Dear Friends

I am looking for the provider details of instrument - Byron Bender (or  super 
protein wire model bender), which is used to build protein wire model using 
Torsion angle for teaching purpose. I could not find any such provider.

I greatly appreciate your help

Thank you

Dr. B. Syed Ibrahim
Assistant Professor,
Centre for Bioinformatics
Pondicherry University
India - 605 008



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Re: [ccp4bb] 3D stereo and pymol

2018-01-03 Thread David Schuller
The Mate desktop should also work; it is a continuation of the old Gnome 
2 desktop.


- dave schuller

On 01/03/18 04:42, Wim Burmeister wrote:
I answer a bit late, but I repost a message on 3D graphics from Mai 
2017 :


Hello,

we just wanted to share our experience in finding a configuration 
which allows to use 3D graphics under linux using Nvidia GeForce 3D 
glasses.


We had quite a hard time to find a configurations which works correctly.

We finally used Debian linux with a xfce desktop. Other recent 
desktops use a tiling which is not compatible with 3D graphics.


The hardware consists of

  * a DELL Precision T5810 desktop computer with an Nvidia Quadro
M4000 (8 Gbyte memory, 4 DP) graphics card
  * Nvidia GeForce 3D Vision 2 (NVIDIA GEF 3D VISION 2 GLASSES KIT)
active stereo glasses
  * a stereo connector PNY Quadro 4000 3D for the synchronization of
graphics card and glasses
  * an ASUS 24" LED 3D - VG248QE display
  * a DisplayPort-DisplayPort cable

The Nvidia linux drivers from version 367.57 can handle the current 
version of the Nvidia glasses.


For an obscure reason a direct DP-DP connection between graphics card 
and display is absolutely required in order to obtain fully working 
stereo. If a DP-DVI dual link adapter is used, the stereo does not 
work on the top and the bottom part of the screen. This is true for a 
native DELL active adaptor or generic models. The exact reason remains 
unresolved, but the solution is to use a direct DP-DP connection. This 
limits the available choice of displays which require 120 Hz for 
1080*1980 screen resolution and a DP input. We have been choosing a 
“Nvidia 3D ready” model.


There has been a considerate about of exchange about this problem on

https://devtalk.nvidia.com/default/topic/992892/linux/partially-working-stereoscopic-effect-with-3d-vision-under-debian-linux/

The setup comes with a price tag of about 1600 € free of taxes.

coot, pymol and chimera work straight without problems in hardware 
stereo mode. The experience is absolutely great.


Best

Wim

--

Wim Burmeister
Professeur
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs

CS 20192
38044 Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr
Tel:    +33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
website 



//



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Re: [ccp4bb] Radiation damage to the FAD in enzyme structure

2017-11-06 Thread David Schuller
Some alternative interpretations have been suggested, but if you think 
you are seeing radiation damage, you could try collecting data on 
several crystals and binning it by dose received. For comparison see:



The catalytic pathway of horseradish peroxidase at high resolution.
Berglund, et al. (23 May, 2002) Nature 417(6887), 463-8
DOI:
   10.1038/417463a 


If your low dose and high dose structures appear nearly the same, then 
you are seeing something other than radiation damage.




On 11/06/17 06:01, Martin Malý wrote:

Dear colleagues,

I am investigating a structure of a FAD-dependent enzyme. The electron 
density map suggests radiation damage to the FAD. It apparently is 
different from simple change of the redox state and "butterfly"-like 
structure. We did not find in literature possible products of 
radiation damage, like a removal of several atoms of the FAD. Has 
anyone observed such effect?


To describe it in more detail, I can observe negative difference map 
of C2, N3, C4, and O4 atoms of flavine. Moreover, there is positive 
difference map close to O2 and O4 atoms thus it looks as water 
molecules are bound there instead of the missing FAD atoms.


I am attaching parameters of the experiment: performed at synchrotron,
exposition time 210 s, high resolution diffraction limit 1.65 A
( = 2 at shell 1.75-1.65 A). We could see a decrease of
diffraction data statistics during the experiment hence we think there
is significant radiation damage to the crystal.

Thank you very much for ideas.
Regards,
Martin Maly



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Re: [ccp4bb] Clean Ubuntu system disk

2017-06-13 Thread David Schuller
I like to pipe the `du` output straight into a `sort` command. That way 
the biggest directories appear at the end.


cd /
sudo du -sk * |sort -n

That is for directories. If you are looking for the largest files, you 
can try something like this:

ls -lR |sort -nk5




On 06/13/17 04:31, Arnaud J. Hungler wrote:


Dear Jiyong,


To find which directory is using the space disk, you can go to the 
root directory, and use the  'du' tool as root user (or with sudo).


cd /

sudo du -hs * 2> /dev/null


Wait a bit, and every single directory will appear with his size. If 
you see an unexpected big size for a specific directory, cd into this 
one, and re-do the  'du' command until you find the guilty files.



You can as well use a graphical tool like Baobab. (I really like this 
one.)



Best,

Arnaud


*From:* CCP4 bulletin board  on behalf of 苏纪勇 


*Sent:* Tuesday, June 13, 2017 11:14 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] Clean Ubuntu system disk
Dear CCP4BB,

I installed CCP4 in Ubuntu 14.10. After I run several rounds of CCP4, 
I found my disk is nearly full. Only 400Mb space left. I guess I often 
kill the job that temporary files left in my disk. Could one BB tell 
me how to remove the temporary files?


Best regards,

Jiyong




This message and its contents including attachments are intended 
solely for the original recipient. If you are not the intended 
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Re: [ccp4bb] mystery disappearance of CCP4 website(s)

2017-05-25 Thread David Schuller

I can't reach it.

A newspaper site I frequent, www.startribune.com, was down earlier this 
morning, but is back up already.



On 05/25/17 09:12, Andrew Sharff wrote:


You are not alone. They are unreachable from here too!


Andrew


On 25/05/17 14:09, R. Michael Garavito wrote:
I have been trying to reach some of the CCP4 websites 
(www.ccp4.ac.uk/ ) from the US and they all 
seem to be unreachable, even from the http://www.ccp.ac.uk/ site. 
 Any ideas? Or did I miss some announcement.  Most of the other CCPs 
seem to be up.


Michael

//
/R. Michael Garavito, Ph.D./
/Professor of Biochemistry & Molecular Biology/
/603 Wilson Rd., Rm. 513///
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/

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Re: [ccp4bb] Completely Off-Topic

2017-01-12 Thread David Schuller
I wonder if anyone has tried glutamate as a cryprotectant for proteins. 
If the [] is that high, it may make a stable environment for proteins. I 
have no idea what effect it might have on ice formation.


https://amb-express.springeropen.com/articles/10.1186/2191-0855-3-36


 /Bacillus subtilis/ natto: a non-toxic source of poly-γ-glutamic acid
 that could be used as a cryoprotectant for probiotic bacteria



Bhat, et al *DOI: *10.1186/2191-0855-3-36





On 01/11/2017 07:45 PM, Keller, Jacob wrote:


Dear Crystallographers,

Was anyone else aware that in E coli the intracellular glutamate 
concentration is ~100 mM? Also other cell types (yeast, mammalian) are 
10s mM. Anything to say about this? I learned of this just recently, 
and have been amazed about it for more than a week. Did I miss this in 
Biochem 101? Does it matter?


JPK

***

Jacob Pearson Keller, PhD

Research Scientist

HHMI Janelia Research Campus / Looger lab

Phone: (571)209-4000 x3159

Email: kell...@janelia.hhmi.org 

***




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[ccp4bb] Citing the literature

2016-12-23 Thread David Schuller
I looked with distaste at the pile of notes I'd accumulated for my next 
Revere High Science Club lecture, on crystallography, which had been my 
specialty in graduate school and for many years after.


The Carbon Murder, "A Gloria Lamerino Mystery"

by Camille Minichino, 2004, ISBN 0-373-26522-0


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Re: [ccp4bb] AW: unusual monoclinic relation?

2016-12-19 Thread David Schuller

On 12/19/16 11:25, herman.schreu...@sanofi.com wrote:


Dear Andy,

I don’t think you will solve this pre-Xmas


...
There is hope of a pre-Christmas solution. Convert to Eastern Orthodox; 
that will provide an extra two weeks margin, due to the Orthodox use of 
the Julian calendar.


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Re: [ccp4bb] Averaging of different proteins in heteromeric complex

2016-12-16 Thread David Schuller


"The proteins are stoichiometric"

Huh? What is the stoichiometry? I'm expecting a ratio here, like 1:1 or 
some such.


I see two possibilities:

1) The two proteins are completely interchangeable in the structure.

2) The two proteins are not interchangeable, but are being 
crystallographically averaged.


To differentiate, I would want more info, not necessarily crystallographic.

Do pure samples of either protein form the same structure (double hex ring)?

Does the stoichiometry of the complex ever vary?

Is there any data to suggest that the complex behaves any differently 
than pure samples of either protein?


Do you have any non-crystallographic data on complex formation - 
cross-linking results, etc. ?


On 12/16/16 11:45, Graham Robinson wrote:


Dear Crystallographers,

I have solved the structure of a complex, which is the average of its 
component proteins. The problem is as follows:


The complex is composed of two proteins, which share 67%/84% sequence 
identity/similarity in the resolvable region. The proteins are 
stoichiometric (SDS-PAGE of the crystals), and form a dodecamer 
composed of two hexameric rings, stacked on top of one another.


The crystals are H3. Analysis with Xtriage, Pointless, Aimless, Scala 
do not find other space groups likely, and do not find any apparent 
data pathologies. Data processing in H3 (to 1.9 A) is straight forward 
(Rfactor/Rfree: 22.3%/26.4% using one of the proteins as MR model). 
Attempts to solve the structure in other space groups (except P1) 
fail, or produce meaninglessly poor statistics.


