[ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[Pedro M. Matias]

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 
the 30-day money back warranty in case the glasses don't work, and 
that would be an expensive mistake.


Therefore, I'm asking whether anybody in this community has had any 
experience with these glasses, in either Windows or Linux 
environments, using programs such as Coot for 3D stereo 
visualization. I know there are other such system out there but these 
seem to be the cheapest I found so far.


Thanks in advance,

Pedro Matias


Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : [EMAIL PROTECTED]

Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[P Hubbard]

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 these folks via the 
VR920 forum hosted by Vuzix. I've currently no access to a Linux box with 
stereographics, so can't say for sure whether the Nvidia drivers work or not, 
but  according to the Vuzix website the HMD uses DirectX 9 for 3D so it 
probably won't. I hope the Linux hack is available soon!

I agree with you, and think that the old LCD-shutter glasses are better (so 
long as you have the monitor for it). However, the more expensive Z800 
supposedly offers a more pleasant VR experience.

AGS

> Date: Mon, 4 Feb 2008 09:12:56 +
> From: [EMAIL PROTECTED]
> Subject: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional
> To: CCP4BB@JISCMAIL.AC.UK
> 
> 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 
> the 30-day money back warranty in case the glasses don't work, and 
> that would be an expensive mistake.
> 
> Therefore, I'm asking whether anybody in this community has had any 
> experience with these glasses, in either Windows or Linux 
> environments, using programs such as Coot for 3D stereo 
> visualization. I know there are other such system out there but these 
> seem to be the cheapest I found so far.
> 
> Thanks in advance,
> 
> Pedro Matias
> 
> 
> Industry and Medicine Applied Crystallography
> Macromolecular Crystallography Unit
> ___
> Phones : (351-21) 446-9100 Ext. 1669
>(351-21) 446-9669 (direct)
>  Fax   : (351-21) 441-1277 or 443-3644
> 
> email : [EMAIL PROTECTED]
> 
> Mailing address :
> Instituto de Tecnologia Quimica e Biologica
> Apartado 127
> 2781-901 OEIRAS
> Portugal

_
Helping your favorite cause is as easy as instant messaging. You IM, we give.
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Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[Anastassis Perrakis]

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 wrote:


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 the 30-day money back warranty in case the  
glasses don't work, and that would be an expensive mistake.


Therefore, I'm asking whether anybody in this community has had any  
experience with these glasses, in either Windows or Linux  
environments, using programs such as Coot for 3D stereo  
visualization. I know there are other such system out there but  
these seem to be the cheapest I found so far.


Thanks in advance,

Pedro Matias


Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : [EMAIL PROTECTED]

Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[Andrew Raine]

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 these:

http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3

on one of our Linux workstations.  After the original Acer screens were 
swapped for Samsung ones it is excellent.  People like it for the lack 
of flicker and consequent lack of headaches!  It has a wide angle of 
view, and several people can see stereo on the same screen at the same 
time, and there is no cross-talk between different displays in the same 
room.


It needs to be driven by an nVidia FX-series graphics card, with dual 
DVI outputs.  Other cards with dual outputs can be made to work, but the 
nVidia driver can intercept the conventional quad-buffered screen 
swapping instructions and divert the two eye views tot he different 
displays.  Thus most software that is already stereo-capable will work 
without modification.


In case this sounds a little too glowing, I should point out that I have 
no connection with the suppliers or the manufacturers, except as a customer!


Andrew

--
Dr. Andrew Raine, Head of IT, MRC Dunn Human Nutrition Unit,
Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, UK
phone: +44 (0)1223 252830   fax: +44 (0)1223 252835
web: www.mrc-dunn.cam.ac.uk email: [EMAIL PROTECTED]

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[Andrew Raine]

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 cheaper there...?) is the DVI 
"reflector" card that flips the image to be displayed on the screen seen 
in the half-silvered mirror.


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

--
Dr. Andrew Raine, Head of IT, MRC Dunn Human Nutrition Unit,
Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, UK
phone: +44 (0)1223 252830   fax: +44 (0)1223 252835
web: www.mrc-dunn.cam.ac.uk email: [EMAIL PROTECTED]

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[P Hubbard]

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: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional
> To: CCP4BB@JISCMAIL.AC.UK
> 
> 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 these:
> 
> http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3
> 
> on one of our Linux workstations.  After the original Acer screens were 
> swapped for Samsung ones it is excellent.  People like it for the lack 
> of flicker and consequent lack of headaches!  It has a wide angle of 
> view, and several people can see stereo on the same screen at the same 
> time, and there is no cross-talk between different displays in the same 
> room.
> 
> It needs to be driven by an nVidia FX-series graphics card, with dual 
> DVI outputs.  Other cards with dual outputs can be made to work, but the 
> nVidia driver can intercept the conventional quad-buffered screen 
> swapping instructions and divert the two eye views tot he different 
> displays.  Thus most software that is already stereo-capable will work 
> without modification.
> 
> In case this sounds a little too glowing, I should point out that I have 
> no connection with the suppliers or the manufacturers, except as a customer!
> 
> Andrew
> 
> -- 
> Dr. Andrew Raine, Head of IT, MRC Dunn Human Nutrition Unit,
> Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, UK
> phone: +44 (0)1223 252830   fax: +44 (0)1223 252835
> web: www.mrc-dunn.cam.ac.uk email: [EMAIL PROTECTED]

_
Helping your favorite cause is as easy as instant messaging. You IM, we give.
http://im.live.com/Messenger/IM/Home/?source=text_hotmail_join

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[Pedro M. Matias]

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 preferably with Linux or OSX ? (any windows 
hints are welcome as well).


Yes indeed.  We have a 20" one of these:

http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3

on one of our Linux workstations.  After the original Acer screens 
were swapped for Samsung ones it is excellent.  People like it for 
the lack of flicker and consequent lack of headaches!  It has a wide 
angle of view, and several people can see stereo on the same screen 
at the same time, and there is no cross-talk between different 
displays in the same room.


It needs to be driven by an nVidia FX-series graphics card, with 
dual DVI outputs.  Other cards with dual outputs can be made to 
work, but the nVidia driver can intercept the conventional 
quad-buffered screen swapping instructions and divert the two eye 
views tot he different displays.  Thus most software that is already 
stereo-capable will work without modification.


In case this sounds a little too glowing, I should point out that I 
have no connection with the suppliers or the manufacturers, except 
as a customer!


