Re: [ccp4bb] Histogram matching in DM - question
Dear Ed, The question of dealing appropriately with density modification in the presence of heavy atoms has been discussed in the paper on SHARP 2.0 (see Acta D59, 2023-2030, published in 2003) and the solution described in that paper has been available in all versions of SHARP/autoSHARP since then. Essentially, it removes the contribution from the heavy atom(s) before density modification in SOLOMON, and adds it back afterwards. You might want to give it a try if you have had cases where you thought that density modification was doing a sub-optimal job with your metal-containing protein. With best wishes, Gerard. On Tue, Aug 18, 2009 at 04:42:48PM -0400, Edward A. Berry wrote: Peter Grey wrote: Hi everyone, I am trying to use density modification at rather low resolution (4-5A ) for an RNA structure. My first time ever with RNA. I usually use Histogram matching as part of the density modification scheme in DM. But this method is based on density distribution of protein maps I think. Is histogram matching still valid when it comes to RNA or protein/RNA structures ? I have the same question with respect to metalloproteins. Presumably the heavier metal atoms make spikes that are completely off the scale of a normal protein histogram. Is it then a bad idea to use histogram matching? Do the metals get flattened down to the highest density expected for protein on every cycle? Ed -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
[ccp4bb] Postdoctral Position Available
Dear All, The Frontier Research Center for Applied Atomic Sciences of Ibaraki Univ. (Ibaraki, Japan) invites a highly motivated young scientist in the field of neutron/x-ray protein crystallography or biochemistry to join our research team. The Postdoctoral Research Fellow candidate will work on a multidisciplinary project involving protein expression, biochemical and biophysical characterization, and crystallization of some enzymes. The Frontier Research Center for Applied Atomic Sciences is located close to J-PARC (Japan Proton Accelerator Research Complex) and Photon Factory, thus it is very good circumstance for structural biologists and crystallographers. http://www.ibaraki.ac.jp/all/gaiyou/22.htm Experience and expertise in protein expression, and purification are required. The applicants should have hold (or will obtain, soon,) a Ph.D. degree and be under 35 years old. The appointment will be for half a year (from October 1st in 2009 to March 31st in 2010). Salary will be 3,700 yen/hour, 6 hours/day and 5 days (Monday to Friday, except national holiday)/week. To apply, please email or send envelope including (1) a curriculum vita (including publications) (2) an original paper of your masterwork to Masaki UNNO, PhD: e-mail: unn...@mx.ibaraki.ac.jp Address: Ibaraki Quantum Beam Research Center,162-1 Tokai, Shirakata, Naka, Ibaraki 319-1106, Japan. The language is English or Japanese. The deadline for application is 27th August, 2009. Thank you for your interest. ~ Masaki UNNO, Ph.D. Frotier Research Center for Applied Atomic Sciences, Ibaraki University Ibaraki Quantum Beam Research Center 162-1 Tokai, Shirakata, Naka, Ibaraki 319-1106, Japan Tel: 029-352-3239, Fax: 029-287-7872 E-mail: unn...@mx.ibaraki.ac.jp ~
[ccp4bb] Identification of the hydrophobic residues on the dimer interface
Hi, everybody I have a crystal structure as homodimer, from which residues in the dimer interface need to be identified. Using PISA on the EBI website, residues involved in forming hydrogen bonds, salt bridges, disulfide bonds and covalent bonds could be identified. But hydrophobic interaction could also play an essential role on the dimer stablization. So does anybody know: 1. how to find those hydrophobic residues (software or on-line-server) 2. how to confirm that whether they play a role in the dimerization, except for site-mutation. Thanks a lot! Hunter
Re: [ccp4bb] Identification of the hydrophobic residues on the dimer interface
Hi Hunter, 1. how to find those hydrophobic residues PISA will also tell you this - you just need to look at the hydrophobic residues which are highlighted and have a buried surface area (BSA) value in the PISA output. You can take these residues and plot them in your favourite pdb viewer (CCP4mg, PyMol, etc) As for confirming their importance - the only definative test IS site-directed mutagenesis. However, before you dash off and order your primers, Rosetta/Robetta has an in-silico alanine scanning mutatgenesis server which may help direct your efforts: http://robetta.bakerlab.org/alascansubmit.jsp HTH David 2009/8/19 Haitao ZHANG crystalc...@gmail.com: Hi, everybody I have a crystal structure as homodimer, from which residues in the dimer interface need to be identified. Using PISA on the EBI website, residues involved in forming hydrogen bonds, salt bridges, disulfide bonds and covalent bonds could be identified. But hydrophobic interaction could also play an essential role on the dimer stablization. So does anybody know: 1. how to find those hydrophobic residues (software or on-line-server) 2. how to confirm that whether they play a role in the dimerization, except for site-mutation. Thanks a lot! Hunter -- David C. Briggs PhD Father Crystallographer http://drdavidcbriggs.googlepages.com/home Skype: DocDCB