I have good anomalous data from isomorphous SeMet crystals, and the 
anomalous difference density peaks for the Se are approximately 
additive: anomalous peaks for positions where SeMet is unique to one 
of the two proteins are about 1/2 the size of peaks common to both 
proteins. This composite effect is apparent when the structure is 
processed in P1 also.


Crystal contacts are not specific to either of the two proteins, and 
so it appears that the crystal doesn't distinguish between up- and 
down-orientations of the dodecameric rings. Therefore, each subunit in 
the resulting structure is a composite of the two proteins.


Despite the occurrence of heteromeric rings in protein structures, I 
have not been able to find a description of this problem in the 
literature, nor the archives of the CCP4BB.


I am keen to hear from anyone who has observed similar things in 
structures of their complexes, and how best to approach this problem.


Many thanks,

Graham Robinson

Postdoc, University of Geneva

Graham Robinson, Ph.D.

Fitzpatrick Group

Département de Botanique et Biologie Végétale

Université de Genève

30 Quai Ernest-Ansermet

CH-1211, Genève 4

T: +41 (0) 22/379.30.12




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Re: [ccp4bb] Unfilled electron density for structure with tNCS

2016-11-30 Thread David Schuller
There are reasons why MR might fail to find additional copies; perhaps a 
surface loop in the search model interferes with packing. You should 
probably take a look at solvent content.




On 11/30/2016 12:20 PM, Matthew Bratkowski wrote:

Hello all,

I am working on a structure in space group P4 at a resolution of about 
4 angstrom.  Xtriage indicates that translational NCS is present.  I 
am able to solve the structure by molecular replacement with four 
copies in the asymmetric unit, and there are two sets of identical 
copies. However, discontinuous, unfilled Fo-Fc density is present that 
appears to correspond to additional copies of the protein in the 
crystal packing.  I tried having phaser search for additional 
components in the ASU, but in each case the molecular replacement fails.


Is it possible that disordered copies of the protein appear in the ASU 
that is accounting for the unfilled density?  Other than the 
additional density, the structure looks ok.  I did not have too many 
problems with refinement as I was able to get a final Rwork/Rfree of 
around 0.24/0.29, which seems pretty decent considering the low 
resolution.


Any suggestions would be helpful.

Thanks,
Matt




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Re: [ccp4bb] Good 3D Monitor for Molecular Modelling

2016-10-28 Thread David Schuller
The last I heard (which was a while ago), Windows could run the stereo 
emitter over USB with a Geforce card, but Linux still needed a Quadro 
card with the 3 pin mini-DIN connector. I hope this is no longer true, 
but I have not heard clear information to the contrary. Note that the 
text you quote does not mention OS at all.


On 10/28/16 04:18, Johannes Cramer wrote:

Hi Matt,

I guess you are talking about hardware. For a year or so, this should 
have become quite cheap. A recent Nvidia Geforce card, a 120 Hz 3D 
Monitor and a 3D vision kit should do the trick. However, personally I 
only have experiences with the "professional" NVidia quadro grafics 
card series.
Can anyone in the CCP4BB confirm that Geforce cards work with coot, as 
suggested on the pymolwiki site:


  * GeForce Cards from series 400 onward have gained OpenGl
support in recent Nvidia driver iterations (314+). This allows
Pymol to be viewed in 3D using the quad buffered stereo
setting with a GeForce card, 120Hz screen and 3D Vision kit.


Cheers,
Johannes

2016-10-27 20:11 GMT+02:00 Folmer Fredslund >:


Hi Matt,

Have you tried looking at these pages:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo

https://pymolwiki.org/index.php/Stereo_3D_Display_Options


HTH,
Folmer Fredslund


On 2016-10-27 17:20, Matthew Graf wrote:

Hello All,
 I am looking for suggestions on a good, but not too costly, 3D
monitor for visualizing pdb structures and looking at outputs of
modelling programs. I am not personally a structural biologist,
but am on the hunt for someone who is. All help appreciated.

Kind regards,
Matt






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[ccp4bb] Dials

2015-07-08 Thread David Schuller
Does this look like a suitable solution for those who like dials while 
model building?


http://petapixel.com/2015/07/07/review-palettes-modular-photo-editing-controls-are-pricey-but-powerful/

http://www.cnet.com/news/buttons-and-sliders-and-knobs-oh-my-palette-offers-a-more-physical-interface-for-pcs/

http://palettegear.com/

Palette tactile controllers - a core unit hooks up to the computer via 
USB cord. Dials, buttons and sliders can be arranged in flexible 
configurations and snap together magnetically.


They advertise compatibility for Mac and Windows. No mention of Linux. 
It looks like a lot of effort and expense went into aesthetics and this 
makes the price somewhat high.


Still, there has not been a really good solution for a control interface 
with more than one dial for a while now.


Cheers,

--
===
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===
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Re: [ccp4bb] Point group

2015-05-21 Thread David Schuller

On 05/21/15 11:56, Mohamed Noor wrote:

Dear all

I can process my 3.8 A dataset in either P4 or P422 point groups.
Do the scaling statistics look similar for both? If so, go with P422. 
Trying to enforce an incorrect symmetry operator would blow up your stats.



  MR searches and refinement in SG P41 and P41212 results in R/Rfree of around 
30/35 % with 8 and 4 NCS copies, respectively. Pointless doesn't seem to 
complain but Xtriage suggests 25 % twinning in the former (refinement was done 
without twin law) and that the true point group could be P422. So do I go with 
P422?

Secondly, where can I find the DIALS equivalent to XDS FRAME.cbf? The 
statistics are slightly better but I prefer to confirm it visually. I recently 
had a case of pseudosymmetry which makes me suspicious of automated processing 
suggestions.

Thanks.



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Re: [ccp4bb] CYS mod

2015-05-12 Thread David Schuller

So far almost everyone is suggesting BME.

I didn't do the purification  crystallization myself, but I am told:

Buffer was HEPES
cryo was ethylene glycol, glycerol and DMSO.
Some MgSO4 and KPO4
No BME, but maybe some DTT.

Purified from a proteobacterium.




On 05/12/15 15:20, Dyda wrote:

What is in buffer? Perhaps DTT and cacodylate?

Fred
***
Fred Dyda, Ph.D.   Phone:301-402-4496
Laboratory of Molecular BiologyFax: 301-496-0201
DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov
Bldg. 5. Room 303
Bethesda, MD 20892-0560  URGENT message e-mail: 2022476...@mms.att.net
Google maps coords: 39.000597, -77.102102
http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred
***



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Re: [ccp4bb] No MR solution

2015-04-01 Thread David Schuller

On 04/01/15 11:23, Roger Rowlett wrote:


There are 8 possible space groups in the P422 family. Did you search 
in all of these?


What he said. The answer should be YES. Phaser is set up to do this 
easily.


How many search models are likely to fit in the unit cell based on  
Matthews analysis? Then there are questions about model selection and 
preparation. How identical is the search model to the target? Does it 
make sense to search for the domains separately?


If the domains are separate enough to be called domains, it might be 
worthwhile to try this.


Did you truncate the model side chains?

I usually try with the full sequence, and with a poly-Ala truncation. 
Especially if the sequence identity between model and target is low.


BTW, you didn't mention anything about the similarity or identity of the 
model. That's important in figuring out whether you should have been 
successful or not. Much more so than the resolution of the data.


There are lots of ways to skin the cat depending on the problems 
encountered. 3.0 A may be challenging for a low identity search model.


__
Roger Rowlett
Gordon  Dorothy Kline Professor
Department of Chemistry
Colgate University

On Apr 1, 2015 11:06 AM, Sekharreddy M vijayasekk...@gmail.com 
mailto:vijayasekk...@gmail.com wrote:


HI All,
  I am trying to find MR solution for one of the protein
crystals with 3.0A resolution, but not able find solution using
Phaser (PHENIX).The protein has two domains.and the probable best
space group identified was p4212(HKL2000).

 I am novice in using crystallization tools for solving
structures.I am stuck at this stage  and I appreciate any help in
this regard.

Thank you.




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Re: [ccp4bb] nVidia quadro

2015-03-25 Thread David Schuller
You could check the nVidia page of officially supported displays. It 
includes a search tab so you can check for Built-in Emitter.

http://www.nvidia.com/object/3d-vision-displays.html

Performing that search brings up 5 contenders. Good luck finding any of 
these products still for sale.




On 03/25/15 12:00, Andreas Schenk wrote:
Thank you for assembling all that information about NVidia 3D vision 2 
on Linux.


Is there a good list somewhere with monitors that have a built-in 
emitter and are confirmed to work under Linux?
I looked at the list at 
http://www.heise.de/preisvergleich/?cat=monlcd19widexf=5848_3D-f%E4hig+%28aktiv%29#xf_top 
and it seems that a lot of manufacturers are marketing their monitors 
as 3D Vision2 ready or 3D capable just because they support running at 
120 Hz, even if they don't have a built-in emitter.


Best,
Andreas


On 25.03.2015 05:16, Kay Diederichs wrote:
Sorry to come late into the discussion, and just to mention: it would 
be wrong if readers of CCP4BB get the impression that  Quadro cards 
that support quad buffered stereo have to be high-end. To the 
contrary, an entry-class Quadro K620 together with a €250 Nvidia 3D 
Vision 2 compatible monitor (with built-in emitter) gives you very 
nice stereo on Linux. There is more info at 
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo#Nvidia_3D_Vision_2 
.


