Well, it's not exactly a solution that could be quickly implemented in
the short
term, but given the rise of open-source crystallography software, I wonder if
modules could be written to let the viewer see 3D objects on a 2D
display using
"head tracking." You'd have to nod your head slightly ba
Yangming,
This topic has been discussed before - basically there are no easily
discernable trends - some proteins crystallize better with a tag, others -
without, and yet others - don't care whether the tag is there or not. I tend
to try either, just to see what works better (time and effort permi
Dear Yanming
Lots of proteins have been crystallized with His-tags on. However, in
general one would assume that a flexible tag could have a negative effect.
I am not aware of a systematic comparison of crystallization of tagged and
untagged proteins, but the following paper is relevant to this t
Could you find out whether this error persists across different
distributions?
Would one solution be to use MIFit instead of xtalview? MIFit is the
official successor of the now unsupported xtalview and as far as I know
also available for free for academic users.
Tim
--
Tim Gruene
Institut
Hi All,
Maybe, I should not have asked this question:
Can anybody give me the hints (or point to the references) on the impact
of His tag on crystallization experiments. In perticular:
1, With or without His tag, which one is better for crystallization?
2, If I successfully crystallized N-termi
Dear Michelle,
this is not strange at all. You simply have
a MR solution that refers to a different origin.
You cannot display the original model plus the
MR solution in the same coordinate system (with
respect to the same origin). Of
course they clash.
Greetings
Marius
> Dear all,
>
> I refin
Dear all,
I refined a protein structure in the space group P6(1)22, with one copy in the
asymmetric unit, resolution ~1.8 A, Rwork=0.20, Rfree=0.22.
Then I tried to feed Phaser (version 1.3.3) with this structure. It found
quickly a very prominent solution, but the first euler angle is 180 inst
Dear colleagues,
someone out there who has installed XtalView
with the new SUSE Linux 10.3.
When launching Xfit, there is an error message
xfit: xcb_io.c: _XAllocID: Assertion `!(dpy -> flags & etc. etc.
when googeling for this error, it is well reported to
occur for the newest Linux systems. Any
Hi Ian,
Thank you very much for your detailed information.
I checked the effect of weighter term (wa) in CCP4i for the R/Rfree. When I
used wa=0.01 , the value is 0.225/0.277 FOM =0.799. The values changed to
0.204/0.269 (FOM=0.806) for wa= 0.05, 0.195/0.268 (FOM=0.807) for wa=0.1 and
Hi Anastassis,
Thank you very much for your suggestions. I answered the questions as follows.
I used NCS before rigid body refinement. After that I did not put NCS
restraints in the restrained refinement and TLS+restrained refinement because
it raised the R/Rfree quite a lot.
The resolution is
Dear Sun,
If we take Ian's formula for the ratio of R(free) to R(work) from his
paper Acta D56 (2000) 442-450 and make some reasonable approximations,
we can reformulate it as:
R(free)/R(work) = sqrt[(1+Q)/(1-Q)] with Q = 0.025pd^3(1-s)
where s is the fractional solvent content, d is the reso
Hi Sun Tang
Unfortunately there's no such thing as a fixed value for the maximum acceptable
Rfree-Rwork difference that applies in all circumstances, because the 'normal'
difference depends on a number of factors, mainly the observation/parameter
ratio, which depends in turn on the resolution a
What is the resolution? Are you using ncs restraints (you probably
should, on the coordinates but not on the Bs)? How does your
Ramachandran plot look?
You might tighten the geometry even more. Aside from all theoretical
arguments about how big the rmsd's should be, if they're rather
loose, t
Hi -
I don't think there is something necessarily wrong with the values
you report.
A few questions to see *if* something is wrong are:
- as you wrote to Tim you have NCS: do you use NCS restraints ?
- what is the resolution / B factor of the data ?
- have the data been checked for twining ?
Hi Tim,
Thank you for your and information and suggestions. There are two indepdent
molecules in the asymmetric unit and one molecule does not have very good
density, especially in the N-terminus.
Do you think that I should remove the region in the refinement?
Best,
Sun
Tim Gruene <[EMAIL P
I would agree that the difference is suspiciously high. I. Tickle and
others have published analytical expressions for how to estimate the ratio
between R and Rfree, just google for "tickle rfree" to find the
references.
You easily achieve a large difference by adding too many waters which jus
Peter and Miguel,
thanks for the help with Refmac, it appears to be working correctly!
still issues with PHASER though..
thanks a bunch!
Ainsley
P.J.Briggs wrote:
Dear Ainsley
I'm not sure which file you took from Garib's page, however the CCP4i
"install" options (under the "System Administ
Pedro,
The DV920 works even with frame-sequential stereo, but with a native
resolution of 640x480, they aren't useful for real work. Plus, they're
not all that comfortable -- I returned them after a couple of week.
According to the Vuzix rep I spoke to on the phone, we are still years
away from
Hi Boaz,
Thank you for your opinions. The resolution is 2.8A and I remembered some
people may think the structure is over-refined when the difference between
Rfree/Rwork is greater than 6.
What do you think the greatest acceptable difference between the two?
Best,
Sun
Boaz Shaanan <[EMAIL
Hi, Jeroen
The Vuzix VR920 should provide a cheap 3D stereo alternative to CRT
monitors, because it contains two small LCD screens - if one displays
a right eye view and the other a left eye view we'd have a situation
similar to older display systems, with side-by-side stereo and a 3D
viewer
Hello All,
I refined a structure with Refmac in CCP4i and the R/Rfree is 0.215/0.277. The
difference between R and Rfree is too much even though I used 0.01 for
weighting term in the refinement (the default value is 0.3). The RMSD for bond
length and bond angle is 0.016 A and 1.7 degree.