Andrew

--
Dr. Andrew Raine, Head of IT, MRC Dunn Human Nutrition Unit,
Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, UK
phone: +44 (0)1223 252830   fax: +44 (0)1223 252835
web: www.mrc-dunn.cam.ac.uk email: [EMAIL PROTECTED]


Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : [EMAIL PROTECTED]

Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[P Hubbard]

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 +
> From: [EMAIL PROTECTED]
> Subject: Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional
> To: CCP4BB@JISCMAIL.AC.UK
> 
> 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 cheaper there...?) is the DVI 
> "reflector" card that flips the image to be displayed on the screen seen 
> in the half-silvered mirror.
> 
> 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
> 
> -- 
> Dr. Andrew Raine, Head of IT, MRC Dunn Human Nutrition Unit,
> Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, UK
> phone: +44 (0)1223 252830   fax: +44 (0)1223 252835
> web: www.mrc-dunn.cam.ac.uk email: [EMAIL PROTECTED]

_
Helping your favorite cause is as easy as instant messaging. You IM, we give.
http://im.live.com/Messenger/IM/Home/?source=text_hotmail_join

[ccp4bb] WG: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[Gregor Witte]

 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 afterglowing
too long for 3D-model-building and thus it will produce a bad headache after
some hours, but maybe it's worth a try... Even if I doubt it with regard to
the price...
Actually I've just written an email to the german reseller with loads of
questions about the TFT and the possible use with linux/coot.

  Unfortunately there's only a german web-page ... You can find it at 
http://www.alternate.de/html/product/details.html?articleId=193317 
and you have to klick on "Ausfuehrliche Details" for the specs) (euro 599,-)

There's also a 19" TFT & 3D-glasses set available (  ...?articleId=193301 )


Gregor


-
Dr. Gregor Witte
University of Munich
Gene Center/Institute of Biochemistry
mail: [EMAIL PROTECTED]
 


-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Im Auftrag von
Anastassis Perrakis
Gesendet: Montag, 4. Februar 2008 11:34
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

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 wrote:

> 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 the 30-day money back warranty in case the glasses 
> don't work, and that would be an expensive mistake.
>
> Therefore, I'm asking whether anybody in this community has had any 
> experience with these glasses, in either Windows or Linux 
> environments, using programs such as Coot for 3D stereo visualization. 
> I know there are other such system out there but these seem to be the 
> cheapest I found so far.
>
> Thanks in advance,
>
> Pedro Matias
>
>
> Industry and Medicine Applied Crystallography Macromolecular 
> Crystallography Unit ___
> Phones : (351-21) 446-9100 Ext. 1669
>   (351-21) 446-9669 (direct)
> Fax   : (351-21) 441-1277 or 443-3644
>
> email : [EMAIL PROTECTED]
>
> Mailing address :
> Instituto de Tecnologia Quimica e Biologica Apartado 127
> 2781-901 OEIRAS
> Portugal

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[Jeroen Mesters]

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
stable picture at just 60 Hz refresh rate in contrast to CRTs that look
stable at 85 - 100 Hz.

The cheapest solution is still the good old CRT (there are still a few
around) with nuvision stereo glasses.
For example, you can still buy the Samsung SyncMaster 1100MB that has
sufficient rates (Vert x Hori 160 Hz x 130 kHz) to do the job.

If you can, wait a few years ...

Jeroen.

p.s. There are also some (more expensive) active stereo beamers around
(we own an Infocus DepthQ) and they provide a nice active stereo picture
on the wall:
- http://www.digital-image.de/
- http://www.depthq.com/



Pedro M. Matias wrote:
> 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 preferably with Linux or OSX ? (any windows
>>> hints are welcome as well).
>>
>> Yes indeed.  We have a 20" one of these:
>>
>> http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3
>>
>>
>> on one of our Linux workstations.  After the original Acer screens
>> were swapped for Samsung ones it is excellent.  People like it for
>> the lack of flicker and consequent lack of headaches!  It has a wide
>> angle of view, and several people can see stereo on the same screen
>> at the same time, and there is no cross-talk between different
>> displays in the same room.
>>
>> It needs to be driven by an nVidia FX-series graphics card, with dual
>> DVI outputs.  Other cards with dual outputs can be made to work, but
>> the nVidia driver can intercept the conventional quad-buffered screen
>> swapping instructions and divert the two eye views tot he different
>> displays.  Thus most software that is already stereo-capable will
>> work without modification.
>>
>> In case this sounds a little too glowing, I should point out that I
>> have no connection with the suppliers or the manufacturers, except as
>> a customer!
>>
>> Andrew
>>
>> -- 
>> Dr. Andrew Raine, Head of IT, MRC Dunn Human Nutrition Unit,
>> Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, UK
>> phone: +44 (0)1223 252830   fax: +44 (0)1223 252835
>> web: www.mrc-dunn.cam.ac.uk email: [EMAIL PROTECTED]
>
> Industry and Medicine Applied Crystallography
> Macromolecular Crystallography Unit
> ___
> Phones : (351-21) 446-9100 Ext. 1669
>   (351-21) 446-9669 (direct)
> Fax   : (351-21) 441-1277 or 443-3644
>
> email : [EMAIL PROTECTED]
>
> Mailing address :
> Instituto de Tecnologia Quimica e Biologica
> Apartado 127
> 2781-901 OEIRAS
> Portugal

Re: [ccp4bb] Still cannot read .mtz + another ?

[Miguel Ortiz-Lombardía]

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 Task tar.gz file. Instead, it contain three executables (for refmac5,
libcheck and makecif) that you simply install in the directory that contain
the CCP4 executables ($CBIN) with the same names that had the old versions
of these programs. That way they are called when you use a CCP4i task.

I hopt this helps,


Miguel

2008/2/4, C.Ainsley Davis <[EMAIL PROTECTED]>:
>
> 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 version of REFMAC. I downloaded the
> file from Garib's page)  I try to use the ccp4 GUI to install the file,
> but it doesnt like it. It says something about it being unable to read
> the contents.  If I gunzip then tar the file i get 3 files which I am
> not sure what to do with. There is also a new library file Garib
> recommends downloading, but in any case I cannot install the 5.4 version
> of REFMAC and cannot find any documentation online on how to install it!
>
> Thanks again CCP4 BB!
>