To have higher resolution than 1920x1080 you may need some 
combination of higher-end monitor and (separate) emitter, and that 
would indeed require a 3-pin DIN connector and an expensive Quadro 
card. Also, an expensive Quadro is of course faster - but entry cards 
are, in contrast to popular belief, fast enough for crystallographic 
electron density + model inspection and modelling.


In summary, the computer gamers have been supporting us 
crystallographers to the point that Stereo is quite affordable.


best,

Kay

On Tue, 24 Mar 2015 18:05:20 +, Oganesyan, Vaheh 
oganesy...@medimmune.com wrote:



Colleagues,

I’d like to thank everyone who took time to answer my question 
regarding Quadro cards that support quad buffered stereo. I now hope 
to build a workstation with Quadro 5000.


Regards,

Vaheh Oganesyan
www.medimmune.com




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===
   David J. Schuller
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Re: [ccp4bb] chloride or water

2015-01-21 Thread David Schuller

On 01/21/15 15:04, Pavel Afonine wrote:

   (And why not make every water into UNX for good measure as well?)

Why not indeed, except that I would not call it water but Dummy Atom 
with an element type of your choice.




there was a time long ago when budding crystallographers were taught to 
refer to solvent atoms rather than waters if there was doubt.


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Re: [ccp4bb] active 3D monitors: successor of Asus VG278HR?

2015-01-09 Thread David Schuller

On 01/09/2015 12:11 AM, Jens Kaiser wrote:

In addition to what others have -- correctly -- stated I want to add one
more thing:

Yes, you are right, if you do not get your hands on a monitor with
built-in emitter, you'll need ad least a K4000 and in many cases the
VESA din bracket (~$50). You do not have to buy the expensive ($800+) 3D
Vision pro emitter, though, for about $150 you can get the 3D Vision 2
(the 2 is important!) kit, that includes the DIN-to-Phone jack cable
(officially for connection to DLP) you'll need to connect the graphics
card to the emitter. Don't use the DP-DVI adapter, there's not enough
bandwidth - go straight out of the DVI and you'll be fine (this
realization cost me a day).

This is getting rather distant from the central topic, but here is 
clarification on a couple points mentioned above:


1)
3D Vision Pro uses a wireless signal to communicate between the 
emitter and the glasses. It costs more. The glasses must also be Pro 
compatible, and the intended purpose is for a roomful of viewers at a time.


3D Vision 2 is probably what you want; it uses infrared to communicate 
between the emitter and the glasses. Line of sight is necessary.
NVidia 3D Vision 2 Wireless Glasses Kit includes emitter, one pair of 
glasses, cables and accessories. Model number is 942-11431-0007-001

Extra 3D Vision 2 glasses: model number 942-11431-0003-001

2)
 DP as mentioned above is Displayport. The issue you had with the 
DP-DVI adapter is probably that you were dealing with a Displayport to 
single link DVI adapter. It is the single link DVI, not the Displayport 
that does not have adequate bandwidth for a 1920x1080x120Hz display. The 
same problem would probably occur if you used the DVI port with a single 
link DVI cable. I would expect a stereo-ready monitor to come with a 
dual link DVI cable. DP-dual link DVI adapters are available, if you 
look hard enough.
You can distinguish between single link and dual link DVI by the number 
of pins; see Wikipedia for details.


---
Current specifications for Displayport (1.2+) and HDMI(2.0+) have enough 
bandwidth for 1920x1080x120Hz, but there don't seem to be any 
Displayport stereo monitors on the market. I would guess this is due to 
a lack of consumer demand, with 3D television and gaming not having 
caught on.
The introduction of organic LED (OLED) screens, which is expected in the 
next few years, should also benefit stereo technology, but once again we 
are at the mercy of the gaming market.
3D headsets (e.g. Oculus Rift) are due for introduction in the next year 
or so, which should be fine for one person but not so much for sharing.


Cheers,

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



Re: [ccp4bb] Demonstration for 2nd graders?

2015-01-08 Thread David Schuller
This one is probably above second grade, but the equipment setup is 
pretty easy


http://ipl.physics.harvard.edu/wp-uploads/2013/03/15c_s07_5.pdf
Measuring the wavelength of light with a ruler




On 01/08/15 13:35, John Lee wrote:

Hi everyone,

Slightly off topic here but I got myself volunteered by my 2nd grade 
son to do a show and tell at his class. I have the rock candy 
experiment ready with some background info on what I do.


Can anyone direct me to some resources or your personal demo's that 
you have done?


Thanks a bunch

-John





--
===
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===
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Re: [ccp4bb] HKL2000 Display

2014-12-03 Thread David Schuller
Yes, it is probably the wrong detector type, or the wrong parameters, 
perhaps binned vs. unbinned.



On 12/03/14 07:25, David Waterman wrote:

Hi Muhammed,

It looks a lot to me like denzo thinks your detector has a larger 
image size than the actual number of elements in the array. However, I 
don't use denzo so I'm not commenting from experience.


Cheers

-- David

On 3 December 2014 at 04:09, Muhammed bashir Khan 
muhammad.bashir.k...@univie.ac.at 
mailto:muhammad.bashir.k...@univie.ac.at wrote:


Hi All;

Could somebody explain why my Display image in HKL2000 look like that.
Image attached.
Thanks for help in advance.

Bashir


Department of Biochemistry
University of Alberta
Edmonton Canada






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===
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===
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Re: [ccp4bb] are mathematician scientists ?! (previously Free Reflections as Percent and not a Number)

2014-11-29 Thread David Schuller

On 11/29/14 07:47, Alexandre OURJOUMTSEV wrote:

Dear Tim,

as you know I avoid making public comments and prefer enjoying the comments 
done by others, however this time is hard to resist :-)

I was surprised by your mail : do you mean that mathematicians are NOT SCIENTISTS ?! Do 
you mean that they are nasty persons who fight against normal biologists, do 
not let them developing new techniques and prevent them from achieving their holy goals ?
...
It has been written that mathematics is the language of science, so I 
guess that makes mathematicians linguists.


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Re: [ccp4bb] Formulation of my own mother liquor

2014-11-21 Thread David Schuller

The most important thing is that you do it the same way every time.
But you might also put some thought into flexibility, in case you need 
to explore cryoprotectants, etc.


On 11/21/14 11:48, amro selem wrote:

Dear All,
first i wish you nice weekend, then i wanna ask about formulation of 
my own mother liquor, i want to optimize a condition containing

 0.2m MgCl2, 0.1m Tris , PH 8; and 20% PEG6K as pricipitant. (PACT)
the question is , should i make a stock solution from every ingredient 
by dissolving it in miliQ water. then mix all stuff  together  and add 
water till final concentration with out adjusting final pH. OR 
dissolve the PEG in pH adjusted buffer and then mix all ingredients , 
so the final pH will be 8.

any suggest any idea or any one knows what the company do.
CHEERS
Amr




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===
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Re: [ccp4bb] how to combine two derivative datasets that are not isomorphous?

2014-11-18 Thread David Schuller
You don't mention any quality indicators on your derivatives, nor 
resolution.


Presuming they actually have some decent phasing power, you may be able 
to generate phases  maps using SIR phasing + solvent flattening. If you 
can do that for each isomorphous set, then you could combine them using 
multiple space group noncrystallographic averaging.


Or, if the derivatives contain atoms with anomalous scattering, you 
could solve a derivative alone with SAD methods, or a derivative + 
native set with SIRAS. Once you get crude maps, you can once again try 
to combine the two sets with multiple space group averaging.


As for MR, there are lots of things you can try. Once again, you have 
provided no detail on what the sequence similarity is, or any other 
factor that would allow us to judge the likelihood of success.
You could search again with the model clipped down to poly-Ala. You 
could search again with any external loops trimmed off. If it is a 
multiple domain molecule, you could search individually with single 
domains. You could find additional search models, and search with a 
suite rather than single model. MR programs will suck up as much free 
time as you can provide them.



On 11/18/14 15:01, joy yang wrote:

Hi All,

I have two derivative datasets (heavy atom A and B) and two native 
datasets (a and b), A and a are isomorphous, B and b are isomorphous, 
however, a and b (or A and B) are not isomorphous.


I was able to make two difference patterson maps (FA-Fa and FB-Fb) and 
search for heavy atoms against them, the possible positions of heavy 
atom A and B are very close to each other in the unit cell (which 
seems to me that I am very close to a right phase, though not there 
yet), I am wondering if there is any means for me to combine the 
information from FA-Fa and FB-Fb as the two native datasets are not 
isomorphous? And also, I have a homology model which I tried molecular 
replacement and failed, is there any means for me to combine the 
information from the model too?


Best,

Bei



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



Re: [ccp4bb] workstation crystallography

2014-11-11 Thread David Schuller
I will comment on specific features you might look for in a 
crystallographic workstation, rather than brand names. I usually build 
from parts rather than buy intact machines.


CPU: 3+ GHz per compute core is good these days. For a standard single 
user desktop, 4 CPU cores is fine. More cores will allow you to run 
multiple independent jobs, but will not speed up a single job. Server 
chips may have 6 or 8 cores (or maybe even more, but then they start 
cutting the clock speed). It's up to you to decide what kind of workload 
this machine is likely to experience. (Those server CPUs will lack 
on-chip graphics, but see the next point)


Graphics:
1) First question: do you want stereo 3D? If so, that places 
restrictions on which graphics cards and which monitors are supported.


2) If the answer to 1 is no, then you have more freedom. I would not 
recommend on-CPU graphics for a couple reasons.
a) Better graphics performance with separate graphics cards. Any 
mid-range or better card should do.
b) An add-in graphics card will allow the CPU to run faster. This is 
because the turbo feature built into modern CPU/GPU chips will slow 
down the compute cores based on the total thermal load of all CPU/GPU cores.


