Hi, I am planning to purchase a crystallization robotic system (dispenser,
screen maker and imager). As far as I know the following components are
available.
1. Protein Dispenser- mosquito, phoenix
2. Screen maker - alchemist II, Freedom EVO (Tecan) and Microlab star line
(Hamilton). Freedom E
On Sep 17, 2008, at 8:21 PM, Engin Ozkan wrote:
As a grad student we had access to stereo, I did not use it much. I
have to say I do not know why new students would be swayed just by
them. As a young grad student, I was amazed by chemistry in action
(and I still am), and did not need ste
Ironically as this stereo discussion ensues, it seems NVidia is
pushing 3d glasses once again (http://tech.slashdot.org/tech/08/09/17/1530202.shtml
) . Those 120Hz LCD's are welcome reprieve from the bulky SGI
monitors in our x-ray core now.
More on topic, however, as a 'newer' generation (
Hi All,
In the portion of the MOREP logfile where it lists the RF peaks, what does
Rf and Rf/sigma mean? Is Rf - peak height and Rf/sigma - peak heights
measured as deviations from mean? Looking into the CCP4 tutorial on MOLREP
(http://www.ccp4.ac.uk/dist/examples/tutorial/html/mr-tutorial.html) t
An advantage with stereo viewing is that you can increase the slab in
a crowed active site and still make sense of it. In my experiance,
valuable for understanding structure function relationships in
flexible proteins.
Paula Lario
On 17-Sep-08, at 8:21 PM, Engin Ozkan <[EMAIL PROTECTED]>
From another member of the new generation...
I could not agree more with Scott. Stereo is not essential, my lab of
thirteen crystallographers does not even have the capability, and noone
has ever asked for it (including our older PI). And I have refined and
built in one year one 3.9 A and
Christian,
I think it would be great to continue this discussion on CCP4bb, especially as
we learn more about all the new stereo-capable display products now hitting the
market.
It would be even more wonderful if a few volunteers could monitor this
discusson and then summarize their distille
if you have bad/poor experimental phases and you are building de novo/
from scratch by hand,
in my opinion stereo is very handy and makes map interpretation much
easier.
-tommi
On Sep 17, 2008, at 6:02 PM, Steve Lane wrote:
Warren et al.:
The following is based largely on a survey conducte
Lutz:
I would like to second your point about people (students or otherwise)
seeing a 3D structure. We semi-frequently have high-school students come
through the lab, and the thing that always impresses them the most is
being able to rotate a 3D represenation of a molecule, especially when
they u
Hi All,
I am trying to make a quite classic demonstration of electron density
map
sliced and contoured as (smoothed) isoheight curves. The sliced
section is
random and NOT along any main cell axes. I am curious if there is any
crystallographic software can handle this, which will save me f
Dear all,
following this discussion and enjoying AGAIN 3D on a Mac - at least
in Pymol -, I'd like to add my two cent opinion.
Whether or not stereo is important in research might be a matter of
debate, true! But, we are focussing on membrane proteins and normally
these structures are at
Dear all,
I would like to continue the discussion on the availability of 3D-LCD monitors
that work with Linux or Mac (started in the discussion
"Progresss with Stereo 3D under Mac OS X Leopard").
(We do have a running stereo capable system with Linux-PC & SGI-CTR-monitor &
CrystalEyes.)
Now we
Hi Nat:
On Sep 17, 2008, at 11:14 AM, Nathaniel Echols wrote:
those of us who came of age (technologically speaking) in an era of
ubiquitous bright, high-contrast (and increasingly massive) LCD
screens
can't bear to look at a CRT display any more.
The day I stopped using CRTs in the presen
My use goes back to Evans and Sutherland workstations, FRODO, SGI's with
O, Duncan's graphics program suite, and COOT, on multiple platforms.
I don't use dials at all, and multiple uses with a three-button mouse are
far more favorable.
I still prefer O to COOT for a number of reasons. The main re
>
> I find that depth-cue/fog is a sufficient cue for me to determine the
> "3-dimensionality" of what I am viewing on my 2-dimensional monitor,
> and I find that most 3D systems tend to give me a headache long before
> I would get one without them.
>
Even when the depth-cue/fog isn't enough, simp
Just to put my two cents in on this as I would fall into that new generation
so to speak:
I started out with the SGI and linux systems with stereo, O, and dials about
eight years ago. Never used the dials and rarely seen anyone else use
them. Over the past few years I have transition to coot, pc
Dear Steve,
despite your survey/perception, bottom line is, comes paper writing
time, nothing beats stereo viewing of the molecules or the packing of
them in the crystal lattice: facts become apparent that are otherwise
easily overseen in two dimensions!
Stereo-free macromolecular crystallog
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
Very well phrased Steve, and I do agree - however stereo is helpful
e.g. looking at binding pockets etc.
I think it depends very much on your workflow what you are actually
doing if you really need lots of stereo. In my case I run everything
on my MacbookPro but I occasionally walk over to ou
I think I figured out the problem: the directory path where I had
unpacked the source tree was different from that defined in ccp4.setup
I guess I forgot once again that Linux and Windows are quite
different operating systems...