-- 
http://www.pangea.org/mol/spip.php?rubrique2
~~~
Je suis de la mauvaise herbe,
Braves gens, braves gens,
Je pousse en liberté
Dans les jardins mal fréquentés!

Georges Brassens

[ccp4bb] Still cannot read .mtz + another ?

[C.Ainsley Davis]

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 version of REFMAC. I downloaded the 
file from Garib's page)  I try to use the ccp4 GUI to install the file, 
but it doesnt like it. It says something about it being unable to read 
the contents.  If I gunzip then tar the file i get 3 files which I am 
not sure what to do with. There is also a new library file Garib 
recommends downloading, but in any case I cannot install the 5.4 version 
of REFMAC and cannot find any documentation online on how to install it!


Thanks again CCP4 BB!

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[Harry Powell]

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) to make 
sure you have enough light reflected from the "horizontal" monitor to 
be about the same as the light transmitted from the vertical one.



On 4 Feb 2008, at 12:09, Harry Powell wrote:


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 has a refractive index) will be polarized in any case (that's 
why your Polaroid™ sunglasses let you see below the waves...). My 
physics is too rusty to remember, but I think the vertical monitor in 
this case needs to be polarized vertically, since the reflected 
polarized light will be horizontal.


No idea where you can buy large sheets of Polaroid™  though.

IMWBW, though...

On 4 Feb 2008, at 11:30, P Hubbard wrote:


 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 +
> From: [EMAIL PROTECTED]
> Subject: Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional
> To: CCP4BB@JISCMAIL.AC.UK
>
> 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 cheaper there...?) is the DVI
> "reflector" card that flips the image to be displayed on the screen 
seen

> in the half-silvered mirror.
>
> 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
>
> --
> Dr. Andrew Raine, Head of IT, MRC Dunn Human Nutrition Unit,
> Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, UK
> phone: +44 (0)1223 252830 fax: +44 (0)1223 252835
> web: www.mrc-dunn.cam.ac.uk email: [EMAIL PROTECTED]

Helping your favorite cause is as easy as instant messaging. You IM, 
we give. Learn more.

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, 
Hills Road, Cambridge, CB2 2QH





Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills 
Road, Cambridge, CB2 2QH

[ccp4bb] Synchrotrons and Lasers for Structural Systems Biology

[Victor Lamzin]

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 their point of view on how the new synchrotron light 
sources including the X-ray free electron lasers under development will 
shape biological structural research in the next decades to come.


The symposium will be followed by the 4th Annual Meeting of the 
EC-funded BIOXHIT project, 17th - 18th April 2008. Project’s highlights 
will be presented in the area of crystallisation technologies, 
synchrotron beamlines, beamline endstations and data collection, data 
processing and structure determination, databases and networking, 
training, implementation and dissemination.


Attendance to the meetings is free of charge.

The registration deadline for the symposium and the BIOXHIT Meeting is 
Saturday, 5th April 2008, http://www.structures-in-biology.org


Gerard Bricogne, Kim Henrick, Victor Lamzin, Sine Larsen, Sean 
McSweeney, Colin Nave, Anastassis Perrakis, Manfred Weiss (the 
organising committee)

Re: [ccp4bb] WG: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[Jeroen Mesters]

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 tried to insert a black picture in between the normal ones but this
had too many unwanted side-effects. Currently, they are working on an
additional graphics chip incorporated into the screen that calculates an
intermediate picture between two pictures so the changes are more
gradual and they claim this provides a very nice movie quality
Too bad again, this technology is also not what we are looking for! It
would actually destroy the stereo effect!

CRTs are still the best and the cheapest solution for now.

Jeroen.


Gregor Witte wrote:
>  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 afterglowing
> too long for 3D-model-building and thus it will produce a bad headache after
> some hours, but maybe it's worth a try... Even if I doubt it with regard to
> the price...
> Actually I've just written an email to the german reseller with loads of
> questions about the TFT and the possible use with linux/coot.
>
>   Unfortunately there's only a german web-page ... You can find it at 
> http://www.alternate.de/html/product/details.html?articleId=193317 
> and you have to klick on "Ausfuehrliche Details" for the specs) (euro 599,-)
>
> There's also a 19" TFT & 3D-glasses set available (  ...?articleId=193301 )
>
>
> Gregor
>
>
> -
> Dr. Gregor Witte
> University of Munich
> Gene Center/Institute of Biochemistry
> mail: [EMAIL PROTECTED]
>  
>
>
> -Ursprüngliche Nachricht-
> Von: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Im Auftrag von
> Anastassis Perrakis
> Gesendet: Montag, 4. Februar 2008 11:34
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional
>
> 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 wrote:
>
>   
>> 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 the 30-day money back warranty in case the glasses 
>> don't work, and that would be an expensive mistake.
>>
>> Therefore, I'm asking whether anybody in this community has had any 
>> experience with these glasses, in either Windows or Linux 
>> environments, using programs such as Coot for 3D stereo visualization. 
>> I know there are other such system out there but these seem to be the 
>> cheapest I found so far.
>>
>> Thanks in advance,
>>
>> Pedro Matias
>>
>>
>> Industry and Medicine Applied Crystallography Macromolecular 
>> Crystallography Unit ___
>> Phones : (351-21) 446-9100 Ext. 1669
>>   (351-21) 446-9669 (direct)
>> Fax   : (351-21) 441-1277 or 443-3644
>>
>> email : [EMAIL PROTECTED]
>>
>> Mailing address :
>> Instituto de Tecnologia Quimica e Biologica Apartado 127
>> 2781-901 OEIRAS
>> Portugal
>> 

Re: [ccp4bb] Still cannot read .mtz + another ?

[C.Ainsley Davis]

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 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 file
linked as "refmac 5.4 for linux", which arrives on your system as
"refmac5.4_linintel.tar.gz". Unpacking this I get three files:

refmac_linintel
makecif_linintel
libcheck_linintel

These are updated executables for the refmac5, makecif and libcheck
programs that should be in the "bin" directory of your CCP4 distribution
(do "cd $CBIN" to get there) - you should move the current executables
out of the way, and then copy and rename the new files into the bin
directory.

For the new dictionary, I would suggest downloading the file and
unpacking it somewhere like the lib/data/ subdirectory of your CCP4
distribution. This should create something like
/your/path/ccp4-6.0.2/lib/data/dic

You can then change the environment variable "CLIBD_MON" to point to
/your/path/ccp4-6.0.2/lib/data/dic/, either on the command line or in
ccp4.setup (probably better to do the latter).

I'm pretty sure that this should work - sorry if it sounds complicated.
And yes it would probably be useful if Garib did indeed include some
information about updating on the actual page - but we don't have any
control over that.

Hope that this helps, best wishes

Peter Briggs
CCP4

C.Ainsley Davis wrote:
  

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 version of REFMAC. I downloaded the
file from Garib's page)  I try to use the ccp4 GUI to install the file,