Monitor: Get one with LED backlighting. Lasts longer and is more efficient.

RAM: More RAM is good, and it is relatively cheap at present. 8 GB 
minimum, recommended 16 GB.


Storage (disk is now an anachronism): I strongly recommend a quality 
SSD, at least for the OS. It makes a noticable difference in speed. 120 
GB or more for the OS. If you need multi-terabytes of storage space for 
data (and who doesn't?), get hard drives for that.


Ports: Gigabit (at least) ethernet to get on the network.
USB3.0 for connecting peripherals like portable drives. By next year I 
will be recommending USB3.1, which will have higher data throughput, 
higher power throughput and convenient symmetrical connectors.


Cheers,


On 11/11/14 08:27, abhishek jamwal wrote:

Dear ccp4 bb members,

I need to buy a desktop workstation for the purpose of running 
crystallography related applications. I have short-listed HP's Z420 
and Dell's T7600, I chose this because their configuration description 
looks impressive (8 cores, 16 threads, 3.6 GHz processor etc.). 
However, I have no practical idea about their performance.


Can anyone , who has experience with these workstations comment on 
 performance ? And whether these workstations are optimal/suboptimal 
for the desired purpose ?


what other options do I have apart from dell and hp ? Please suggest.

*Is desktop iMac a good option for this purpose ?*


many thanx in advance


abhishek








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   David J. Schuller
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Re: [ccp4bb] Molecular Replacement model preparation

2014-10-05 Thread David Schuller
Since there is a hinge, you could try searching with the two domains 
separately.


On 10/05/14 03:34, Luzuokun wrote:

Dear all,
I’m doing molecular replacement using Phaser. My protein is predicted 
to have two domain with a “hinge” linking them. The model sequence 
identity is 0.27. But the MR result is poor. I’ve tried other 
programme (Molrep, MrBump, Balbes,,,_.) But no improvement was 
observed. I think that this is due to the “open” or “closed” 
conformation around the hinge. I was told that I could place the Z 
axis along the hinge 
(http://xray0.princeton.edu/~phil/Facility/Guides/MolecularReplacement.html 
http://xray0.princeton.edu/%7Ephil/Facility/Guides/MolecularReplacement.html), 
 could anyone tell me more details about how to do next?


Thanks!
Lu Zuokun



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Re: [ccp4bb] Space group numbers

2014-10-02 Thread David Schuller
With the successful introduction of racemic crystallization to 
macromolecular, a large number of possible space groups have been opened 
up to this audience. You can find examples in the PDB of space groups P 
-1 (i.e. P 1-bar), I -4 2 d, etc.




On 10/02/14 06:51, George Sheldrick wrote:
The strange thing is that small molecule crystallographers do not 
suffer from this problem, because they don't use space group numbers! 
This is just as well, because instead of just 8 combinations of 
primitive orthorhombic space groups and settings, they have to 
consider 111  (if I have counted correctly).


George


On 10/02/2014 11:50 AM, Frank von Delft wrote:
I second that!  The default should be symmetry based... cells stretch 
and shrink, but symmetry is harder to change.  (i.e. from crystal to 
crystal.)


(I thought all CCP4 programs have supported this for ages.)



On 02/10/2014 10:25, Kay Diederichs wrote:
On Tue, 30 Sep 2014 13:29:02 +0100, Phil Evans 
p...@mrc-lmb.cam.ac.uk wrote:


Be careful: the International Tables space group number may be 
ambiguous. For example sg number 18 may refer to P 21 21 2 or its 
permuted settings P 21 2 21 or P 2 21 21, if you follow the 
proper IUCr convention that primitive orthorhombic space groups 
have abc
I would like to point out that there is an alternative 
interpretation of the International Tables (Vol A, 4th ed. 1995). In 
that interpretation (which e.g. XDS follows) space group 18 has the 
'standard' space group symbol, P21 21 2 (bold letters in Table 
3.2). This is of course not ambiguous at all; the pure 2-fold then 
corresponds to the c axis and there is always a permuation of axes 
to achieve this. As a result, the axes are not necessarily ordered 
such that abc . The latter ordering is just a convention which 
was chosen for convenience and the convention refer(s) to the 
cell obtained by the transformations from Table 9.3.1 (citing from 
table 9.3.2) - in other words, the convention is fulfilled _after_ 
the transformation (which of course is just order-permuting while 
keeping right-handedness) - nothing new here.


In my understanding, CCP4 developers have (years ago) understood 
this convention as a condition, which lead them to  invent CCP4 
space group symbols 1017 and 2017 as well as 1018, 2018, 3018. This 
also seems to be the reason for the default being SETTING 
CELL-BASED in POINTLESS.


Users of XDS should be aware that by default, POINTLESS therefore 
permutes the axes such that abc . This however may lead to space 
groups 1017 / 2017 / 1018/ 2018/ 3018 - indicated in the MTZ file, 
but not in the POINTLESS log file (last I checked).


In consequence, XDS will use the space group 17 or 18 (which is what 
POINTLESS reports), but the user must provide  the correct ordering 
(which does not necessarily mean abc) of cell parameters in 
XDS.INP. The easiest way, for XDS users, would be to run POINTLESS 
with the SETTING SYMMETRY-BASED option (I wish the latter were the 
default because the default SETTING CELL-BASED has no advantages 
that I can see). Or they use the good old manual way of 
inspecting, by eye, the systematic absences along H00 0K0 00L - this 
cannot fail.


To me, symmetry trumps cell metric so SETTING SYMMETRY-BASED 
should be the default.


I'm harping on this because I have recently seen how a Molecular 
Replacement solution was not obtained in space group 18 because of 
the misleading (I'd say) ordering abc .


I'm probably also harping on this because it took me so many years 
to discover this failure mode, and I would like to prevent others 
from falling into this trap.


HTH,

Kay



The space group names are unambiguous (though also watch out for R3 
 R32 which are normally indexed as centred hexagonal, but could be 
indexed in a primitive cell)


Phil


On 30 Sep 2014, at 13:07, Simon Kolstoe simon.kols...@port.ac.uk 
wrote:



Dear ccp4bb,

Could someone either provide, or point me to, a list of 
space-groups relevant to protein crystallography just by space 
group number? I can find lots of tables that list them by crystal 
system, lattice etc. but no simple list of numbers.


Thanks,

Simon








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   David J. Schuller
   modern man in a post-modern world
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Re: [ccp4bb] L-Dopa Stabilization?

2014-07-03 Thread David Schuller

On 07/03/14 17:05, Edward A. Berry wrote:
I see, L-dopa is a phenolic (o-quinolic actually) compound, same as 
what gets oxidized

in sliced apples to turn them brown.


At least, that's the way it used to be.

http://www.okspecialtyfruits.com/arctic-apples/about-our-nonbrowning-apples
Truly nonbrowning Arctic^® apples are a brilliantly engineered solution 
to a real-world problem...


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



[ccp4bb] FORTRAN still rules?

2014-05-08 Thread David Schuller

http://arstechnica.com/science/2014/05/scientific-computings-future-can-any-coding-language-top-a-1950s-behemoth/


 Scientific computing's future: Can any coding language top a 1950s
 behemoth?


   Cutting-edge research still universally involves Fortran; a trio of
   challengers wants in.

---

Includes a JPEG image of a Hollerith card for the younguns  who have 
never seen one.


Julia may be the first language since Fortran created specifically with 
scientific number crunching in mind.


Fortran has been consistently regarded as the fastest language 
available for numerical work, and it remains the standard used for 
comparatively benchmarking supercomputers. But what does it mean for a 
language to be fast?


Julia's published benchmarks http://julialang.org/benchmarks/ show it 
performing close to or slightly worse than C, and Fortran, as usual, 
performing better than C for most tasks.


http://julialang.org/benchmarks/

The epigraph that opens this article notwithstanding, there is a 
reasonable chance that the language of choice for scientific computing 
in another decade will be called Julia.


Discuss.

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===
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Re: [ccp4bb] small molecule crystallography

2014-03-24 Thread David Schuller
Coincidentally, I just spent my day trying to index a lattice of ~ 10 x 
10 x 11 A.


Mounting samples: if the compound is stable, just glue it to the end of 
a steel pin. No muss, no fuss.


We had to attenuate our synchrotron beam heavily to make it work; motors 
can only turn so fast.


We did 10 degree rotations to get enough spots per frame per imaging. 
Detector setup allowed for ~ 1 A resolution.


Indexing was a challenge for many of the samples, heavily overloaded 
spots and streaks seemed to be causing the most problems.


We tried various of the usual macromolecular programs for indexing; 
HKL2000, iMosFlm, XDS, DPS. None of them seem to be optimised for this, 
but some of them actually worked in some instances.






On 03/24/14 14:04, Andreas Förster wrote:

Dear all,

I've been approached by a materials student with a petri dish full of 
big, sturdy, salty, yellow crystals.  He claims I have the best kit 
for single-crystal diffraction on campus.


I would very much appreciate advice on how to deal with this, anything 
in the range from won't work to use software X to analyze data in 
space group P-43N would be welcome.


Thanks.


Andreas







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Re: [ccp4bb] account creation for CCP4wiki (and XDSwiki)

2014-03-12 Thread David Schuller

On 03/12/14 11:52, Kay Diederichs wrote:

...
Account creation now uses a Captcha which is not of the boring type, 
but rather challenges your expertise in telling cats from dogs.



