Re: [ccp4bb] proton scattering by X-rays

[Mark van der Woerd]

Not very well. When you look in the originally quoted article, there is really 
not much difference in the ED for H+ and H- (which are conveniently both shown 
in Fig 2). You build a model that is consistent with 'book knowledge' (i.e. 
normal hydrogen has only one bond) and take it from there. 

You have a point that the resolution isn't very good at 0.89A (sorry!)  but I 
suspect that the number of recorded reflections is much more important than the 
nebulous number of 0.89A (i.e. you can start to see these little details 
because you finally have an over-determined system parameters). 

What you CAN do in fact is appropriately subtract "spherical electron density" 
from the experimental density and see what is left (i.e. directional ED that is 
'surplus'). I tried to quickly find a paper on that, they exist, and they show 
that experimental density does confirm what we learn in chemistry class, 
orbitals are not imaginary. 

Mark

 

 

-Original Message-
From: Doug Ohlendorf 
To: CCP4BB 
Sent: Mon, Feb 2, 2015 11:29 am
Subject: Re: [ccp4bb] proton scattering by X-rays


But, how with x-rays can one experimentally tell the difference between a 
hydrogen and a filled orbital (say of N)? I will grant that the electron 
density for a bound H should extend farther from the heavy atom but I believe 
you would need resolution better than 0.89 Ang to see this difference.

Doug

Douglas H. Ohlendorf   Phone:  612-624-8436
Professor  FAX:612-624-5121
Dept. of Biochemistry, Molecular Biology & Biophysics
Twin Cities Campus, University of Minnesota
Lab web site:   http://biosci.cbs.umn.edu/bmbb/ohlen_lab/index.html


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Colin Nave
Sent: Monday, February 02, 2015 9:04 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] proton scattering by X-rays

“As you say the proton itself is invisible to X-rays.”
Not quite! The ratio of scattering between electrons and protons should go as 
the inverse square of the masses.
Ratio of mass 1:1860, ratio of scattering 1:3459600. A small correction but 
doubtless it has been incorporated in to SHELX.
Colin


From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ian Tickle
Sent: 02 February 2015 13:35
To: ccp4bb
Subject: Re: [ccp4bb] proton scattering by X-rays


Peter, if it's a covalently-bonded H atom it surely can't be a bare proton, it 
must have at least some partial electron around it for the (possibly partial) 
covalent bond, enough to diffract X-rays anyway.  As you say the proton itself 
is invisible to X-rays.
Cheers
-- Ian

On 2 February 2015 at 13:08, Peter Moody 
mailto:pcem1bigfi...@gmail.com>> wrote:
Dear BB

I have (again) realised how limited by understanding of our subject is.

In Nature’s online site 
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14110.html?WT.ec_id=NATURE-20150129
 there is a paper describing an X-ray structure determined with sub-atomic data 
(nice!).  The figures show density for H+ as well as H-. In my simple way I had 
assumed that any X-ray scattering from the nucleus was negligible, and that the 
electrons are responsible for this. I would expect a proton (i.e. H+) alone to 
be invisible to X-rays, and certainly not to look similar to a hydride (with 
two electrons in (electron density) maps. What have I missed?  Could someone 
please explain, or point me to a suitable reference?

Best wishes, Peter
(please use peter.mo...@le.ac.uk to reply directly)

http://www2.le.ac.uk/departments/biochemistry/staff/moody



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Re: [ccp4bb] proton scattering by X-rays

[Mark van der Woerd]

Hi Peter,

Try to think of it as a quantum chemist:
What you call H+ is not "H+ floating in space". They are hydrogens bound to the 
rest of the structure by means of electrons. These electrons can be described 
by wave functions, which relate to probabilities where they (electrons) might 
be.

If we consider for simplicity water, we learn in a simple model that each O-H 
bond contains two electrons. On average, they "like to be" closer to O and than 
to H. But it does not mean "H has none". 

You need high-quality, high-resolution data to actually visualize this and in 
small molecule work this is commonly done. In macromolecular work not so much, 
but my search easily found an example (see 
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC16211/ for Crambin) where you can 
"see" the electrons between N and H in the backbone.