but it doesnt like it. It says something about it being unable to read
the contents.  If I gunzip then tar the file i get 3 files which I am
not sure what to do with. There is also a new library file Garib
recommends downloading, but in any case I cannot install the 5.4 version
of REFMAC and cannot find any documentation online on how to install it!

Thanks again CCP4 BB!



  

Re: [ccp4bb] an over refined structure

[Anastassis Perrakis]

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 ? (phenix.xtriage)
- is the N-term domain of one copy really invisible (then indeed do  
remove ...!)

- has TLS been used ?
- did you add waters ? (too many?)

I guess then we can make better suggestions if something is wrong and  
if so how its best to fix.


A.

> 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.

Re: [ccp4bb] an over refined structure

[Tim Gruene]

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 just 
model noise. There may be other reasons for which more knowledge about the 
structure is required. Do you have large unmodelled regions, like loops 
that do not show in the density map?


Tim


--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A


On Mon, 4 Feb 2008, Sun Tang wrote:


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 may be wrong with the over-refined structure? What is the reason for 
leading to an over-refined structure? How to avoid it?

Best wishes,

Sun Tang


-
Be a better friend, newshound, and know-it-all with Yahoo! Mobile.  Try it now.

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[Warren DeLano]

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 having 1024x768 or better resolution in sub-$1,000 consumer VR
glasses.

Cheers,
Warren

> -Original Message-
> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On 
> Behalf Of Pedro M. Matias
> Sent: Monday, February 04, 2008 8:49 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional
> 
> 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 with mirrors. 
> Afterglow and flicker wouldn't be a problem because each LCD 
> would always receive the same eye view. In Linux with an 
> NVIDIA Quadro card, this might (?) be achieved by option "4" 
> TwinView clone mode stereo, provided each LCD can be 
> perceived as a single display.
> 
> Regards,
> 
> Pedro.
> 
> At 14:24 04-02-2008, Jeroen Mesters wrote:
> >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 
> >stable picture at just 60 Hz refresh rate in contrast to 
> CRTs that look 
> >stable at 85 - 100 Hz.
> >
> >The cheapest solution is still the good old CRT (there are 
> still a few
> >around) with nuvision stereo glasses.
> >For example, you can still buy the Samsung SyncMaster 1100MB 
> that has 
> >sufficient rates (Vert x Hori 160 Hz x 130 kHz) to do the job.
> >
> >If you can, wait a few years ...
> >
> >Jeroen.
> >
> >p.s. There are also some (more expensive) active stereo 
> beamers around 
> >(we own an Infocus DepthQ) and they provide a nice active stereo 
> >picture on the wall:
> >- http://www.digital-image.de/
> >- http://www.depthq.com/
> >
> >
> >
> >Pedro M. Matias wrote:
> > > 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 preferably with Linux or 
> OSX ? (any 
> > >>> windows hints are welcome as well).
> > >>
> > >> Yes indeed.  We have a 20" one of these:
> > >>
> > >> 
> > 
> http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_om
> > nia_mimo&SubCatID_=3
> > >>
> > >>
> > >> on one of our Linux workstations.  After the original 
> Acer screens 
> > >> were swapped for Samsung ones it is excellent.  People 
> like it for 
> > >> the lack of flicker and consequent lack of headaches!  It has a 
> > >> wide angle of view, and several people can see stereo on 
> the same 
> > >> screen at the same time, and there is no cross-talk between 
> > >> different displays in the same room.
> > >>
> > >> It needs to be driven by an nVidia FX-series graphics card, with 
> > >> dual DVI outputs.  Other cards with dual outputs can be made to 
> > >> work, but the nVidia driver can intercept the conventional 
> > >> quad-buffered screen swapping instructions and divert 
> the two eye 
> > >> views tot he different displays.  Thus most software that is 
> > >> already stereo-capable will work without modification.
> > >>
> > >> In case this sounds a little too glowing, I should point 
> out that I 
> > >> have no connection with the suppliers or the 
> manufacturers, except 
> > >> as a customer!
> > >>
> > >> Andrew
> > >>
> > >> --
> > >> Dr. Andrew Raine, Head of IT, MRC Dunn Human Nutrition Unit, 
> > >> Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, UK
> > >> phone: +44 (0)1223 252830   fax: +44 (0)1223 252835
> > >> web: www.mrc-dunn.cam.ac.uk email: 
> [EMAIL PROTECTED]
> > >
> > > Industry and Medicine Applied Crystallography Macromolecular 
> > > Crystallography Unit ___
> > > Phones : (351-21) 446-9100 Ext. 1669
> > >   (351-21) 446-9669 (direct)
> > > Fax   : (351-21) 441-1277 or 443-3644
> > >
> > > email : [EMAIL PROTECTED]
> > >
> > > Mailing address :
> > > Instituto de Tecnologia Quimica e Biologica Apartado 127
> > > 2781-901 OEIRAS
> > > Portugal
> 
> Industry and Medicine Applied Crystallography Macromolecular 
> Crystallography Unit ___
> Phones : (351-21) 446-9100 Ext. 1669
>(351-21) 446-9669 (direct)
>  Fax   : (351-21) 441-1277 or 443-3

Re: [ccp4bb] an over refined structure

[Ian Tickle]

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 and the solvent content (a 
greater solvent content means a bigger cell volume which means more reflections 
for a given number of ordered atoms in the a.u. and hence a bigger obs/param 
ratio).  The Rfree-Rwork difference also depends on Rwork itself (i.e. you tend 
to get higher values of Rfree-Rwork for higher values of Rwork), so it's better 
to think in terms of the Rfree/Rwork ratio (which is independent of Rwork).

So for example at very high resolution a 'normal' value for Rfree-Rwork might 
be only 0.02 (so 0.05 which is what many people consider acceptable would 
actually be unacceptably high), whereas at low resolution it might be 0.1 (so 
0.05 would be unacceptably low).  Also you need to bear in mind that Rfree 
tends to have a quite high uncertainty, particularly at low resolution (because 
it's usually based on a relatively small number of observations), so the 
deviation has to be quite big (e.g. > 3 SU) before it can be considered to be 
statistically significant.

So Rfree needs to be compared not with Rwork at all but with the value of the 
optimal Rfree/Rwork expected on the basis that the model parameterisation and 
weighting of X-ray terms and restraints are optimal and the errors in the model 
have the same effect as the random experimental errors in the data (i.e. a 
statistical 'null hypothesis').  As Tim just pointed out we tried to do this in 
our Acta D (1998) papers: there you can compare your observed Rfree/Rwork ratio 
either with the theoretical value or with the value found for 'typical' 
structures in the PDB at the same resolution.

An abnormal Rfree/Rwork ratio could arise from a number of causes, not just 
over-fitting (I assume that's what you mean by 'over-refinement' - it's not 
clear to me how a structure can be 'over-refined' since a fundamental 
requirement of the maximum likelihood method is that the structure is always 
refined to convergence, and refining beyond that will by definition produce no 
further statistically significant changes in the parameters).

For example the number of parameters being refined may be either too low, or 
too high (over-fitting), or the values of the weighting parameters may not be 
appropriate, or there may be something badly wrong with the atomic model (e.g. 
