I second this opinion. At the end of next week our Pilatus 200K will be
delivered. Soon after that I will be able to report on its characteristics.
But really, Boaz nailed it: reliability and service are very important. It does
not matter how good something is on paper if you cannot keep it ru
Stephen,
Stephen,
Although your peptide is smaller than the one I once worked on, here are some
thoughts that might be applicable.
1. Check and play with the radius of integration in the molecular replacement.
The default is probably not appropriate for your case but the value should be
much
No. :-)
When you are a reviewer for structural papers in journals (I do this work
sometimes), and when you see an article that has (in this example) Tom's
structure in it, but he and/or his mentor is not an author, then you call the
editor and tell them "you may have a problem". I realize that
Earlier today, I thought this and did not write it. It is a slightly different
theme on your suggestion:
I hear there are now (but have not seen examples of) "journals" (web sites)
where you do exactly what Tom did: you put your data there, which "proves" that
you did the work (first) and you
I think that in statistics you can build a model that describes (and predicts)
the uncertainty. So if you have done similar (!) replicate experiments, from
which you can build the model, you can apply it to a single observation and
provide a reasonably good guess for the value that you were meas
I don't think there is such a rule, but in the old days, when we only had
Hampton Screen I and II, the rule was:
- Set up screen 1, look at the drops and you should expect some kind of
precipitation in 50% of the drops. If much less than that, increase your
protein concentration. If much more t
BTW, a l-o-n-g time ago, I worked on a project with crystals that only grew in
the cold room. BUT... we found out that the crystals could in fact be
transferred to a regular lab under condition that you warmed them up very
slowly. So I would harvest the crystals into capillaries (this was before
oxygen so they can survive, their eyes may get
damaged.
Too far removed from CCP4. This cannot happen in the cold room while harvesting
crystals.
Mark
-Original Message-
From: Jacob Keller
To: mjvdwoerd
Cc: CCP4BB
Sent: Fri, Jul 13, 2012 5:10 pm
Subject: Re: [ccp4bb] harvesting
Hi Evette:
Technically:
The expansion ratio of liquid to gaseous nitrogen is approximately 1:700, that
is, 1 liter of liquid becomes 700 liters of gas (at room temperature). When you
are in a room that is 3 (~10ft) meters tall, 6 (~18ft) meters wide and 10
(~30ft) meters long and you assume t
Rex,
\begin{shameless self-advertizing}
Once upon a time we did a systematic study how to optimize crystal size. The
study was done with knowledge of the protein solubility (which is not normally
available, of course) and we showed that you can still do it when you do not
have this informatio
Hi Donghui,
Yes. Crystals for restriction enzyme Bsob I were ugly and did not diffract well
without detergent and were beautiful with good diffraction in presence of OBG.
You can find it in the publication. We did not find any detergent molecules in
the structure.
Now, when to try such things.
Hi Christine,
I would try to optimize both conditions, provided that you do not have
contradicting information (like a diffraction pattern that shows a small
lattice - "salt"). Have you tried an additive screen? Have you tried adding a
detergent?
My experience is mixed with things of that nat
There is a really nice web site that shows how colors are perceived by various
color-blind readers. One of the journals I recently published in recommends it
for consideration. If you are interested, have a look. The web site is made
especially for people who publish scientific articles with col
Provided that you guess the number of copies and your guess is reasonably
close, my experience is that Phaser will do the job. But you have to tell it
how many copies you expect, or it will never make sense of the data. When I did
my structure with 6(?) copies some years ago, I guessed a number
Hi Prem,
In addition to other remarks made:
- You could dissolve one or more crystals in water and have mass spec done to
verify that your crystals are a complex. It takes many crystals (20-30) to make
sure on an SDS-PAGE. You will probably need to silver stain the gel to enhance
the sensitivit
With the starting remark that Wayne is "larger than life" in my mind, we could
call SAD the "Teeter Method"? I think it has a very nice ring to it and perhaps
Wayne would approve.
I learned something new today. Until now I thought that of course it is called
"dispersion". That is because in t
Paul,
Wait a while, and then CENTOS 6 (or not wait a while). In my opinion neither of
your choices are as stable as CENTOS. The big drawback is that CENTOS does not
have the latest gadgets - but gadgets and stability are mutually exclusive, by
definition. I have lately been annoyed because I o
Hans,
Most natural toxins from snakes, scorpions etc are 50+/-some peptides. And
quite a few of those have been studied and crystallized (see pdb for a list).
Having worked on one of these structures as a graduate student, I can share my
experience:
- Purification is harder than you would thi
Hmmm, so you would, when collecting large data images, say 4 images, 100MB in
size, per second, in the middle of the night, from home, reject seeing
compressed images on your data collection software, while the "real thing" is
lingering behind somewhere, to be downloaded and stored later? As o
Reluctantly I am going to add my 2 cents to the discussion, with various
aspects in one e-mail.