The main difference between what you think of as H+ and H- is one and two 
bonds, respectively. The density in their figures does not look all that 
different, but says "something should be here". We then propose H in the 
location and show that it adequately explains the experimental data.

HTH

Mark 

 

 

 

-Original Message-
From: Peter Moody 
To: CCP4BB 
Sent: Mon, Feb 2, 2015 11:33 am
Subject: [ccp4bb] proton scattering by X-rays


 
   
Dear BB
  


   
I have (again) realised how limited by understanding of our subject is.
  


   
In Nature’s online site 
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14110.html?WT.ec_id=NATURE-20150129
 there is a paper describing an X-ray structure determined with sub-atomic data 
(nice!).  The figures show density for H+ as well as H-. In my simple way I had 
assumed that any X-ray scattering from the nucleus was negligible, and that the 
electrons are responsible for this. I would expect a proton (i.e. H+) alone to 
be invisible to X-rays, and certainly not to look similar to a hydride (with 
two electrons in (electron density) maps. What have I missed?  Could someone 
please explain, or point me to a suitable reference?
   


  
Best wishes, Peter 

  
(please use peter.mo...@le.ac.uk to reply directly)
   
   
http://www2.le.ac.uk/departments/biochemistry/staff/moody
   
 
 

Re: [ccp4bb] Control the crystallization process in the presence of small volatile organic molecules

[Mark van der Woerd]

Chen,

Dioxane is not easy to work with, exactly for the reasons you describe. 

There is one thing you did not mention, which I know to be an additional issue: 
the quality of the dioxane. I do not know if you need good quality (whatever 
that is) but it is a fact that crystallization works with dioxane from some 
manufacturer/lots and not with others. I have never figured out why this is so. 

For a paper on kinetics and reservoir volume discussion, I would read the work 
by Forsythe et al 
(http://journals.iucr.org/d/issues/2002/10/01/ic0013/vidsup.html,  
doi:10.1107/S0907444902014208)
Basically you will find that this paper says that well volume does not matter 
much. Content of your drop matters a lot. In your case, having a very volatile 
component, equilibration would be really fast. 

One way to get away from all that is to do batch experiments, where there is no 
active transport from a drop into a well. But your question remains very good: 
you need an "oil" (?) that will not permit water or a volatile organic 
substance to escape. I am not sure what would do the trick. 

Dioxane is a decent cryo-protectant by itself. I would think about adding 
"gooey" things like low molecular weight PEG to try to get the drops better 
behaved. Evaporation of the dioxane will still be an issue, but with a higher 
viscosity you may not have to "chase your crystals" through the drop. 

Hope this helps a little.

Mark

 

 

 

-Original Message-
From: Chen Zhao 
To: CCP4BB 
Sent: Wed, Jan 22, 2014 11:00 pm
Subject: [ccp4bb] Control the crystallization process in the presence of small 
volatile organic molecules




Dear all,


I am now optimizing a hit which contains about 30% 1,4-dioxane using 
hanging-drop vapor diffusion at 25 degree. I am having a hard time to reproduce 
the results: most of the times the drops are either dry in one day or full of 
precipitate, and only occasionally could I get small crystals. Is there a way 
to control the vapor diffusion process, like using oil to seal the reservoir? 
(I know paraffin is permeable to dioxane) Also if someone could refer me to 
studies on the effects of reservoir volume and surface area to the 
crystallization kinetics, that would be very helpful.


I am also seeking for recommendations for freezing crystals in this condition. 
What kind of cryoprotectant has a higher chance? Another problem is that when I 
tried to freeze the crystals, the drop dries super rapidly, and the crystals 
will dissolve if I add reservoir buffer. But I would assume good cryoprotectant 
could do the job. On the other hand, this points back to my previous question 
on "dioxane-impermeable" oil. If this magic oil exists, I could use it to seal 
the drop when freezing.


Thank you for help!


Sincerely,
Chen

Re: [ccp4bb] cryoprotection ideas for salt based condition

[Mark van der Woerd]

Mahesh,

Have you tried to see what happens when you do not freeze the crystals at all? 
Do you get good resolution data? Do the crystals suffer radiation damage?