mistraced chain).  Given the values you are reporting I think the latter is 
very unlikely, possibly you just need to tweak the X-ray and/or restraint 
weights.

HTH

Cheers

-- Ian

> -Original Message-
> From: [EMAIL PROTECTED] 
> [mailto:[EMAIL PROTECTED] On Behalf Of Sun Tang
> Sent: 04 February 2008 16:56
> To: Boaz Shaanan
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] an over refined structure
> 
> 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 PROTECTED]> wrote:
> 
>   Hi,
>
>Why do you think this structure is over-refined ? The 
> Rfree/Rwork difference of 6.2% seems fine, although you 
> didn't mention resolution. If anything, an over-refined 
> structure would show a smaller difference, as far as I know. 
> If all the other criteria (Ramachandran outliers, etc., map) 
> are OK you should just be happy with your structure.
>
>Cheers,
>
>Boaz
>   
>   - Original Message -
>   From: Sun Tang <[EMAIL PROTECTED]>
>   Date: Monday, February 4, 2008 18:41
>   Subject: [ccp4bb] an over refined structure
>   To: CCP4BB@JISCMAIL.AC.UK
>   
>   > 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 may be wrong with the over-refined structure? 
> What is the 
>   > reason for leading to an over-refined structure? How 
> to avoid it?
>   > 
>   > Best wishes,
>   > 
>   > Sun Tang
>   > 
>   >
>   > -
>   > Be a better friend, newshound, and know-it-all with Yahoo! 
>   > Mobile.  Try it now.
> 
> 
>   Boaz Shaanan, Ph.D. 
>   Dept. of Life Sciences 
>   Ben-Gurion University of the Negev 
>   Beer-Sheva 84105 
>   Israel 
>   Phone: 972-8-647-2220 ; Fax: 646-1710

Re: [ccp4bb] an over refined structure

[Sun Tang]

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 PROTECTED]> wrote: 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 just 
model noise. There may be other reasons for which more knowledge about the 
structure is required. Do you have large unmodelled regions, like loops 
that do not show in the density map?

Tim


--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A


On Mon, 4 Feb 2008, Sun Tang wrote:

> 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 may be wrong with the over-refined structure? What is the reason for 
> leading to an over-refined structure? How to avoid it?
>
> Best wishes,
>
> Sun Tang
>
>
> -
> Be a better friend, newshound, and know-it-all with Yahoo! Mobile.  Try it 
> now.


   
-
Be a better friend, newshound, and know-it-all with Yahoo! Mobile.  Try it now.

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[Pedro M. Matias]

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 with mirrors. Afterglow and flicker wouldn't be a problem 
because each LCD would always receive the same eye view. In Linux 
with an NVIDIA Quadro card, this might (?) be achieved by option "4" 
TwinView clone mode stereo, provided each LCD can be perceived as a 
single display.


Regards,

Pedro.

At 14:24 04-02-2008, Jeroen Mesters wrote:

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
stable picture at just 60 Hz refresh rate in contrast to CRTs that look
stable at 85 - 100 Hz.

The cheapest solution is still the good old CRT (there are still a few
around) with nuvision stereo glasses.
For example, you can still buy the Samsung SyncMaster 1100MB that has
sufficient rates (Vert x Hori 160 Hz x 130 kHz) to do the job.

If you can, wait a few years ...

Jeroen.

p.s. There are also some (more expensive) active stereo beamers around
(we own an Infocus DepthQ) and they provide a nice active stereo picture
on the wall:
- http://www.digital-image.de/
- http://www.depthq.com/



Pedro M. Matias wrote:
> 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 preferably with Linux or OSX ? (any windows
>>> hints are welcome as well).
>>
>> Yes indeed.  We have a 20" one of these:
>>
>> 
http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3

>>
>>
>> on one of our Linux workstations.  After the original Acer screens
>> were swapped for Samsung ones it is excellent.  People like it for
>> the lack of flicker and consequent lack of headaches!  It has a wide
>> angle of view, and several people can see stereo on the same screen
>> at the same time, and there is no cross-talk between different
>> displays in the same room.
>>
>> It needs to be driven by an nVidia FX-series graphics card, with dual
>> DVI outputs.  Other cards with dual outputs can be made to work, but
>> the nVidia driver can intercept the conventional quad-buffered screen
>> swapping instructions and divert the two eye views tot he different
>> displays.  Thus most software that is already stereo-capable will
>> work without modification.
>>
>> In case this sounds a little too glowing, I should point out that I
>> have no connection with the suppliers or the manufacturers, except as
>> a customer!
>>
>> Andrew
>>
>> --
>> Dr. Andrew Raine, Head of IT, MRC Dunn Human Nutrition Unit,
>> Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, UK
>> phone: +44 (0)1223 252830   fax: +44 (0)1223 252835
>> web: www.mrc-dunn.cam.ac.uk email: [EMAIL PROTECTED]
>
> Industry and Medicine Applied Crystallography
> Macromolecular Crystallography Unit
> ___
> Phones : (351-21) 446-9100 Ext. 1669
>   (351-21) 446-9669 (direct)
> Fax   : (351-21) 441-1277 or 443-3644
>
> email : [EMAIL PROTECTED]
>
> Mailing address :
> Instituto de Tecnologia Quimica e Biologica
> Apartado 127
> 2781-901 OEIRAS
> Portugal


Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : [EMAIL PROTECTED]

Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[P Hubbard]

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 just need 
to solve the polarization problem as some LCD TVs run at 120 Hz now). I think 
most people would prefer that too.

By the way, image inversion/mirroring can be done using Nvidia Windows 
drivers... but I'm not 100% sure about doing it in Linux as I've never tried it.

P.S: I shouldn't suggest these companies are over charging - though to me they 
seem to charge an awful lot of money given the components and skill/technology 
level needed to make them. Maybe I'm way off mark?!

AGS

Date: Mon, 4 Feb 2008 12:09:33 +
From: [EMAIL PROTECTED]
Subject: Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional
To: CCP4BB@JISCMAIL.AC.UK








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 has a 
refractive index) will be polarized in any case (that's why your Polaroid™ 
sunglasses let you see below the waves...). My physics is too rusty to 
remember, but I think the vertical monitor in this case needs to be polarized 
vertically, since the reflected polarized light will be horizontal.



No idea where you can buy large sheets of Polaroid™  though. 



IMWBW, though...



On 4 Feb 2008, at 11:30, P Hubbard wrote:



 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 +

> From: [EMAIL PROTECTED]

> Subject: Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

> To: CCP4BB@JISCMAIL.AC.UK

> 

> 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 cheaper there...?) is the DVI 

> "reflector" card that flips the image to be displayed on the screen seen 

> in the half-silvered mirror.

> 

> 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

> 

> -- 

> Dr. Andrew Raine, Head of IT, MRC Dunn Human Nutrition Unit,

> Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, UK

> phone: +44 (0)1223 252830 fax: +44 (0)1223 252835

> web: www.mrc-dunn.cam.ac.uk email: [EMAIL PROTECTED]



Helping your favorite cause is as easy as instant messaging. You IM, we give. 
Learn more. 


Harry

-- 

Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
Cambridge, CB2 2QH








_
Shed those extra pounds with MSN and The Biggest Loser!
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Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[Harry Powell]