I have heard that this algorithm can be fooled by cosmetic surgery.

http://www.condenaststore.com/-sp/No-Caption-Advertisement-for-cosmetic-surgeon-There-s-a-picture-of-a-dog-New-Yorker-Cartoon-Prints_i8542378_.htm


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===
   David J. Schuller
   modern man in a post-modern world
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   schul...@cornell.edu


Re: [ccp4bb] preparation of citrate buffer pH3-6.5

2014-01-30 Thread David Schuller

RE citrate buffer preparation

The Calbiochem buffers has some generally useful information about 
buffers; pKa and such.


http://www.antibodybeyond.com/books/Calbiochem_Buffers_Booklet_CB0052_E.pdf
http://wolfson.huji.ac.il/purification/PDF/Buffers/Calbiochem_Buffers_Booklet.pdf

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Re: [ccp4bb] Phasing with Many Monomers/AU

2014-01-20 Thread David Schuller
Is the monomer the biggest unit you have to search with? If there is a 
dimer, tetramer, etc. that is conserved, you could try searching with that.




On 01/19/14 14:30, Chris Fage wrote:
Thank you all for your responses. I already have a few ideas about how 
to approach the problem.


One of my concerns with so monomers per asymmetric unit at lower 
resolution was the failure of MR software. Neither PHENIX nor Phaser 
MR have made progress. I am fairly new to anomalous methods, having 
solved only two structures by SeMet-based SAD. I've certainly picked 
up on a number of tricks from the recent messages on heavy atoms, but 
I thought my case might be a little unusual. I am confident the space 
group is P1, as it was the only viable option when I indexed four 
clean albeit low-res datasets.


The monomers are ~38 kDa, and the crystals diffracted to 3.4-3.0 at a 
synchrotron.


The conditions for both native and SeMet crystals are:
8-12% PEG 2000 MME, 0.2 M ammonium sulfate, 0.1 M sodium acetate pH 5.5.

Macromolecular seeding of native crystals into SeMet drops yields the 
needle-like crystals.


Any further input is greatly appreciated!

Regards,
Chris


On Sat, Jan 18, 2014 at 11:14 AM, Chris Fage cdf...@gmail.com 
mailto:cdf...@gmail.com wrote:


Hello Everyone,

I am currently trying to phase a structure with an asymmetric unit
predicted to contain 20-24 monomers (space group P1). The native
crystals, while beautiful in appearance (see attached), only
diffract to ~3.4-3.0 angstroms at best, and SeMet-derived crystals
grow with poor morphology (small needles). Also, based a
fluorescence scan, I know that mercury does not bind appreciably.
Other than screening for a new space group, what options might I
have for phasing this many monomers at lower resolution? Is there
any real chance of solving the structure in this space group?

Thank you in advance for any suggestions!

Regards,
Chris





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===
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===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
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Re: [ccp4bb] A question on crystal optimization

2013-12-25 Thread David Schuller
I don't know why you would concern yourself with the outward morphology 
of the crystal, rather than its diffraction quality. I have grown some 
gorgeous little gems which did not diffract well.



On 12/24/13 23:49, Acoot Brett wrote:

Dear All,

I am optimizing a crystal. In one of the optimizing conditions I find 
the crystal is cubic-like shape (the crystal is not large, but 
absolutely not the traditional tiny crystal. The crystal has some 
kind of faces and edges but not so sharp, and it is absolutely not 
round). But after 1 day the crystal changed into sphere form (the 
cubic not obvious).


Will you please introduce your experience on how to get the sharp face 
and sharp edge crystal for my situation)?


There is source says if the crystal grows too faster, the sharpness 
would be lost. Will you please also let me know how to slow down the 
growth rate of the crystal?


Cheers,

Acoot



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[ccp4bb] Heavy atom sites

2013-12-15 Thread David Schuller
I have some SIRAS data of a known structure. I want to get the 
isomorphous and anomalous occupancy and phasing power from my data. 
What's the best software to do this?


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   David J. Schuller
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Re: [ccp4bb] Stereo monitor

2013-11-21 Thread David Schuller

On 11/21/13 07:50, mesters wrote:

...(both handle the dual link DVI-D standard)...


Are there any monitors on the market yet which can produce stereo 3D 
from a Displayport 1.2 input? With or without a built-in emitter.



--
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   David J. Schuller
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[ccp4bb] Fred Sanger obit

2013-11-20 Thread David Schuller

http://www.bbc.co.uk/news/science-environment-25020112


 Frederick Sanger: Double Nobel Prize winner dies at 95



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[ccp4bb] Fourier transforms

2013-11-18 Thread David Schuller

http://nautil.us/blog/the-math-trick-behind-mp3s-jpegs-and-homer-simpsons-face


 The Math Trick Behind MP3s, JPEGs, and Homer Simpson's Face

Posted By Aatish Bhatia on Nov 06, 2013


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Re: [ccp4bb] bluetooth monitor

2013-10-29 Thread David Schuller

IMHO Bluetooth is way too slow for a monitor connection.

On 10/29/2013 01:05 PM, Brett, Thomas wrote:

Hi all:
I was wondering if anyone had economical suggestions on a bluetooth LED or LCD 
monitor. I would like to have a wall mounted monitor that one could easily 
connect laptops and imacs to for structure display, doing tutorials on building 
into maps, etc.
thanks
-tom


Tom J. Brett, PhD
Assistant Professor of Medicine
Division of Pulmonary and Critical Care
Washington University School of Medicine
Campus Box 8052, 660 S. Euclid
Saint Louis, MO 63110
http://brettlab.dom.wustl.edu/



--
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===
   David J. Schuller
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   MacCHESS, Cornell University
   schul...@cornell.edu


Re: [ccp4bb] bluetooth monitor

2013-10-29 Thread David Schuller
The best technology would be Wigig, but I don't think it's on the 
market yet.


Some wireless monitor connection solutions appear to be available using 
Intel WiDi and Miracast. Check your favourite vendor for availability 
and requirements.



On 10/29/2013 01:05 PM, Brett, Thomas wrote:

Hi all:
I was wondering if anyone had economical suggestions on a bluetooth LED or LCD 
monitor. I would like to have a wall mounted monitor that one could easily 
connect laptops and imacs to for structure display, doing tutorials on building 
into maps, etc.
thanks
-tom


Tom J. Brett, PhD
Assistant Professor of Medicine
Division of Pulmonary and Critical Care
Washington University School of Medicine
Campus Box 8052, 660 S. Euclid
Saint Louis, MO 63110
http://brettlab.dom.wustl.edu/



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


Re: [ccp4bb] About molecular replacement

2013-09-12 Thread David Schuller
Perhaps some correct solutions were thrown out due to packing 
considerations.


There are a few methods to address that possibility. You could use a 
search model with large loops trimmed, especially is a sequence 
comparison shows they are probably not conserved. Or you could search 
with a suite of structures from the family.



On 09/12/13 17:21, Dhanasekaran Varudharasu wrote:

Dear crystallographers,

  I have solved a structure of a 
glucose binding protein of CE4 family. When I try to solve the 
structure using the same CE4 family enzyme as search model, it failed 
for many case. Finally, I solved the with a same family enzyme used as 
search model. As soon as I solved the structure, I superposed my final 
refined model with structures of CE4 family enzymes which did not 
produce the good molecular replacement solution for my enzyme. I found 
that all are having (Beta/alpha)7 fold and superpose very well with my 
model. Whereas, some loop region are not superpose very well. My doubt 
is why molecular replacement failed thought over-all fold is same?.



--
*Dhanasekaran Varudharasu*
Post-Doctoral Fellow
Department of Oral Biology
Rutgers school of Dental Medicine
Rutgers Biomedical and Health Sciences
Newark, NJ 07103
USA






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Re: [ccp4bb] non-diffracting xtals

2013-08-19 Thread David Schuller

On 08/19/13 16:49, Mahesh Lingaraju wrote:

Hello people

I recently obtained hexagonal rod like crystals (150x50x20 um) which 
turned out to be non diffracting. What is the usual convention for 
cases like this ? do people usually give up on the condition or still 
try to optimize it ?


It depends: are other crystal forms available, and have you exhausted 
all of the commonly available screening kits?


Are there any ligands which you might try adding to the crystallization 
to firm up the lattice?


The crystals are also not very reproducible. I believe it is because 
of ammonium acetate in the condition causing fluctuations in the pH 
because of its volatility. Is there any way to work around such a 
problem ?


When I was young and stupid, I set up some hanging drop crystals with 
ammonium in the drop, but not in the reservoir. I got some xtals that 
depended on the resulting pH change. Then I figured out that I should 
put the ammonium salt in both the drop and the reservoir.
You don't mention your conditions, but if you are doing something 
similar, you might change your procedures.


Or you could try substituting something else for the ammonium. Or 
increase the amount of buffer. And try a range of pH conditions.


Cheers,

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===
   David J. Schuller
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Re: [ccp4bb] 5D data storage

2013-07-12 Thread David Schuller
It seems like every couple of years I see an article about a new high 
density optical format. Then they don't make it to the marketplace. I 
think it has something to do with resistance from the music  movie 
business over piracy concerns. But anyway, I have learned not to get too 
excited until a product is actually available for purchase.



On 07/11/13 18:47, Scott Classen wrote:

I stumbled across this interesting abstract today, and though I'd rekindle the 
perennial data storage debate on ccp4bb.

Apparently these researchers have figured out a way to store 360TB of data on a disc 
(not sure of the actual dimensions). The memory crystal should have a thermal stability of 1000ºC 
and the data should remain readable forever.