- It is easy to overlook that our "business" is to answer
biological/biochemical questions. This is what you (generally) get grants for
to do (showing that these questions are of critical importanc
Phoebe,
Just automate the archiving and come up with a reasonable scheme how to. Ours
is that data sets are called:
userid_yearmonth_projectid_#
Userid is derived from the login into CrystalClear (oops, free advertizing),
projectid is set by the PI (so she can remember 10 years from now what
Rex,
There are people more qualified to answer your question 1 than I am, so I am
going to politely defer that answer. The answer depends on the unit cell
dimensions, detector distance etc, and yes, there are more observations
rejected due to overlap than would be the case in monochromatic da
PEG is a polymer and it can be made by anionic or cationic polymerization.
Whichever you use, you go "the other way" to terminate the reaction at an
appropriate time (so you have the molecular weight you want). So when you start
with an acid, you terminate with a base and vice versa. If you te
James,
I would have a look at the paper by Judge et al:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1300446/pdf/10465769.pdf
Specifically, in this paper you will find that the crystallization behavior of
lysozyme changes drastically with pH. At the time the paper wasn't really
written to
All,
Pardon the slightly off-topic question.
We would like to use Pymol and generate movies with it on a WINDOWS computer.
We are very familiar with Pymol and how to make the correct views etc. We write
the individual frames out into PNG files.
So what is left to do, is to "stitch together" t
Dave,
We have used CentOS for years and I am very happy with it. We also use NVIDIA
hardware. CentOS does not work out of the box with NVIDIA, but NVIDIA has an
installation package for their drivers on their web site that does work out of
the box in combination with CentOS. That is, you run
Having grown crystals with dioxane as precipitant, I can tell you that
harvesting them isn't easy - as is the case for most crystals grown in volatile
precipitants. At the time, we used an increased amount of dioxane plus
2-propanol as additive to further stabilize the crystal. (Yes, that make
Methods for vapor diffusion in microgravity have long existed (and the 'trick'
is that you cannot have 'free liquid', as we do in standard vapor diffusion
plates, because it does not 'stay'). Having worked at NASA, I have said the
same thing: vacuum and cooling should be easy - but alas, they
I was going to comment that I have learned the following: "respect" does not
mean the same thing in all places in the world. Some time back I had a protein
here that I thought needed extra respect and I had learned from a Rigaku
employee how to do this - I bowed very very deeply in front of th
There is a reasonable experiment you can do:
Take the unit cell of your (presumed) crystal complex and put the search model
into the until cell in a way that seems reasonable (use coot, or your favorite
program). Make structure factors (with CCP4 or your favorite program) and throw
away the
Hi Francis,
There is an older paper that mentions this idea: Tsao et al, Acta Cryst B48
(1992), 75-88. However, when you look at the paper, small-angle scattering data
is not the only thing that was used. In particular, if my memory serves me
right, the 60-fold averaging applied to the proble
Hi Claudia,
There is an option that has not been mentioned yet and has a very obvious
advantage: CentOS. I am mentioning this because it is identical in
functionality to Red Hat and therefore it will take the least of your time to
move to a new system. We like CentOS because it is derived fro
Todd,
Once upon a time I studied at an institution of higher learning. Its specialty
is (and was) the education of and participation in medical sciences (I guess
that?could be?an oxymoron, sorry). With that comes the securely keeping and
sharing (as needed) of patient data. The institutional bu
Tassos,
The most obvious answer (and possibly incorrect) is that DNA itself has a
different dn/dc value and when you say that you have a DNA binding protein,
chances are that some or all of it may be bound to DNA, which would change the
nature of the beast (and the MW). Perhaps you can delibe
There have been excellent examples given for cases in which the original data
would have been very valuable for discussion and understanding. However, it has
always been my understanding that scientists are required to keep the original
data on which their conclusions are based. It is also my un
We have a tiered system:
a) Personal files. Small and many, change often. Typical: CCP4, coot, CNS and
other files. Backed up daily.
b) X-ray images. Not so many, but large. Large in total. Never change once
established. Backed up every two hours.
c) Archive. Mostly X-ray images but also some pe
But Tassos, you and Gerard both should know better (Mark vR already knows,
clearly). THAT is not Dutch diplomacy, because it always starts like this:
No, no, no, you are completely wrong!
Actually, the way I learned about Cicero is better explained with Gaius Julius
Ceasar. There is a tempora
Mark,
What bothers me about your message is that you already have talked to Rigaku.
Until now we have never been able to create a problem that they could not
diagnose and help me solve from remote. In danger of offending ccp4 readers:
specialized Rigaku experts are a remarkable source for inf
I completely agree with Marius. Our (my) constraints are not $500 in price
difference, but the fact that I maintain a system for scientific computing AND
an X-ray system AND I am expected to be a scientist who publishes and writes
grants. Thus, our approach has been to automate and minimize my
I followed Kay's advice (after deciding that I knew better, of course, but we
won't elaborate on that :-) and I am very pleased AND have had no trouble
(knock on wood) to get everything working just fine. We make sure we have both
64 bit and 32 bit libraries and so far everything has worked ou
I agree with Bill.