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 has a refractive index) will be polarized in any case (that's 
why your Polaroid™ sunglasses let you see below the waves...). My 
physics is too rusty to remember, but I think the vertical monitor in 
this case needs to be polarized vertically, since the reflected 
polarized light will be horizontal.


No idea where you can buy large sheets of Polaroid™  though.

IMWBW, though...

On 4 Feb 2008, at 11:30, P Hubbard wrote:


 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 +
> From: [EMAIL PROTECTED]
> Subject: Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional
> To: CCP4BB@JISCMAIL.AC.UK
>
> 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 cheaper there...?) is the DVI
> "reflector" card that flips the image to be displayed on the screen 
seen

> in the half-silvered mirror.
>
> 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
>
> --
> Dr. Andrew Raine, Head of IT, MRC Dunn Human Nutrition Unit,
> Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, UK
> phone: +44 (0)1223 252830 fax: +44 (0)1223 252835
> web: www.mrc-dunn.cam.ac.uk email: [EMAIL PROTECTED]

Helping your favorite cause is as easy as instant messaging. You IM, 
we give. Learn more.

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills 
Road, Cambridge, CB2 2QH

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[esko . oksanen]

   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 monitors. While this 
is relatively easy to do, the problem is that your mouse pointer is in 
either screen and you never know which one... In practice it was fine for 
looking at stereo, but for building a model etc. it was pretty useless. It 
also turned out that the medical imaging people etc. usually have a _third_ 
LCD on the side to rotate the image. I don't know if you could make 
Xorg.conf to turn a quad-buffered stereo signal useful for this or 
alternatively make the software (PyMol, coot, etc.) support this type of 
stereo, but without that I would not recommend this system for 
xtallography..

  The mirror at least in the Planar system is definitely half-silvered (so 
it will turn the polarisation of the upper monitor) and it's positioning had 
to be pretty precise to get a nice image. So while you might build such a 
system your self, it might take some time and machining...

  Esko

Esko Oksanen, M.Sc.
European Molecular Biology Laboratory, Grenoble Outstation
6 rue Jules Horowitz
BP 181
38042 Grenoble Cedex 9
FRANCE
tel. +33-4-76207633
mob. +33-6-67416110
Skype ejoksane
[EMAIL PROTECTED]


Quoting Harry Powell <[EMAIL PROTECTED]>:

> Hi
> 
> Just looking at the diagrams, I don't think the glass is half-silvered 
> - it looks like a large sheet of Polaroid(TM). 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 has a refractive index) will be polarized in any case (that's 
> why your Polaroid(TM) sunglasses let you see below the waves...). My 
> physics is too rusty to remember, but I think the vertical monitor in 
> this case needs to be polarized vertically, since the reflected 
> polarized light will be horizontal.
> 
> No idea where you can buy large sheets of Polaroid(TM)  though.
> 
> IMWBW, though...
> 
> On 4 Feb 2008, at 11:30, P Hubbard wrote:
> 
> >  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 +
> > > From: [EMAIL PROTECTED]
> > > Subject: Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional
> > > To: CCP4BB@JISCMAIL.AC.UK
> > >
> > > 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 cheaper there...?) is the DVI
> > > "reflector" card that flips the image to be displayed on the screen 
> > seen
> > > in the half-silvered mirror.
> > >
> > > 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
> > >
> > > --
> > > Dr. Andrew Raine, Head of IT, MRC Dunn Human Nutrition Unit,
> > > Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, UK
> > > phone: +44 (0)1223 252830 fax: +44 (0)1223 252835
> > > web: www.mrc-dunn.cam.ac.uk email: [EMAIL PROTECTED]
> >
> > Helping your favorite cause is as easy as instant messaging. You IM, 
> > we give. Learn more.
> Harry
> -- 
> Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills 
> Road, Cambridge, CB2 2QH
> 
> 
> 

[ccp4bb] an over refined structure

[Sun Tang]

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 may be wrong with the over-refined structure? What is the reason for 
leading to an over-refined structure? How to avoid it?

Best wishes,

Sun Tang

   
-
Be a better friend, newshound, and know-it-all with Yahoo! Mobile.  Try it now.

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[David J. Schuller]

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) "XRandR" spec. 

http://www.x.org/wiki/Projects/XRandR

Many of the Linux drivers have added support just within the last few
months, so unless you're on the bleeding edge you probably don't have
this yet.

BTW, there is recent activity on open source drivers for common graphics
cards with the "RadeonHD" and "Nouveau" projects.


Cheers,

-  
===
With the single exception of Cornell, there is not a college in the
United States where truth has ever been a welcome guest - R.G. Ingersoll
===
  David J. Schuller
  modern man in a post-modern world
  MacCHESS, Cornell University
  [EMAIL PROTECTED]

Re: [ccp4bb] an over refined structure

[Sun Tang]

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 PROTECTED]> wrote: Hi,
  
  Why do you think this structure is over-refined ? The Rfree/Rwork difference 
of 6.2% seems fine, although you didn't mention resolution. If anything, an 
over-refined structure would show a smaller difference, as far as I know. If 
all the other criteria (Ramachandran outliers, etc., map) are OK you should 
just be happy with your structure.
  
  Cheers,
  
  Boaz

- Original Message -
From: Sun Tang <[EMAIL PROTECTED]>
Date: Monday, February 4, 2008 18:41
Subject: [ccp4bb] an over refined structure
To: CCP4BB@JISCMAIL.AC.UK

> 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 may be wrong with the over-refined structure? What is the 
> reason for leading to an over-refined structure? How to avoid it?
> 
> Best wishes,
> 
> Sun Tang
> 
>
> -
> Be a better friend, newshound, and know-it-all with Yahoo! 
> Mobile.  Try it now.


Boaz Shaanan, Ph.D. 
Dept. of Life Sciences 
Ben-Gurion University of the Negev 
Beer-Sheva 84105 
Israel 
Phone: 972-8-647-2220 ; Fax: 646-1710 
Skype: boaz.shaanan

‎ 

   
-
Never miss a thing.   Make Yahoo your homepage.

Re: [ccp4bb] Still cannot read .mtz + another ?

[P.J.Briggs]

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 file
linked as "refmac 5.4 for linux", which arrives on your system as
"refmac5.4_linintel.tar.gz". Unpacking this I get three files:

refmac_linintel
makecif_linintel
libcheck_linintel

These are updated executables for the refmac5, makecif and libcheck
programs that should be in the "bin" directory of your CCP4 distribution
(do "cd $CBIN" to get there) - you should move the current executables
out of the way, and then copy and rename the new files into the bin
directory.

For the new dictionary, I would suggest downloading the file and
unpacking it somewhere like the lib/data/ subdirectory of your CCP4
distribution. This should create something like
/your/path/ccp4-6.0.2/lib/data/dic

You can then change the environment variable "CLIBD_MON" to point to
/your/path/ccp4-6.0.2/lib/data/dic/, either on the command line or in
ccp4.setup (probably better to do the latter).

I'm pretty sure that this should work - sorry if it sounds complicated.
And yes it would probably be useful if Garib did indeed include some
information about updating on the actual page - but we don't have any
control over that.

Hope that this helps, best wishes

Peter Briggs
CCP4

C.Ainsley Davis wrote:
> 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 version of REFMAC. I downloaded the
> file from Garib's page)  I try to use the ccp4 GUI to install the file,
> but it doesnt like it. It says something about it being unable to read
> the contents.  If I gunzip then tar the file i get 3 files which I am
> not sure what to do with. There is also a new library file Garib
> recommends downloading, but in any case I cannot install the 5.4 version
> of REFMAC and cannot find any documentation online on how to install it!
> 
> Thanks again CCP4 BB!

-- 
___
Peter J Briggs, [EMAIL PROTECTED]   Tel: +44 1925 603826
CCP4,   [EMAIL PROTECTED]  Fax: +44 1925 603825
http://www.ccp4.ac.uk/
Daresbury Laboratory, Daresbury, Warrington WA4 4AD

Re: [ccp4bb] an over refined structure

[price]

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, things that are built incorrectly may be shoved back into 
density, making mistakes harder to spot.
Have you made sure that all your side chains are not just in the 
density, but in nice, non-strained rotamers?
The backbone and side chains are rather couple in refinement, 
especially if you don't have very high resolution data - this means 
that if you originally had the backbone slightly wrong, you may have 
built the side chains in the wrong rotamers.  They'll look like they 
fit the density, but everything will be a bit strained until you fix 
them.  Particularly if your Ramachandran plot is a bit scruffy, try 
optimizing the backbone geometry (by something such as lego in O), 
then refitting the side chains.


Phoebe Rice


At 11:33 AM 2/4/2008, you wrote:

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 PROTECTED]> wrote:
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 just
model noise. There may be other reasons for which more knowledge about the
structure is required. Do you have large unmodelled regions, like loops
that do not show in the density map?

Tim


--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A


On Mon, 4 Feb 2008, Sun Tang wrote:

> 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 may be wrong with the over-refined structure? What is the 
reason for leading to an over-refined structure? How to avoid it?

>
> Best wishes,
>
> Sun Tang
>
>
> -
> Be a better friend, newshound, and know-it-all with Yahoo! 
Mobile. Try it now.




Be a better friend, newshound, and know-it-all with Yahoo! Mobile. 
Try 
it now.


---
Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
fax 773 702 0439
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html 

[ccp4bb] an over refined structure

[George M. Sheldrick]

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 resolution, p is
the effective number of parameters refined per atom after allowing for
the restraints applied, d^3 means d cubed and sqrt means square root.

The difficult number to estimate is p. It would be 4 for an isotropic 
refinement without any restraints. I guess that p=1.5 might be an 
appropriate value for a typical protein refinement (giving an R-factor
ratio of about 1.4 for s=0.6 and d=2.8). In that case, your R-factor 
ratio of 0.277/0.215 = 1.29 is well within the allowed range!

However it should be added that this formula is almost a 
self-fulfilling prophesy. If we relax the geometric restraints we
increase p, which then leads to a larger 'allowed' R-factor ratio!

Best wishes, 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. +49-551-39-2582

Re: [ccp4bb] an over refined structure

[Sun Tang]

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 
0.186/0.267 (FOM=0.807) for wa=0.2, respectively. It seemed that increase in wa 
decreases both R and Rfree with R more than Rfree. 

Which wa value is the best one in this case?

Thank you very much for your valuable help.

Best,

Sun

Ian Tickle <[EMAIL PROTECTED]> wrote: 
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 and the solvent content (a 
greater solvent content means a bigger cell volume which means more reflections 
for a given number of ordered atoms in the a.u. and hence a bigger obs/param 
ratio).  The Rfree-Rwork difference also depends on Rwork itself (i.e. you tend 
to get higher values of Rfree-Rwork for higher values of Rwork), so it's better 
to think in terms of the Rfree/Rwork ratio (which is independent of Rwork).

So for example at very high resolution a 'normal' value for Rfree-Rwork might 
be only 0.02 (so 0.05 which is what many people consider acceptable would 
actually be unacceptably high), whereas at low resolution it might be 0.1 (so 
0.05 would be unacceptably low).  Also you need to bear in mind that Rfree 
tends to have a quite high uncertainty, particularly at low resolution (because 
it's usually based on a relatively small number of observations), so the 
deviation has to be quite big (e.g. > 3 SU) before it can be considered to be 
statistically significant.

So Rfree needs to be compared not with Rwork at all but with the value of the 
optimal Rfree/Rwork expected on the basis that the model parameterisation and 
weighting of X-ray terms and restraints are optimal and the errors in the model 
have the same effect as the random experimental errors in the data (i.e. a 
statistical 'null hypothesis').  As Tim just pointed out we tried to do this in 
our Acta D (1998) papers: there you can compare your observed Rfree/Rwork ratio 
either with the theoretical value or with the value found for 'typical' 
structures in the PDB at the same resolution.

An abnormal Rfree/Rwork ratio could arise from a number of causes, not just 
over-fitting (I assume that's what you mean by 'over-refinement' - it's not 
clear to me how a structure can be 'over-refined' since a fundamental 
requirement of the maximum likelihood method is that the structure is always 
refined to convergence, and refining beyond that will by definition produce no 
further statistically significant changes in the parameters).

For example the number of parameters being refined may be either too low, or 
too high (over-fitting), or the values of the weighting parameters may not be 
appropriate, or there may be something badly wrong with the atomic model (e.g. 
mistraced chain).  Given the values you are reporting I think the latter is 
very unlikely, possibly you just need to tweak the X-ray and/or restraint 
weights.

HTH

Cheers

-- Ian

> -Original Message-
> From: [EMAIL PROTECTED] 
> [mailto:[EMAIL PROTECTED] On Behalf Of Sun Tang
> Sent: 04 February 2008 16:56
> To: Boaz Shaanan
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] an over refined structure
> 
> 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  wrote:
> 
>  Hi,
>   
>   Why do you think this structure is over-refined ? The 
> Rfree/Rwork difference of 6.2% seems fine, although you 
> didn't mention resolution. If anything, an over-refined 
> structure would show a smaller difference, as far as I know. 
> If all the other criteria (Ramachandran outliers, etc., map) 
> are OK you should just be happy with your structure.
>   
>   Cheers,
>   
>   Boaz
>  
>  - Original Message -
>  From: Sun Tang 
>  Date: Monday, February 4, 2008 18:41
>  Subject: [ccp4bb] an over refined structure
>  To: CCP4BB@JISCMAIL.AC.UK
>  
>  > 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 may be wrong with the over-refined structure? 
> What is the 
>  > reason for leading to an over-refined structure? How 
> to avoid it?
>  > 
>  > Best wis

Re: [ccp4bb] an over refined structure

[Sun Tang]

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 2.8 A.
I did not check twinning. I will do that soon.
I used PHASER to solve the structure and the density of the N-domain (~ 50 a.a) 
in one molecule is not good, with a lot of broken density for the backbone.
I used the TLS in the refinement. I usually used the initial TLS parameters 