What
Don't know for the phaser problem, I had it once, but it was because I had
phenix installed as well and I had set them both up in the same shell. That
was something suggested already, so I guess it's not your problem.
As for refmac: the tar.gz file you download from Garib's webpages is not a
CCP4i
Dear Ainsley
I'm not sure which file you took from Garib's page, however the CCP4i
"install" options (under the "System Administration" menu) are only for
installing new interfaces and not for updating the programs themselves.
I just took a look at the files on Garib's page, and downloaded the fi
We would like to announce the Symposium on "Synchrotrons and Lasers for
Structural Systems Biology" to be held on 16th April 2008 at the
premises of the EMBL/DESY in Hamburg, Germany. International experts in
the field of the use of synchrotron radiation in biological research
will present thei
Hey all I have checked everything that was mentioned here.
I dont have PHENIX installed ( I am using the current version from
http://diablo/ucsc.edu/~wgscott/debian/deb/ccp4/)
I checked the setup file and its set to 1
Any other ideas?
Next question
I would like to install the newest versio
Hi Gregor,
I think this LCD monitor is not useful since the refresh rate is only 75
Hz, thus in stereo 2 x 37.5 Hz and that is going to give a big headache.
I know Samsung is working on a 100 Hz LCD-TV. Nevertheless, the goal is
not for stereo but to suppress the afterglow effects again.
They tri
Hi all,
I've just read about a cheap TFT-screen & 3D-glasses combination from
"ZALMAN" (ZM-M220W 22" TFT with 2x 3D-glasses). I don't know if one can use
with linux but the technical specs look like it's using the normal Nvidia
driver. I think maybe the refresh-rate is either too low or the after
Dear Pedro,
there is no cheap solution for now, the 3D community has to wait for a
few years more I think to be presented with a good stereo-capable LCD.
The problem is not the refresh rate (as low as 5 ms nowadays) but it is
the after glow effect... that is one of the reasons why LCDs provide a
s
On Mon, 2008-02-04 at 11:24 +, Andrew Raine wrote:
> Are you implying that an appropriately written Xorg.conf can get the
> graphics card to do this instead? The prospect is very appealing!
> Regards,
> Andrew
That should be a piece of cake using the new (and still under
development) "XRand
Okay, I was wrong. On two points...
What I'd forgotten is that LCD displays produce polarized light (and so
do TFT displays, for that matter), so you don't need a sheet of
Polaroid to polarize the light from the vertical display.
The half-silvered mirror is there (of course, I hear the cries)
Hi all,
There's a pretty good description of how it works, and how to make one yourself
here:
http://forums.nvidia.com/index.php?showtopic=32547
I've never used one myself, and I personally feel that LCD stereo with a large
f.o.v. on a single flat panel should be available soon (I think they j
Hi,
We tested a Planar 17" stereo monitor a year or so ago on our Macs (with
the image flipping card) and the problem was that although the stereo effect
was nice, we had to use side-by-side and an extended desktop stereo in eg.
PyMol to get the left and right eye images to the right moni
Hi
Just looking at the diagrams, I don't think the glass is half-silvered
- it looks like a large sheet of Polaroid™. It only needs to polarize
the transmitted light from the vertically oriented monitor, since the
reflected light from the interface between two materials (at least one
of which
Hi Andrew,
Just like the commercial systems, the glass is the only special piece of kit
(which can be bought separately). The LCD monitors are just set up to display
either left or right channel. If you ask me, I think these companies are just a
rip off!
Paul
> Date: Mon, 4 Feb 2008 11:24:32
P Hubbard wrote:
Just an FYI you can build those yourself at a fraction of the price!
You just need the special piece of glass, two identical LCD monitors,
and an edited X config file.
The clever bit of the Omnia system (and the similar one from Planar,
which being from the US might be c
Hi,
Just an FYI you can build those yourself at a fraction of the price! You
just need the special piece of glass, two identical LCD monitors, and an edited
X config file.
They are still bulky though!
AGS
> Date: Mon, 4 Feb 2008 10:46:45 +
> From: [EMAIL PROTECTED]
> Subject: Re: [cc
At USD 7000 it's not exactly the cheap solution I was looking for...
At 10:46 04-02-2008, Andrew Raine wrote:
Anastassis Perrakis wrote:
While we are on the subject, does anyone in general have working in
their labs a stereo-3D solution that does not require CRT monitors
but works on LCD and
Anastassis Perrakis wrote:
While we are on the subject, does anyone in general have working in
their labs a stereo-3D solution that does not require CRT monitors but
works on LCD and preferably with Linux or OSX ? (any windows hints are
welcome as well).
Yes indeed. We have a 20" one of the
Dear all -
While we are on the subject, does anyone in general have working in
their labs a stereo-3D solution that does not require CRT monitors
but works on LCD and preferably with Linux or OSX ? (any windows
hints are welcome as well).
Tassos
On Feb 4, 2008, at 10:12, Pedro M. Matias
Hi,
I've played around with the VR920 - and have used it with WinCoot using
GlovePIE for head tracking. It's fun to fly round your protein but the screen
judder(?) hurts your brain after a few minutes (low quality accelerometers?).
There are people developing Linux drivers; you can contact the
Dear Colleagues,
I found out that eDimensional sells the Vuzix HMD 3D glasses, but
their stereo drivers only work in windows. I suppose that they should
also work under Linux with the Nvidia stereo drivers. However because
we must pay by purchase order and bank transfer, they will not honor
t
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