After a few minutes thinking, in between "jobs working in the yard":
It depends if you need to understand "everything" (I guess that's impossible
these days) --- are you comfortable with publishing and defending research
results that you do not understand? I am not. In quit
I would agree with this statement, my preference is VERY STRONG. We mostly
work on Nucleosome and Nucleosome-nuclear protein complexes. By definition
these are low-resolution structures. They are very difficult to interpret, even
with stereo and I could not imagine even trying to work on thing
Hi Bill,
I thought that Moleman2 in the Uppsala Software Factory suite could do this,
but I haven't tried on residues with the same chain ID and number. Being
optimistic today, nothing in the friendly manual says that you cannot do it, so
that's what I would try.
Mark
-Original
Hi Sampath,
You are asking many questions at once. Since I am right now trying to solve a
very difficult Se-Met structure, here are some ideas:
- Do you have an energy scan on your crystal, showing that there is absorbance
at the correct wavelength for Se? If yes, you have proof that there was
All,
In the past couple of days I have been trying to use Acorn (in the CCP4 suite
of programs). Consistently it starts up fine and after some small amount of
time (5-10 minutes) it has taken up all the physical memory and then it starts
to slowly gobble up all the swap space until the only opt
All,
Below you will find the pertinent information for a job opening at the Howard
Hughes Medical Research Institute. All information can be found at this site:
http://www.hhmi.org/jobs/main?action=job&job_id=548.
If you are interested, please follow the instructions in the advertizement and
I have seen procedures in a reputable lab where they do indeed pick multiple
colonies and mix them; the people with the most experience claim(ed) that this
MUST be done for the particular prep they were doing or else they get very low
yields. The concern would be (in my mind) that if the diffe
Vaheh,
I don't recall precipitation at all, but I do remember that we were prepared to
change the crystallization recipes (i.e. adjust the recipes from previous
'large volume' crystallization to make more nuclei). For example, our first
tests were with lysozyme (sorry, hardly a representative
Once upon a time I worked in a group that was interested in developing
crystallization in microfluidics. This was before the time that Fluidigm
existed and we had not heard of crystallization with the aid of microfluidics
at the time. We had good reason to try to make a system that was as smal
Once upon a time I worked in a group that was interested in developing
crystallization in microfluidics. This was before the time that Fluidigm
existed and we had not heard of crystallization with the aid of microfluidics
at the time. We had good reason to try to make a system that was as smal
All,
I am posting on behalf of Dr. Karolin Luger. Dr. Luger has a job opening for a
post-doctoral researcher.
Job Summary:
Looking for a highly motivated individual with a strong interest in
integrated approaches to problems in structural biology. The lab has
extensive crystallographic and sp
Paul:
We are running Coot under Centos with Nvidia video cards, emitters and glasses.
Although our system is relatively new and therefore has not been used as
extensively as I would like to see, we have never encountered your problem and
hopefully will not. There are programs (VMD) in which y
Shivesh,
In addition to the comments that have been made already, I would try seeding
with the needles (or pieces thereof) - macroscopic, or take a couple of needles
and crush them up into really small pieces and use various dilutions of these
very small pieces for seeding. You could do that
Dear Lin-Woo,
Yes, crystallography programs can be made to work on Linux systems with Dual
Core CPUs. We run CentOS on Dell Precision 690 workstations and everything
works well. We are using Nvidia graphics cards (specifically Quadro FX3450) and
they work very well also. Nvidia Quodro graphic
It could be a hardware problem or it could be a mis-configuration. The card
you list DOES support stereo viewing in all crystallographic applications, I am
sure, because we have the same hardware (except our computers are 64 bit and we
run CentOS operating system, but otherwise identical).
As
We have made the change to 64 bit computers and indeed it is a bit confusing
to have to think 'twice' (32/64 bits). I guess that the argument can be made
that eventually all computers will be 64 (or more) bit and therefore staying
with 32 bits on a new computer is like holding back 'progress'?
I would recommend any one of these things:
1. Increase the concentration of the chemicals present, i.e. add more
iso-propanol OR add more PEG, but use a low molecular weight, like PEG400.
Either one or both. You will need 5% glycerol to get a good (ice-free)
cryo-condition or 10% PEG400 or 10
Although I have not yet tried to compile coot or CCP4, I have found that the
GNU provided packages (gcc, g77) do not make life convenient (how is that for a
euphamism for 'banging your head against the wall)?
Things worked better with gfortran than g77 and again better with the Intel
compil
Toluenes and derivatized benzenes may absorp into your plastic tray? Or into
the tape covering your tray? Just few other destinations.
It would make sense that if the binding of the 'drug' to the protein is tight,
then you do not need much in immediate contact, it will get there. The method
All,
It appears that I have just accidentally uncovered an important feature of the
new ccp4bb: on the old bb your default e-mail reply was to the author of the
original e-mail only, while on the new one the default goes to the bb and not
(explicitly) to the original author.
I would vote
Dear Kay,
Of course we would like to try. We are still (!) working on converting our
facility (as I have discussed off and on with you) to more novel computers,
with more novel programs and a better setup.
Just yesterday I had decided that it would be good to follow your example to
use ifor
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