Here is the news release:

http://www.southampton.ac.uk/mediacentre/news/2013/jul/13_131.shtml

and a PDF abstract from the recent Conference on Lasers and Electro-Optics 
(CLEO’13) in San Jose:

http://www.orc.soton.ac.uk/fileadmin/downloads/5D_Data_Storage_by_Ultrafast_Laser_Nanostructuring_in_Glass.pdf



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===
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[ccp4bb] Stereo images

2013-07-04 Thread David Schuller

http://io9.com/rare-3d-camera-found-containing-photos-from-wwi-669397198


 Rare 3D Camera Found Containing Photos from WWI
 http://io9.com/rare-3d-camera-found-containing-photos-from-wwi-669397198


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Re: [ccp4bb] Extracting .pdb info with python

2013-06-06 Thread David Schuller

You could use FORTRAN. It's good at formatted I/O.

On 06/06/13 00:37, GRANT MILLS wrote:

Dear CCP4BB,

I'm trying to write a simple python script to retrieve and manipulate 
PDB data using the following code:


#for line in open(PDBfile.pdb):
#if ATOM in line:
#column=line.split()
#c4=column[4]

and then writing to a new document with:

#with open(selection.pdb, a) as myfile:
#myfile.write(c4+\n)

Except for if the PDB contains columns which run together such as the 
occupancy and B-factor in the following:


ATOM608  SG  CYS A  47  12.866 -28.741  -1.611 
1.00201.10   S
ATOM609  OXT CYS A  47  14.622 -24.151  -1.842 
1.00100.24   O


My script seems to miscount the columns and read the two as one 
column, does anyone know how to avoid this? (PS, I've googled this 
like crazy but I either don't understand or the link is irrelevant)


Any advice would help.
Thanks for your time,
Grant



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Re: [ccp4bb] atomic coloring for the color blind

2013-06-01 Thread David Schuller

How about Braille for those who are blind to all colours?

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Re: [ccp4bb] Diffraction image viewer with display of resolution circles

2013-05-23 Thread David Schuller
The version of ADXV we have has some nice resolution ring features. 
There is a mode with the typical 5 rings of evenly spaced resolution. 
There is Anchor1 which draws a circle about the beam centre and 
through a selected point. There is Pick3 which constructs a circle 
from 3 selected points. Anchor1 is good for tweaking the beam centre 
from ice rings.


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===
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Re: [ccp4bb] Cauliflower looking crystals

2013-05-06 Thread David Schuller
I haven't seen cauliflower but I have seen brussel sprouts. Condtions 
(esp. pH) were changing over the course of crystallization, and the 
stalks and sprouts were different crystal forms.


On 05/06/13 06:17, Browning Christopher wrote:

Hi Everybody,

I was wondering if anybody had a similar case to mine. The protein I'm 
working on is a tough one. Its around 75 KDa in size, and it purifies 
well, but soon after the full length protein starts to autolyse. 
Consequently, I don't get any hits after setting up the screens.


To get around this I digest the protein with trypsin and end up with a 
stable fragment of around 25KDa. When I screen this I get many hits, 
but none of them look like something that can be made into single 
crystals. All the hits give me large lobe-like clusters and they look 
like cauliflower heads but they are optically active. I currently have 
the protein in 300mM NaCl buffer. Would dropping or increasing the 
salt or even using a different salt make any difference? Any ideas?


Cheers,

Chris



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Re: [ccp4bb] detectors on home sources

2013-04-30 Thread David Schuller
The Excillum MetalJet (TM) source is technically very interesting, with 
its liquid metal jet anode, but I have no idea how well it works for 
typical in-house crystallography use.




On 04/30/13 15:00, Fareed Aboul-Ela wrote:
I'm involved in advising my institute on an X-ray home source for a 
core facility.  The vendors are offering some new configurations. 
Whatever the claimed advantages/disadvantages, I'm hesitant to make a 
decision without consulting someone with direct experience with them.  
In particular, has anyone had any experience with using the 
photon100 CMOS detector being offered by Bruker, or the pilatus 
200K detector being offered by Rigaku?  I'd also appreciate hearing 
from anyone with experience with the latest Bruker microfocus rotating 
anode generator (called the Turbo or TXS)?


Many thanks for sharing your experiences.

Fareed Aboul-ela
Associate Professor
Zewail University
Zewail City of Science and Technology
Giza, Egypt
faboul...@zewailcity.edu.eg mailto:faboul...@zewailcity.edu.eg



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Re: [ccp4bb] Poor electron density in some of the chains in an asymmetric unit

2013-04-29 Thread David Schuller

On 04/29/13 12:26, Roger Rowlett wrote:
FYI, I do know of one example of a solved structure where some of the 
molecules in the ASU are poorly defined. In 1EKJ, 4 of the 8 molecules 
in the ASU have low B-factors (mid 30s) and 4 have high B-factors 
(50s-60s). In the unit cell these layers alternate. It is possible, if 
everything else has been excluded, that your crystal has a similar 
crystal-packing issue.


Another is 3HDH.
Pig short chain L-3-hydroxyacyl-CoA dehydrongenase revisited: sequence 
analysis and crystal structure determination.

Barycki, et al (1999) Protein Science 8: 2010-2018.

Examination of the map in the region of subunit C revealed that
the electron density was considerably weaker for the third subunit
compared to the other subunits...

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[ccp4bb] Crystals in the news

2013-04-29 Thread David Schuller

http://news.discovery.com/earth/rocks-fossils/sea-squirt-crystal-solved-130429.htm


 Crystal Puzzle Solved with Sea Squirt

RE vaterite

Science 26 April 2013: 454-457.[DOI:10.1126/science.1232139]





http://www.kare11.com/news/article/1023782/391/Strange-ice-phenomena-unfolds-at-Minn-lake


 Strange 'chandeliering ice' phenomena unfolds at Medicine Lake


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Re: [ccp4bb] CCP4 Update victim of own success

2013-04-11 Thread David Schuller

On 04/11/13 13:36, Ethan Merritt wrote:

On Thursday, April 11, 2013 10:22:59 am Antony Oliver wrote:

Eugene - that's great. I too run a small suite of Macs (12) and was trying to 
find a practical way of updating all those machines remotely. The command line 
version of CCP4um will be very useful.

Another option for a set of machines in the same network is to install a single
master copy of ccp4 on one machine exported to the others via NFS, and have all 
the
machines run it from there.  Then you only need to update one copy.
Works fine for me.

Ethan

My method is to run the updater graphically on one machine, then spread 
it around with rsync. Although being able to run it on the command line 
would allow me to accomplish that from my own desk, without crossing 
campus to another building. Even with gigabit, running X remotely is 
rather slow and bothersome.


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Re: [ccp4bb] Scaling with SCALA high and low resolution data sets

2013-03-20 Thread David Schuller

On 03/20/13 13:25, Kyriacos Petratos wrote:

Dear All,

we have two data sets at about 0.9 and 1.9 Ang. resolution collected 
from a single crystal.
Integration with iMosflm seems to be fine like the scaling within each 
of the data sets.
When we try to merge and scale both of them with 'Scala' we get 
extremely high scale factors for the lower resolution images varying 
between approximately 30 and 200!
Do we need to pay attention to some particular options for running the 
program(s)?

Thank you,

Kyriacos
e-mail: petra...@imbb.forth.gr

Is this a space group with alternate settings? Perhaps the two data sets 
were indexed with different settings.


Did you limit the low resolution for the 0.9 A data set to exclude 
overloads?


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Re: [ccp4bb] Philosophical question

2013-03-19 Thread David Schuller

On 03/19/13 10:34, Jacob Keller wrote:
Never one to shrink from philosophizing, I wonder generally why the 
codon conventions are the way they are? Is it like the QWERTY 
keyboard--basically an historical accident-


QWERTY didn't just happen. It was designed. Don't kids today know how 
to use Wikipedia or Google?


http://en.wikipedia.org/wiki/QWERTY

Still used to this day, the QWERTY layout was devised and created in 
the early 1870s by Christopher Latham Sholes 
http://en.wikipedia.org/wiki/Christopher_Latham_Sholes, a newspaper 
http://en.wikipedia.org/wiki/Newspaper editor and printer who lived in 
Milwaukee http://en.wikipedia.org/wiki/Milwaukee...
The solution was to place commonly used letter-pairs (like th or st) 
so that their typebars were not neighboring, avoiding jams. Contrary to 
popular belief, the QWERTY layout was not designed to slow the typist 
down,^[5] http://en.wikipedia.org/wiki/QWERTY#cite_note-5 , but rather 
to speed up typing by preventing 
jams.^http://en.wikipedia.org/wiki/QWERTY#cite_note-why-4 


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Re: [ccp4bb] Philosophical question

2013-03-19 Thread David Schuller

On 03/19/13 14:41, Jacob Keller wrote:
I don't understand this argument, as it would apply equally to all 
features of the theoretical LUCA (protein and DNA sequences, etc). To 
make it logically sound, I think you have either to include some kind 
of super-high boundary to getting to other possible conventions (you 
probably imply this) or, as I have suggested, it may be a particularly 
good, if not the best, solution (a global minimum, one might say). The 
first hypothesis is similar to the QWERTY keyboard, which is cemented 
in place by many factors, whereas the second is more survival of the 
fittest.



It would not be a safe idea to assume that LUCA was a single cell with a 
single chromosome (i.e. like a modern bacterium.) It would also not be 
safe to assume that viruses and horizontal gene transfer were not around 
at that time.


As I mentioned privately, I think the relevant slogan would be winner 
take all rather than survival of the fittest.


Another possible explanation for having a recognition tag at the 
beginning of each transcribed gene: to distinguish between host and 
virus. This does not imply that Met has any specific advantage over any 
any other tag which might have been chosen.