Those are two important questions. First, if your crystals do not diffract well 
before you freeze them, usually (but not always) they will also not diffract 
well after you freeze them and you can try cryo-conditions until you see blue 
in the face, but they will never improve. In that case, you need new/better 
crystals. Second, many well-diffracting crystals do not necessarily need to be 
frozen at the home source. Of course they do need to be frozen at the 
synchrotron, but if you can get good (enough) data at home...

On to recipes: try increasing dioxane. Try adding alcohols (somewhat similar to 
dioxane, maybe iso-propanol). Expect this to be a pain: very volatile agents 
make it difficult to harvest crystals. Of course try the mixtures without 
protein or crystals for freezing conditions and how well you can mix the 
components. Salt and organics are often not compatible. 

Try to regrow your crystals in sodium malonate (replace Ammonium sulfate with 
malonate). Try to regrow them in the presence of small amounts of the 
cryo-protectants you have already tried. For the ones that work, repeat with 
higher amounts. Very often crystals are much happier when you don't soak/tinker 
with them and freeze them straight out of the drop. 

Good luck.

Mark

 

 

 

-Original Message-
From: Mahesh Lingaraju 
To: CCP4BB 
Sent: Wed, Jan 22, 2014 10:38 am
Subject: [ccp4bb] cryoprotection ideas for salt based condition


Hello folks, 


I have crystals for a protein which form in 0.1 M MES pH 6-6.75, 10% dioxane 
and 1.6-2 M Ammonium sulphate. Based on little experience I have finding the 
right cryoprotection for salt based conditions; I have tried glycerol (15-25%), 
Ethylene glycol (20-25%), DMSO (15-20%) and increasing ammonium sulphate 
concentration in presence of 5-10% glycerol. The crystals disintegrate in any 
kind of PEG based cryo. I made all these solutions in the mother liquor and 
tested if they freeze clearly before using them. However when I loop the 
crystals and try to soak them in these cryo- mother liquor, a lot of salt 
crystals suddenly form around the protein crystal and I see diffraction only 
from these salt crystals. The best I have been able to get so far is ~ 9Å 
diffraction (Home-source) with DMSO as the cryoprotectant.


I have also tried using 1 M sodium malonate as the cryoprotectant but my 
crystals are not too stable in this mother liquor probably because I had to 
lower the ammonium sulphate by ~ 7-10% to make the drop not form salt crystals 
instantly when exposed to air. 


Other than trying to make the crystals more cryo-ready by finding other hits or 
may be growing the same crystals with some cryoprotectant, I was wondering if 
any of you have ideas based on your experience or suggestions in case I am 
doing everything wrong in the first place.


Thanks for all the help, 


Mahesh  

Re: [ccp4bb] DNA Protein co- Crystallization

[Mark van der Woerd]

Acoot,

Remember that when you crystallize something, you want to build a lattice of 
*the same thing*. So it is better to make a homogeneous complex (if it is not 
mandatory). This means that the stoichiometry of the protein and DNA has to be 
a constant (we used 1:1.05 with excess DNA because the protein alone would not 
crystallize at all) and also that the complex shape has to be as stable as 
possible. If you can get a DNA sequence with specificity, that would help 
because you are more sure that the complex is homogeneous.

These experiments are always expensive because the DNA cost is high. You are 
facing trials with multiple DNA sequences and I would guess that you are lucky 
if "multiple" equals three in the case the binding is well behaved (sequence 
specific), you have a good grasp on the sequence length (say +/- 1) and then 
you still have to decide what the best "end sequence" is. Frequently these ends 
make crystal contacts with something else (it is fashionable to think that you 
can build a pseudo-continuous DNA helix throughout the crystal by lining up 
subsequent molecules) but in the end it is not known what these contacts are 
until you solve the structure. Trial and error, as usual.

Mark


-Original Message-
From: Acoot Brett 
To: CCP4BB 
Sent: Fri, Jan 3, 2014 9:23 pm
Subject: Re: [ccp4bb] DNA Protein co- Crystallization



Dear All,


For the question, I think for a protein-DNA interaction, the protein may 
interact with any sequences of DNA, which will give a lot of combination of 
protein-DNA sequence for crystallization screening.  Or do anyone regard to 
just try the crystallization of the protein-one specific sequence DNA fragment 
for the trial (for example the DNA sequence with the highest binding affinity)? 
In another word, does the easiness of the crystallization has relation with how 
strong the protein interacts with the DNA sequence?