Industry and Medicine Applied Crystallography
Macromolecular Cr
Hi Daniel,
Sorry to hear about your problem with mrbump. You say that you put the
Fasta35 executable in the ccp4i bin directory(note the "i"). This
directory is probably not in your system PATH. I would recommend that
you put it into the $CCP4/bin which should be in your system path
provided
Hi all,
We' ve just encountered a problem concerning the installation of MrBump on our
Linux machine. MrBump needs Fasta35 for operation, but during installation
does not recognise the already installed Fasta35, even if Fasta35 is placed in
the ccp4i bin. Under the same location the recognition of
Warren et al.:
The following is based largely on a survey conducted here about 6 months
ago (the survey questions are at the bottom of this msg).
Among the "older" generation of PIs, there is a strong perception that
stereo and SGI dials are very important to users. This perception is not
at all
Hi folks:
My apologies to those who will find this irrelevant, but hopefully
they didn't read beyond the subject line. I've gotten many questions
about this, so ...
After the update to 10.5.5, you have to update (again) X11, preferably
to 2.3.1.
Why Apple didn't include this in the 10.
Not wishing to pooh-pooh attempts to get Apple to right their wrongs
(I am an Apple user myself) but I get along perfectly well without
stereo, thank you very much.
I find that depth-cue/fog is a sufficient cue for me to determine the
"3-dimensionality" of what I am viewing on my 2-dimensional moni
Dear CCP4ers,
I am compiling ccp4-6.0.99e from source and get the errors listed
below when the compilation gets to lib/ccif/libccif.a. I re-ran
configure with the --with-rxdispencer option as recommended but the
error persists.
My system is a Fedora Core 8
Linux xtal2.itqb.unl.pt 2.6.23.1-42
On Sep 16, 2008, at 5:26 PM, Warren DeLano wrote:
> Also, do crystallographers still consider stereo 3D to be a
> high-priority or must-have feature in a graphics workstation?
Yes, I do. Really, how can you do without?
As for LCD stereo: yes, please!
On Sep 16, 2008, at 5:26 PM, Warren DeLano wrote:
Also, do crystallographers still consider stereo 3D to be a
high-priority or must-have feature in a graphics workstation?
Hi Warren:
I'd put lack of stereo 3D in the same categories as lack of grant
support or involuntary celibacy.
I'm st
People's feelings about using stereo seem to be highly idiosyncratic,
but for many of us who are pro-stereo, the preference is VERY STRONG.
Pat
On Sep 16, 2008, at 8:26 PM, Warren DeLano wrote:
CCP4bb,
Some graphics news: Full operating-system support for stereo 3D
has at
last been resto
I think that you are looking for A.J.C. Wilson, Acta Cryst. 17 (1964)
1591-2.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582
On Wed, 17 Sep 2008, Ian Tickle
Sorry I should have copied this to the BB as it may be of general
interest:
-Original Message-
From: Ian Tickle
Sent: 17 September 2008 11:05
To: 'Jan Dohnalek'
Subject: RE: [ccp4bb] Topp fails: TOP: Open failed: File:
/people/./myfile.pdb
OK try this one: looking at the program I s
All - I've been trying to track down a paper (or papers) where it was
shown that the epsilon values (symmetry factors) for space groups with
pure rotation axes are not integers as is usually assumed (but still
integers for screw axes). It's almost certainly in Acta Cryst.,
probably in the 60's or
Hi Jan
We had this problem, I think it's because the character strings used to
store pathnames are only 80 chars long, so if you have a long pathname
(you didn't show your full pathname!) then it has a problem. You can
either fix the program, or do as we did make a soft link in the current
direct
Hi all,
Using the 6.0.2 distribution of CCP4, the top program keeps failing
because it just can't see the pdb files. The files can be accessed by
the text viewer of CCP4. (the button VIEW)
I have tried to put them in other directories to make the path string
shorter, etc. None of those helped.
I
Remember, there's a whole mailing list & wiki dedicated to PyMOL, so no need to
clutter up CCP4bb with PyMOL-specific questions!
https://lists.sourceforge.net/lists/listinfo/pymol-users
http://pymolwiki.org
More complete answer:
# assuming that movie has already been defined in PyMOL
# (su
ALMN can plot the rotation function as a map - although I challenge
anyone to make much sense of it! More or less the same methodology as
MOLREP.
More useful - it lists all peaks generated by the symmetry operators in
Eulerian, and polar angles and gives the direct cosines of the rotation
ax
Hi Warren & CCP4ers,
first of all, it is great that at least one application, MacPyMOL,
works again in stereo under Leopard! It is good if developers like you
and users like us tell Apple how important a working stereo 3D is.
Personally, I consider stereo 3D as VERY important and would like t
Hi,
There are detailed instructions on the net but as far as I can
remember all you need before starting to generate the frames is the
following command:
set ray_trace_frames, 1
Also, why do you need such a high resolution. I know that computers
have a lot of power to burn but if you wan
38 matches
Mail list logo