(with only residues in group, no coordinates for the center) for all the TLS 
refinement. When I used the refined TLS parameters, the refinement would go 
divergence.
I only added about 120 water molecules for the whole structures.
I will update the information after I try further refinement.

Best wishes,

Sun

Anastassis Perrakis <[EMAIL PROTECTED]> wrote: 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 ? (phenix.xtriage)
- is the N-term domain of one copy really invisible (then indeed do  
remove ...!)
- has TLS been used ?
- did you add waters ? (too many?)

I guess then we can make better suggestions if something is wrong and  
if so how its best to fix.

A.

> > 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.


   
-
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Re: [ccp4bb] Question about strange MR solution

[Marius Schmidt]

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 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
> instead of 0 
> degrees (the others are 0, as well as the fractional coordinates).
> This solution 
> is not symmetry-related with the structure that I used as search
> model: indeed, 
> there are a lot of clashes. However, when I refine this solution, I
> obtain 
> immediately R factors as good as the search model, and also the
> electron density 
> map looks perfect. Of course, I used the same reflections file to
> refine the 
> initial structure and the MR solution rotated of 180 degrees.
> 
> How can I explain this? The analysis with Truncate (moments and
> cumulative 
> intensity distribution) don't suggest any twinning, as well as the 
> Padilla-Yeates test. Is it possible, that I refined the structure in
> the wrong 
> space group?
> 
> Thank you in advance,
> 
> Michele Lunelli

[ccp4bb]

[Marius Schmidt]

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. Anyone an idea how
to go around it (should I install an older Linux)?
ccp4 is working fine.

Best regards
Marius




Dr.habil. Marius Schmidt
Asst. Professor
University of Wisconsin-Milwaukee
Department of Physics Room 454
1900 E. Kenwood Blvd.
Milwaukee, WI 53211

phone: +1-414-229-4338
email: [EMAIL PROTECTED]
http://users.physik.tu-muenchen.de/marius/

[ccp4bb] Question about strange MR solution

[Michele Lunelli]

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 instead of 0 
degrees (the others are 0, as well as the fractional coordinates). This solution 
is not symmetry-related with the structure that I used as search model: indeed, 
there are a lot of clashes. However, when I refine this solution, I obtain 
immediately R factors as good as the search model, and also the electron density 
map looks perfect. Of course, I used the same reflections file to refine the 
initial structure and the MR solution rotated of 180 degrees.


How can I explain this? The analysis with Truncate (moments and cumulative 
intensity distribution) don't suggest any twinning, as well as the 
Padilla-Yeates test. Is it possible, that I refined the structure in the wrong 
space group?



Thank you in advance,

Michele Lunelli

[ccp4bb] His tag

[Yanming Zhang]

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-terminal, what information can I get 
to assist my set-up of C-terminal crystallization set-up.


Sorry for taking up your time because of my inadequate knowledge
Thank you for your help
Yanming

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[David M Shechner]

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 back-and-forth 
to see the
3D effect, and it could only be used by one viewer per monitor, but at 
least the

hardware required would be only ~$50 or so, and would work equally well on any
type of display.  Check this out, as a demonstration (where the hardware is
rendered by gutting the innards of a $40 'Wiimote.'):

http://uk.youtube.com/watch?v=Jd3-eiid-Uw

Anyone want to get it working in coot?

Cheers,
d.s.

Re: [ccp4bb] His tag

[Artem Evdokimov]

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 permitting).
C-terminal tags are messier to remove because most known proteases require
considerable P(-X) segments. There are at least two clever ways to cleave
C-terminal His-tags 'cleanly' but they're generally not worth the trouble,
IMHO. N-terminal tags are easy to cleave since several 'clean' site-specific
proteases are available (TEV, TVMV, thrombin, etc.).

I am not sure what exactly do you mean by your second question - however
there are cases when even one amino acid difference results in huge changes
in crystallization behavior. The effect greatly depends on the location of
the change - if your proposed tag location is on or near a crystal contact
then the change will likely be huge. Then again, there are (we think) clever
ways to play with protein surfaces to elicit crystallization behavior - case
in point is our recent structure where three amino acid changes resulted in
huge improvement of crystals for a 2300 amino acid heterotetrameric protein.
Morale of this shameless self-promotion is that small changes of protein
surface can have profound effects on crystallization, and since tags are on
the surface the effects may range from none to huge.

Happy protein engineering,

Artem

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Yanming Zhang
Sent: Monday, February 04, 2008 8:54 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] His tag

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-terminal, what information can I get 
to assist my set-up of C-terminal crystallization set-up.

Sorry for taking up your time because of my inadequate knowledge
Thank you for your help
Yanming

Re: [ccp4bb] His tag

[Bostjan Kobe]

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 topic:

Carson M, Johnson DH, McDonald H, Brouillette C, Delucas LJ.
His-tag impact on structure.
Acta Crystallogr D Biol Crystallogr. 2007 Mar;63(Pt 3):295-301. Epub 2007
Feb 21.
PMID: 17327666 [PubMed - indexed for MEDLINE]

I would expect the same protein with the tags on different ends would often
crystallize under similar conditions, as long as the tags do not interfere
with the packing in the crystal.

Bostjan

On 5/2/08 11:54 AM, "Yanming Zhang" <[EMAIL PROTECTED]> wrote:

> 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-terminal, what information can I get
> to assist my set-up of C-terminal crystallization set-up.
> 
> Sorry for taking up your time because of my inadequate knowledge
> Thank you for your help
> Yanming

---
Bostjan Kobe
ARC Federation Fellow
Professor of Structural Biology
School of Molecular and Microbial Sciences
  and Institute for Molecular Bioscience
Office: Building 76 Room 452
Cooper Road
University of Queensland
Brisbane, Queensland 4072
Australia
Phone: +61 7 3365 2132
Fax: +61 7 3365 4699
E-mail: [EMAIL PROTECTED]
URL: http://profiles.bacs.uq.edu.au/Bostjan.Kobe.html
Notice: If you receive this e-mail by mistake, please notify me, and do not
make any use of its contents. I do not waive any privilege, confidentiality
or copyright associated with it. Unless stated otherwise, this e-mail
represents only the views of the Sender and not the views of The University
of Queensland.

[ccp4bb]

[Tim Gruene]

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 fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A


On Tue, 5 Feb 2008, Marius Schmidt wrote:


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. Anyone an idea how
to go around it (should I install an older Linux)?
ccp4 is working fine.

Best regards
Marius




Dr.habil. Marius Schmidt
Asst. Professor
University of Wisconsin-Milwaukee
Department of Physics Room 454
1900 E. Kenwood Blvd.
Milwaukee, WI 53211

phone: +1-414-229-4338
email: [EMAIL PROTECTED]
http://users.physik.tu-muenchen.de/marius/