Acoot
 
 
 
 
 
  On Saturday, 4 January 2014 11:02 AM, rajakumara eerappa  
wrote:
  
  

My suggestions are
1 try complementary and non-complementary overhangs which can form Watson-crick 
and/ or Hoogstein base pairing.
2. If it binds self-complementary duplexes then try them also.
3. Peg conditions with slight acidic pH are more suitable.
4. Divalent cation salts (Ca, Mg, Mn) in crystallization.


Wish you good luck
Raj



On Friday, January 3, 2014, venkatareddy dadireddy  wrote:

Hi,


I'm working on DNA binding protein, looking to co-crystallize protein- DNA 
complex and have no previous experience. Your suggestion would be very precious 
on the following queries.
1. My protein is 646 amino acid long and it exists as homodimer. It is also 
having around 20 amino acid extra sequence from vector. Will vector 
sequence affect   crystallization?
2. Its homologous protein shows good affinity for 31-mer. Shall I use same 
length   of DNA for co- crystallization.
3. What is the length of DNA to be used?
4. What is purity of oligos to be used? Is it HPLC pure or normal desalted 
ones. I have read on CCP4 mails for screening purpose normal oligos are 
fine. Please   comment on that.
3. Any other suggestions on Protein DNA co- crystallization.



Thanks
venkat







  
 
  
 

Re: [ccp4bb] DNA Protein co- Crystallization

[Mark van der Woerd]

Hi Venkat,

1. My protein is 646 amino acid long and it exists as homodimer. It is also 
having around 20 amino acid extra sequence from vector. Will vector 
sequence affect   crystallization?

Only experience can tell. You should try, if possible, to crystallize both 
constructs with and without the extra 20 amino acids. It is important to make 
sure that you try at least the option with 20 amino acids removed. They might 
interfere, for example, in DNA binding.

2. Its homologous protein shows good affinity for 31-mer. Shall I use same 
length   of DNA for co- crystallization.

Yes. 

But... you really want to have some reliable data for YOUR protein. 
Crystallization of protein-DNA complexes is a little more tricky because you 
have to decide not only how to crystallize it, but also which DNA sequence you 
want and how long the sequence should be. If you can do some binding 
experiments, that would really help. Determine which sequence binds best (if 
any, it is advantageous if you have sequence specificity) and what the optimal 
DNA length is. Alternatively, do some protection experiments: with which 
sequences can you see DNA digestion in the presence of your protein? What is 
the protein-protected sequence?

3. What is the length of DNA to be used?

If you have experimental information, you try (example when 31 is best:) 30, 
31, 32, 33, maybe 34. The additional DNA base pairs that will stick out of your 
protein may be important for crystallization and you will want to screen 
multiple lengths and vary the base pairs that stick out. Note that you can (in 
principle) have a non-blunt DNA sequences, i.e. one strand longer than the 
other. You should try that too.

4. What is purity of oligos to be used? Is it HPLC pure or normal desalted 
ones. I have read on CCP4 mails for screening purpose normal oligos are 
fine. Please   comment on that.

My experience is that you will want HPLC grade.

3. Any other suggestions on Protein DNA co- crystallization.


Characterize your protein and protein-DNA complex carefully before you try to 
crystallize. There are many variables and any information you can get from 
other experiments can help you in your choice how to go about crystallization 
of the complex.

Note: if your protein is an enzyme, you may want to consider deactivating the 
enzyme. For example, many enzymes require a Mg co-factor. If you replace Mg 
with Ca, your complex may be more stable/robust and the crystallization may 
work better. 

Hope this helps.