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Re: [ccp4bb] stereo monitor for DELL T7600

2013-03-01 Thread David Schuller

On 03/01/2013 06:52 AM, mesters wrote:


Just make sure the graphics card has not only miniDisplay 
connectors... The 3D monitors mostly have HDMI and DVI-D.
Do not confuse the DVI-D with single/simple DVI as the bandwidth will 
be too low for stereo.





1) Monitors with 120 Hz stereo support and Displayport connections are 
finally becoming available.


2) I find your use of the terminology confusing.
DVI-D means digital only, as opposed to DVI-I, (integrated) which has 
both digital and analog.
DVI-dual link has more digital conductors for a wider signal path. This 
will be need for 129 Hz stereo applications at HD resolution. The cable 
needs to be dual link as well.


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Re: [ccp4bb] Sighting of Protein Crystals in Vivo?!

2013-02-17 Thread David Schuller

On 02/16/13 00:46, Zhijie Li wrote:

Hi Jacob,
Interesting topic.
This reminds me the posters I saw on ACA 2010, on the femto-second 
infrared laser based instrument . That instrument utilizes the 
nonlinear optical properties of  crystals of chiral molecules to 
detect very small crystalline materials from amorphous background: the 
crystals will double the frequency of the laser, turning the infrared 
light to visible light. I cannot recall the exact name of the 
technology now, unfortunately.


Multpile photon fluorescent microscopy, or two-photon excitation 
microscopy, sometimes implemented as scanning confocal microscopy. One 
implementation is acronymmed SONICC.


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Re: [ccp4bb] electron density assignment

2013-02-04 Thread David Schuller
Generate an anomalous map and look for peaks. Many metals would generate 
anomalous.



On 02/04/13 07:39, Gang Dong wrote:


Dear all,

Here are some hexmeric densities we observed in our 1.6-A resolution 
2Fo-Fc map. They are located in between two dimers. Although 7 waters 
would fit nicely in the densities, we are not sure whether they might 
be something else (metals?). Any suggestions are welcome. Thanks! Gang



...

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Re: [ccp4bb] off topic - legacy hardware help needed

2013-01-24 Thread David Schuller

On 01/24/2013 03:19 AM, James Stroud wrote:

It seems like the problem is that the Indigo has an IP address that is not part 
of the subnet that it is on, so this makes network access impossible. Is this 
correct?

If so, you can just spoof the proper subnet in isolation. You can run dd-wrt on 
a compatible router and assign any subnet you want (ensuring to disconnect it 
from the WAN, lest a disgruntled IT guy shows up at your office). Then, just 
access the SGI via IP as you normally would from another machine on the 
isolated subnet and edit the config files to change the IP address. This 
doesn't require tracking down any legacy hardware.
Yes, something like that. I don't think you even need to involve a 
router, just find a computer with an extra ethernet port, configure it 
with an address compatible with that on the old SGI, and plug both into 
a switch. SSH or telnet across and configure a new address on the SGI, 
then reboot and replug.




On Jan 23, 2013, at 5:07 PM, Dave Roberts wrote:


Hi all,

By the way, thanks for all the suggestions on the linux versions.  I went 
against my better judgement and just stuck with Fedora, mainly because I'm 
familiar with it.  I have to admit, I kind of like it. I was able to get it up 
and running, run nfs to mount local drives, and install all the necessary 
crystallography software with no hitch - quick.  It's kind of nice.  And it set 
up my wireless printer automatically - so all is great.

Anyway, we have an old Indigo SGI that runs our NMR.  It's a console only 
system, and we access it via the network from another old SGI (toaster model - 
blue).  The console does not have a video card (nor space for one), so I can't 
plug in to it and see what's happening.

Anyway, our network was recently updated, and in doing so it has made access to 
our console system unavailable.  We can't get there because the IP's that used 
to be needed are no more.

So, I can get the disk out, and I have a variety of unix/linux systems that I 
could plug it in to.  But, alas, I have no motherboards or systems that take 
SCSI (that I have a sled for or a way to put it in). I need to be able to mount 
the drive on some sort of system, edit a few config files to fix the network, 
then plug it all back in.  All without messing up boot tables and such (not a 
big deal, just thought I'd throw that out there).

Is there a cable that simply allows me to plug in the back of a SCSI drive then 
connect to an IDE port on a newer motherboard (or better yet, an external USB 
port)?  Just curious - that would be worth it to me.

Any thoughts?

Thanks

Dave



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Re: [ccp4bb] Crystallography Near Absolute Zero?

2013-01-23 Thread David Schuller

On 01/23/13 10:11, Jacob Keller wrote:
Is anyone aware of any datasets taken at near absolute zero? I was 
wondering what would happen...


http://www.ncbi.nlm.nih.gov/pubmed/12718921
New techniques in macromolecular cryocrystallography: macromolecular 
crystal annealing and cryogenic helium.


Hanson BL 
http://www.ncbi.nlm.nih.gov/pubmed?term=Hanson%20BL%5BAuthor%5Dcauthor=truecauthor_uid=12718921, 
Schall CA 
http://www.ncbi.nlm.nih.gov/pubmed?term=Schall%20CA%5BAuthor%5Dcauthor=truecauthor_uid=12718921, 
Bunick GJ 
http://www.ncbi.nlm.nih.gov/pubmed?term=Bunick%20GJ%5BAuthor%5Dcauthor=truecauthor_uid=12718921.
J Struct Biol. http://www.ncbi.nlm.nih.gov/pubmed/12718921# 2003 
Apr;142(1):77-87.



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[ccp4bb] Golden Jubilee of Ramachandran Plot

2013-01-18 Thread David Schuller

http://eventheodd.blogspot.in/2013/01/golden-jubilee-of-ramachandran-plot.html


 Golden Jubilee of Ramachandran Plot
 
http://eventheodd.blogspot.in/2013/01/golden-jubilee-of-ramachandran-plot.html

Exactly fifty years from now i.e. in the year 1963, G. N. Ramachandran 
et. al published breakthrough original research in Journal of Molecular 
Biology. Ramachandran plot still remains a touchstone for protein form 
and structure (example, in validating a homology models). This plot is 
remarkable because it came ahead of time (it was proposed in 1963 when 
there were no computers, mechanical calculators were the cutting edge of 
technology)

...


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Re: [ccp4bb] Crystallization buffer pH optimization

2013-01-17 Thread David Schuller

That may be the CALBIOCHEM Buffers Booklet, which is free online as a PDF.

On 01/17/2013 12:38 AM, Mike John wrote:

Hello,

Shameful and sorry for asking this simple question, it looks like this 
when first starting a new setup in

so-called structural biology.

I remmeber a book of, probably, Hampton, in which there are tables of 
pH optimization for many buffers. For example for buffer TRIS, the 
table will list how many drops NaOH/HCl needed to change pH from 7.0 
to 7.2, etc. This is useful for crystallization pH optimization, where 
can I buy or download this info?  Alternatives?


Thank you very much!

Mike





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Re: [ccp4bb] [COOT] favorite linux flavor, or as most of you would say, flavour ;)

2013-01-17 Thread David Schuller
A year or two ago we switched from Fedora to Scientific Linux 6. It is a 
free repackaging of Red Hat Enterprise, so it should be a 
straightforward shift from Fedora. It is supported long term, and has 
backing from several large labs (fermilab, CERN, etc)


CCP4, Coot, etc. seem to be well-supported in it. Anything package for 
RH Enterprise should be fine.



On 01/17/13 11:33, David Roberts wrote:
I'm sorry to re-hash this issue, but I just wanted to know what the 
present general consensus is on linux flavors.  I teach a 
crystallography class every 2 years, and I have a small cluster of 
computers running fedora, but the deal is that by the time I get 
around to my class, fedora has routinely gone up at least 2 levels 
since my last upgrade, meaning that the latest software and things are 
difficult at best to load on.


I'm OK with any linux, I just want one that will be able to run the 
majority (if not all) of the typical crystallography packages (cns, 
ccp4, coot, etc...).  I also would like one that works well with nfs 
and local file sharing.  I can upgrade fedora, no problem, but I 
thought I may branch out if others think there are better flavors out 
there.


Thanks so much

Dave Roberts



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Re: [ccp4bb] protein degradation in crystal

2013-01-16 Thread David Schuller
Were the crystals which run different on gels from the same drop, or 
separate drops?


Yes, it is possible that the protein is being cleaved in the crystal 
(self-cleavage?); but it may also be that it is being cleaved in the 
mother liquor, and that crystallization is enriching one form or 
another. Remember that crystallization is a useful purification technique.


There should be enough protein in a crystal to get some mass spec data, 
which will tell you the size of the components, and which should be 
precise enough to tell you the cleavage site. This will tell you what 
type of protease you are dealing with.


Then as possible remedies:

You could include an appropriate protease inhibitor during purification 
to limit degradation.


You could add a bit of protease to encourage proteolysis to go to 
completion. You want your sample to be homogeneous, so whether this is 
useful depends on whether the cleaved part is the interesting part.


You could engineer the gene with a stop codon at or near the cleavage 
site. This is what we did with HO-1, with some success.

DOI: 10.1002/pro.5560070820

You could engineer the cleavage site to eliminate cleavage.

Cheers,

On 01/16/13 06:14, LISA wrote:

Hi All,
I have an 36KD protein which can be crystallize in two days. Most of 
the crystals are very big. But all cystals have poor resolution,lower 
than 3.8 A. I picked some crystals, washed them in the mother solution 
and then run SDS-PAGE. It is surprised to find that different cystals 
have different components. Some crystals have several small bands 
below the band of the protein. And in some crysals the bigger size 
band (as the construct should be) almost disappared and have smear. 
Does the protein was degradated in the crystals? Did someone met the 
similar problem as I? Thanks


All the best
lisa



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Re: [ccp4bb] protein degradation in crystal

2013-01-16 Thread David Schuller
Were the crystals which run different on gels from the same drop, or 
separate drops?


