[ccp4bb] 3D Glasses - Vuzix HMD by eDimensional
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
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_mimoSubCatID_=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
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_mimoSubCatID_=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
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] Still cannot read .mtz + another ?
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
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
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
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 ?
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
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
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
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_mimoSubCatID_=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] an over refined structure
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 Skype: boaz.shaanan ââ'¬Å½
Re: [ccp4bb] an over refined structure
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
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_mimoSubCatID_=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
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! http://biggestloser.msn.com/
Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional
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
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
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.
[ccp4bb] an over refined structure
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
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 wishes, Sun Tang -
Re: [ccp4bb] an over refined structure
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. - Looking for last minute shopping deals? Find them fast with Yahoo! Search.
Re: [ccp4bb] Question about strange MR solution
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]
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
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
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
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
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
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]
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/