Mark



 

 

 

-Original Message-
From: venkatareddy dadireddy 
To: CCP4BB 
Sent: Fri, Jan 3, 2014 4:26 am
Subject: [ccp4bb] DNA Protein co- Crystallization


Hi,


I'm working on DNA binding protein, looking to co-crystallize protein- DNA 
complex and have no previous experience. Your suggestion would be very precious 
on the following queries.
1. My protein is 646 amino acid long and it exists as homodimer. It is also 
having around 20 amino acid extra sequence from vector. Will vector 
sequence affect   crystallization?
2. Its homologous protein shows good affinity for 31-mer. Shall I use same 
length   of DNA for co- crystallization.
3. What is the length of DNA to be used?
4. What is purity of oligos to be used? Is it HPLC pure or normal desalted 
ones. I have read on CCP4 mails for screening purpose normal oligos are 
fine. Please   comment on that.
3. Any other suggestions on Protein DNA co- crystallization.



Thanks
venkat

Re: [ccp4bb] Cyro cooling system

[Mark van der Woerd]

Hi Uday,

I would simply ask Oxford for advice, I have never regretted asking them (or 
most others) for advice. On their web site it is written that the Desktop 
Cooler only goes down to 170K, so that will not do, I don't think. In fact, 
they only make two suggestions when you go through their product selection 
process and neither one of those is very small.

We are very happy with our Oxford system (used for protein crystallography) but 
small it is not.

Mark


 

 

 

-Original Message-
From: Uday Kumar 
To: CCP4BB 
Sent: Mon, Nov 11, 2013 10:22 am
Subject: [ccp4bb] Cyro cooling system


Hello

We are planning to buy a small cryo cooling unit for protein crystal cooling 
which can manage 100 K temp. 

we are limited with space and only small units like Oxford cryosystem Desktop 
cooler or any of that dimensions can fit.

Does anybody has some suggestions in this regard.

Would be nice if someone has some information regarding the use of  Oxford 
cryosystem Desktop cooler for protein crystals.

Thank you

 

Re: [ccp4bb] X-ray pattern has streaks

[Mark van der Woerd]

Yes, and the mosaicity might have been poor to start with, or it might have 
been caused by sub-optimal freezing conditions, assuming that the crystal was 
frozen (not enough information to tell). I recommend doing a room temperature 
diffraction experiment to see which it is and act accordingly - improve the 
crystal or improve the freezing conditions.

Mark

 

 

 

-Original Message-
From: Demetres D. Leonidas 
To: CCP4BB 
Sent: Thu, Oct 3, 2013 7:05 am
Subject: Re: [ccp4bb] X-ray pattern has streaks


Dear Krithika,

what you probably see is the diffraction pattern of a highly mosaic 
crystal due to probably internal disordering.

cheers

Demetres


On 3/10/2013 3:40 μμ, Krithika GOkulnath wrote:
> I introduce myself as Dr.Krithika Gokulnath, CAS in crystallography and 
Biophysics, UNiversity of Madras. I have been working with a cloned protein and 
have been successfully able to crystallise it. However data collection done at 
home source shows a pattern of streaks instead of spots. The crystallization 
set 
up contained 12% PEG 8000, 10mM Magnesium chloride, 200mM Potassium chloride in 
50 mM Tris pH 7.0. The protein is an enzyme which is also in the buffer 
containing the above components excepting the precipitant. It is a tetramer at 
native conditions and molecular weight on SDS-PAGE is 54 Kda. Kindly share your 
suggestions and speculations on what might be the reason for the streaking. The 
streaks are many wide spread and there are no high resolution spots or streaks 
as we might expect in salt crystals.

-- 
---
Dr. Demetres D. Leonidas
Associate Professor of Biochemistry
Department of Biochemistry & Biotechnology
University of Thessaly
26 Ploutonos Str.
41221 Larissa, Greece
-
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Fax. +302410 565290
E-mail: ddleoni...@bio.uth.gr
http://www.bio.uth.gr
---

 

Re: [ccp4bb] Advice on setting up / maintaining a Ubuntu cluster

[Mark van der Woerd]

Dear Sergei,

Many have already given good advice. A somewhat different approach:

You might want to consider using a NAS for user file and program storage. We 
have run a group of Linux PCs for years that way and we are quite pleased with 
it. The NAS would take the place of your file server PC.

Although I don't quite have enough experience with it yet to fully recommend 
it, I do think you might want to consider using FreeNAS (just Google it), 
rather than buying a physical NAS. In a nutshell:

1) It is a free NAS setup, as the name suggests.
2) You need a PC with disk bays, a fair CPU and LOTS of memory. Add number and 
size of the disks you want. The PC generally should be a 64-bit system or else 
you will not be able to install enough memory.  
3) You download the operating system on a USB drive (it does not go on your 
data disks) - this is very easy to do
4) Follow setup instructions and you are ready to start testing. 