Yes, it is possible that the protein is being cleaved in the crystal 
(self-cleavage?); but it may also be that it is being cleaved in the 
mother liquor, and that crystallization is enriching one form or 
another. Remember that crystallization is a useful purification technique.


There should be enough protein in a crystal to get some mass spec data, 
which will tell you the size of the components, and which should be 
precise enough to tell you the cleavage site. This will tell you what 
type of protease you are dealing with.


Then as possible remedies:

You could include an appropriate protease inhibitor during purification 
to limit degradation.


You could add a bit of protease to encourage proteolysis to go to 
completion. You want your sample to be homogeneous, so whether this is 
useful depends on whether the cleaved part is the interesting part.


You could engineer the gene with a stop codon at or near the cleavage 
site. This is what we did with HO-1, with some success.

DOI: 10.1002/pro.5560070820

You could engineer the cleavage site to eliminate cleavage.

Cheers,

On 01/16/13 06:14, LISA wrote:

Hi All,
I have an 36KD protein which can be crystallize in two days. Most of 
the crystals are very big. But all cystals have poor resolution,lower 
than 3.8 A. I picked some crystals, washed them in the mother solution 
and then run SDS-PAGE. It is surprised to find that different cystals 
have different components. Some crystals have several small bands 
below the band of the protein. And in some crysals the bigger size 
band (as the construct should be) almost disappared and have smear. 
Does the protein was degradated in the crystals? Did someone met the 
similar problem as I? Thanks


All the best
lisa



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Re: [ccp4bb] Today ...

2012-12-21 Thread David Schuller
On neither case does an alphanumeric sort coincide with a chronological 
sort. The obvious solution is to petition to have the months renamed 
alphabetically.


On 12/21/12 03:23, Tom Murray-Rust wrote:

Hi Juergen,

Your scheme as printed has two J's - so January and July are 
indistinguishable! I would suggest the letters should instead be 
JFMAYULGSOND.


On 21 Dec 2012, at 01:52, Bosch, Juergen jubo...@jhsph.edu 
mailto:jubo...@jhsph.edu wrote:



May I introduce you to another fool proof way:
12d12 ...
J, F,M,A,Y,J,U,G,S,O,N,D for the months, simply first letter, but if 
taken move to the second letter etc.




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Re: [ccp4bb] Today ...

2012-12-20 Thread David Schuller

On 12/20/12 11:23, Edward A. Berry wrote:
No, No- in scientific circles we go from MSB on the left to LSB on the 
right:

2012 12 20  (still a sort of palindrome).


This is the best method if you are going to incorporate the date into a 
file name. That way alphanumeric and chronological searches come up the 
same.


It's a pity it took us so long to figure this out, and the world is 
ending tomorrow.


http://www.makemeacocktail.com/cocktail/7209/mayan-apocalypse/
Maya Apocalypse cocktail

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Re: [ccp4bb] hkl2000 install

2012-11-19 Thread David Schuller
On 11/18/12 20:48, 王瑞 wrote:
 OK,thank you all of you. I have installed one copy of HKL2000 on our
 desktop computer. But for my notebook's low 1366*768 resolution, the
 HKL2000 can't work ! So what could I do to resolve it ?

http://www.pcworld.com/article/261763/samsung_shows_off_series_9_laptop_with_retina_matching_display.html

Samsung Shows Off Series 9 Laptop With Retina-Matching Display

2560 x 1440 pixels in a 13 inch laptop


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Re: [ccp4bb] vitrification vs freezing

2012-11-16 Thread David Schuller

On 11/16/12 17:33, Adrian Goldman wrote:

Bernard Dixon is merely copying the great essay by George Orwell 'politics and 
the english language'. Its well worth a read.

In it, Orwell lays out about six simple rules for writing good english prose.

Three of them are:
never use the passive voice.
...

Translating into science-speak: The passive voice should never be used.

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[ccp4bb] Sutherland wind Kyoto pPrize

2012-11-11 Thread David Schuller

http://www.i-programmer.info/news/82-heritage/5061-ivan-sutherland-presented-with-kyoto-prize.html



Dr Ivan Sutherland, often dubbed Father of Computer Graphics was one 
of three laureates honored at the 28th Annual Kyoto Prize Ceremony held 
today in Japan,


The Kyoto Prize http://www.inamori-f.or.jp/e_kp_out_out.html is an 
annual international award presented in three categories to honor those 
who have contributed significantly to the scientific, cultural and 
spiritual betterment of mankind...

-

All of us in the crystallographic community have benefited from advances 
in visualization traceable to Sutherland. Congratulations to him.


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Re: [ccp4bb] Assemble Protein-DNA complex

2012-11-09 Thread David Schuller

On 11/09/12 15:43, Tommi Kajander wrote:
It is not very surprising that the affinity gets higher with lower 
salt, right? 


Not at all. I wanted to ask if their assay could distinguish between 
specific binding and nonspecific binding, but I decided not to sidetrack 
the discussion.


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Re: [ccp4bb] Ca or Zn

2012-10-30 Thread David Schuller

On 10/30/12 15:02, Bosch, Juergen wrote:
calculate an anomalous map, you should see the Zn signal even if you 
collected at the SeMet peak.

Jürgen
..


Ca can have a noticeable anomalous signal of its own, if your data are good.

If the possibility to collect new data exists, collecting above and 
below the Zn edge should be informative. (Zn K edge 1.28 A = 9.6586 keV)


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Re: [ccp4bb] Stout and Jensen

2012-10-22 Thread David Schuller

I note that it is on sale at Amazon.com for only $177.07 right now.


On 10/22/12 14:36, Jayashankar wrote:

Dear All,

I would like to buy  the book '' X-ray structure determination'' by 
George.H.Stout and Lyle.H.Jensen.
If in any case , somebody has shelved it and want to give away for 
reasonable price. I would buy it.


sincerely
Dr. Jayashankar Selvadurai (Jay)
Hannover
Germany





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



Re: [ccp4bb] Help Please!

2012-09-18 Thread David Schuller
Those commands which do not work apparently require the version of libc 
that you replaced. If your description is accurate, you did not actually 
delete the file, but merely renamed it.


You can boot up from your Linux (this is Linux, right?) installation 
disk in RESCUE mode and put the file back where it belongs. Anyone 
brave enough to be moving system libraries around probably knows enough 
about Linux to pull it off.




On 09/18/12 12:28, jie liu wrote:

Dear you all

I really need your help. I was trying to install ccp4i Package 
Manager, and got an error saying /lib64/tls/libc.so.6 version 
'GLIBC-2.4' not found.


The file '/lib64/tls/libc.so.6' was actually linked to 
'libc-2.3.4.so'. I thought this one might be out of date. So I found a 
newer version of 'libc-2.5.so' on another linux machine and copied it 
here under the same directory '/lib64/tls'.


Then the stupid thing I did was as follows:
mv  libc-2.3.4.so libc-2.3.4.so.old
mv libc-2.5.so libc-2.3.4.so

Now I can't use any command. I can't ls, rm, mv, cp, pwd, and so on. I 
always got an error saying relocation error: /lib64/tls/libc.so.6: 
symbol _dl_tls_get_addr_soft, version GLIBC_PRIVATE not defined in 
file ld-linux-x86-64.so.2 with link time reference.


It looks like a serious problem. Did I damage the operating system? 
Could you please give some advice on how to fix it?


I am anxiously waiting for your help!

Best regards

Jie Liu



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


Re: [ccp4bb] CCP4-6.3.0 installation

2012-08-04 Thread David Schuller

On 08/04/2012 04:38 PM, james09 pruza wrote:

Dear CCP4bbers,

I am facing CCP4-6.3.0 installation problem. Unable to run make. 
Configuration is done. Getting error while running make (command not 
found). Please help.

Thanks in advance, James


Which operating system are you using? On 
RedHat/Centos/Fedora/ScientificLinux try:

yum install make



Can you tell from the error message whether it is make itself that is 
missing, or something else?


Cheers,

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



Re: [ccp4bb] asking for a reference for cacodylate decomposition in protein crystals upon X-ray exposure

2012-08-02 Thread David Schuller
I do not have the reference you are seeking, but I have seen 
cacodylate-containing xtals diffract to better than 1.2 and hold up very 
well. Also, arsenic has an anomalous signal which may be exploited for 
phasing, peak ~ 1.04 A.



On 07/29/12 18:53, Tatyana Sysoeva wrote:

Hi!

I heard a couple of times that use of cacodylate buffers in 
crystallization is bad, and not only because of the compound toxicity.


As I understood, presence of the cacodylate in a protein crystal will 
cause a particular crystal degradation pattern upon X-ray exposure - 
darkening of the crystals, gas formation

I tried to find some references on that and failed in doing so.
I found some earlier discussions like this one:
http://www.proteincrystallography.org/ccp4bb/message23691.html
but don't have anything to reference in literature. I would appreciate 
if someone can point me to a right direction.


I am sorry if this question is out of the groups topic range.

Thank you in advance!
Sincerely,
Tanya




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



Re: [ccp4bb] harvesting in cold room

2012-07-13 Thread David Schuller

On 07/13/12 17:29, Jacob Keller wrote:
You probably already know this, but nitrogen is not at all 
poisonous--about 78% of the air is nitrogen. I guess you were probably 
worried about asphyxiation?


We have oxygen sensors in our X-ray hutches for precisely that reason.

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



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