FreeNAS offers many options, such as mirroring, striping etc. Different kinds 
of RAIDS are possible. My experience has been that it is very nice to have a 
RAID system that allows for one disk to go bad and you still have a working 
system. It has happened 2-3 times in 5 years, on 3 NASes combined, that we have 
had a disk fail without notice. The FreeNAS home page will lead you to all the 
RAID options you have, how "safe" they are, what the read and write performance 
is etc. 

It is a good idea to build a second system in a different building for backup. 
We use Rsync for backup at night and this works well (it is slow but it does 
not matter). 

You might want to do a resource analysis what your limiting factor is in 
processing crystallographic data. My experience is that the network generally 
is not the limiting factor and disk access generally is not the limit either - 
but it can be, if you are transferring a large number of images from a 
synchrotron. Typically, in my experience, CPU is still the limiting factor. 

Hope this helps.

Mark
 

 

 

 

-Original Message-
From: Sergei Strelkov 
To: CCP4BB 
Sent: Mon, Jul 29, 2013 4:22 am
Subject: [ccp4bb] Advice on setting up / maintaining a Ubuntu cluster


Dear all,

In old times I, just like about any protein crystallographer,
used to work on a cluster of SGI/IRIX workstations with complete NFS-based
cross-mounting of hard disks.

A typical operation included:
1. A single home directory location for every user:
if my home directory was on workstation X, I would by default use
it after logging on any of the workstations in the cluster.
2. A single location for all software for general use.
(And, obviously, 3. The ability to log on any node from
any terminal; today this is done via the 'ssh -X' command).

I wondered if someone could give us an advice on a painless
setup enabling 1. and 2., for a small cluster of Ubuntu computers.
We (will) have about five similar Dell computers in a local (192.168.*.*)
network (wired/wireless). Any tips on the hardware (especially the
LAN and network disks) are also welcome.

Many thanks,
Sergei

-- 
Prof. Sergei V. Strelkov
Laboratory for Biocrystallography
Dept of Pharmaceutical and Pharmacological Sciences, KU Leuven
Herestraat 49 bus 822, 3000 Leuven, Belgium
Work phone: +32 16 330845   Mobile: +32 486 294132
Lab pages: http://pharm.kuleuven.be/anafar

 

Re: [ccp4bb] Harmful effect of X-ray

[Mark van der Woerd]

My first reaction to this question was "well, it depends". The effect of X-rays 
depends on (among other things) the energy (wavelength) and the intensity (and 
of course the dose). But I decided not to write about this until...

In response to Michael's note below, I want to point out that instruments 
constantly improve:

I just re-wrote our safety plan because we have to renew our radiation license 
for our new in-house instrument. On this plan, they ask you to write a 
worst-case scenario. For an in-house sealed tube instrument, producing CuKa 
radiation, we calculated (with the help of the friendly manufacturer, thank 
you) that if you had a direct exposure to the beam, for example because your 
hand would be in the wrong place at the wrong time,  you would burn a 7mm deep 
hole in your hand. Interestingly and surprisingly, when compared to our old 
rotating anode generator, the estimated worst case scenario for the old setup 
was an order of magnitude less severe (less than 1 mm deep burn). The constant 
improvement of instruments also makes them just a little more dangerous. The 
old days of 'tingle' are long gone and you *really* need to watch yourself, 
even on in-house instruments. 

Indeed, if you do not tinker with the safety system and have shielding in place 
at all time, as you say, the exposure is never above background. So: obey all 
the rules and worry very little. 

At the synchrotron, if I recall my safety training correctly, the worst case 
scenario (which is very nearly impossible to accomplish, even if you tried, 
which of course you should not), is instant death. So yes, that gets you kicked 
out, but not the way you imagined. There are many less severe variations, but 
probably all are much more severe than the in-house case. There is a reason for 
all the safety systems.

The original question (what happens and how bad is it), is not that easy to 
answer. Apart from burns, there are of course the known effects of DNA damage 
etc. Since we share a building with people who call their profession "radiation 
health physics", I was reminded with an interesting discussion that there are 
people who study how you can use radiation for your benefit - use enough to 
kill bad things, but not so much to badly harm the good things - and these 
people make a living that way, quite successfully. 

In the end, it is hard to know what anything does to your body and it is best 
to stay on the safe side. Remember ALARA and observe it. It is possibly the 
most sensible safety rule I have seen in my life.

Hopefully now nobody will be tempted to see if it tingles when you stick your 
finger in the beam. 

Mark 

 

 

 

-Original Message-
From: R. M. Garavito 
To: CCP4BB 
Sent: Fri, Jul 12, 2013 10:14 am
Subject: Re: [ccp4bb] Harmful effect of X-ray



Most modern textbooks have sections on the proper protections and measures to 
take, although the information may be dated.  See chapter 6 in Volume III of 
the International Tables for X-ray Crystallography.  With the modern equipment 
and regulatory measures in most countries, you really have to work hard to be 
exposed at dangerous levels (which can lead to skin lesions and burns). 
However, you can get yourself exposed if you intentionally circumvent the 
safety measures and interlocks.  In my experience, X-ray exposure in 
crystallography labs is very low and not dangerous.  Our radiation safety 
people find our labs to be very "clean" with respect to scattered radiation 
around the sample compared to medical X-ray labs.  Talk to your institute's 
safety people for advice.



For in-house equipment, you are most at risk of exposure during aligning the 
equipment.  If you talk to the old crystallographers (or their students who are 
now +50 year old), you might hear stories of aligning collimators and cameras 
by the "tingle" on your eye as you look into the beam.  By the time protein 
crystallography came around (50s-60s), phosphors and film were used for 
alignment so the "danger" comes  mostly from scattered radiation and poor 
shielding.  In all the years I have worked with X-rays without protection (I 
only wore a lab coat to prevent film developer from staining my clothes), 
neither I nor my colleagues have ever had X-ray exposures above background as 
determined by film badges and ring badges.  In fact, we once exposed a film 
badge intentionally to see if anyone cared.  We caught hell for doing that.


For synchrotron sources, chances of being exposed as a general user are now nil 
unless you really work hard to subvert the safety measures (which will get you 
kicked out).



Hope this helps,


Michael




R. Michael Garavito, Ph.D.
Professor of Biochemistry & Molecular Biology

603 Wilson Rd., Rm. 513   

Michigan State University  
East Lansing, MI 48824-1319
Office:  (517) 355-9724 Lab:  (517) 353-9125
FAX:  (517) 353-9334Email:  rmgarav...@gmail.co

Re: [ccp4bb] atomic coloring for the color blind

[Mark van der Woerd]

Professor Rice,

When publishing in NAR (Nucleic Acids Research), it was recommended that we use 
"colors friendly to the color blind". You can read about it here: 
http://jfly.iam.u-tokyo.ac.jp/html/color_blind/

It is quite nice that they went to the trouble of showing us "how they see it". 
And there are plenty of suggestions how to do better. In fact, it turns out 
that you need not stay away from red and green, but define them somewhat 
different and it will work better.

Ever since I made all my illustrations like this once, I try to do it every 
time, for any journal, just in case. I consult this page often, it is quite 
helpful to me. See especially near the bottom of the page "colors unambiguous 
both to color-blinds and non-color-blinds".

Hope this helps you too.

Mark

 

 

 

-Original Message-
From: Phoebe A. Rice 
To: CCP4BB 
Sent: Fri, May 31, 2013 2:35 pm
Subject: [ccp4bb] atomic coloring for the color blind



I feel badly that one of my undergrads had trouble telling an O from a C in a 
pymol homework set because he's color blind. (The assignment involved telling 
me why the a GTP analog (GDPCP) wasn't hydrolyzed).
Is there a handy by-atom coloring scheme I can recommend that works for the 
red-green color blind? 

  thanks,
  "Professor Rice"


++
Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago
773 834 1723; pr...@uchicago.edu
http://bmb.bsd.uchicago.edu/Faculty_and_Research/
http://www.rsc.org/shop/books/2008/9780854042722.asp