Re: [ccp4bb] Histogram matching in DM - question
And to add another small item: the SOLOMON interface in SHARP allows adjustment of the mean density depending on protein, DNA or RNA content. See http://www.globalphasing.com/sharp/manual/denmod2.html#MeanDensity Cheers Clemens On Wed, Aug 19, 2009 at 09:26:34AM +0100, Gerard Bricogne wrote: Dear Ed, The question of dealing appropriately with density modification in the presence of heavy atoms has been discussed in the paper on SHARP 2.0 (see Acta D59, 2023-2030, published in 2003) and the solution described in that paper has been available in all versions of SHARP/autoSHARP since then. Essentially, it removes the contribution from the heavy atom(s) before density modification in SOLOMON, and adds it back afterwards. You might want to give it a try if you have had cases where you thought that density modification was doing a sub-optimal job with your metal-containing protein. With best wishes, Gerard. On Tue, Aug 18, 2009 at 04:42:48PM -0400, Edward A. Berry wrote: Peter Grey wrote: Hi everyone, I am trying to use density modification at rather low resolution (4-5A ) for an RNA structure. My first time ever with RNA. I usually use Histogram matching as part of the density modification scheme in DM. But this method is based on density distribution of protein maps I think. Is histogram matching still valid when it comes to RNA or protein/RNA structures ? I have the same question with respect to metalloproteins. Presumably the heavier metal atoms make spikes that are completely off the scale of a normal protein histogram. Is it then a bad idea to use histogram matching? Do the metals get flattened down to the highest density expected for protein on every cycle? Ed -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * === -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] Identification of the hydrophobic residues on the dimer interface
Hello, PISA gives you quite a lot of information on hydrophobic interactions, down to atomic level (subject to interpretation). In the list of interfaces, PISA gives just the sum hydrophobic effect for each interface. If you click on interface number, it will take you to further details for the interface, which includes list of residues and their hydrophobic contributions. Read on-line documentation if in doubt. Bear in mind that almost all lines in PISA output are hyperlinks to documentation pages, even if they are not highlighted as links. Eugene. On Wed, 19 Aug 2009, Haitao ZHANG wrote: Hi, everybody I have a crystal structure as homodimer, from which residues in the dimer interface need to be identified. Using PISA on the EBI website, residues involved in forming hydrogen bonds, salt bridges, disulfide bonds and covalent bonds could be identified. But hydrophobic interaction could also play an essential role on the dimer stablization. So does anybody know: 1. how to find those hydrophobic residues (software or on-line-server) 2. how to confirm that whether they play a role in the dimerization, except for site-mutation. Thanks a lot! Hunter
[ccp4bb] cyseteine modification
Dear Sir, Is there any other oxidation states of cysteine other than cysteine sulphinic acid and cysteine sulphonic acid. In my protein, the cysteine molecule is definitely overoxidized but the electron density is not corresponding to the sulphinic or the sulphonic acid. The positive density looks as if it can accomodate only one oxygen atom and not more. Thank you for reply in advance. Sincerely Debajyoti Dutta
Re: [ccp4bb] cyseteine modification
Dear Debajyoti There is also the sulfenic acid species (-S-OH) which is actually the first oxidized form of sulfhydryls on the way to sulfonic acid. However sulfenic acids are very susceptible to further oxidation to sulfinic and sulphonic acids, and therefore need a protective chemical environment to remain stable. See for example some previous work of ours on sulfenic and sulfinic forms of active-site cysteines in glutathione reductase (Nature Structure Biology vol 5, 267-271, 1998) and the corrresponding pdb entries 1dnc and 1gsn. Best regards Savvas Savvas Savvides L-ProBE, Unit for Structural Biology Ghent University K.L. Ledeganckstraat 35 9000 Ghent, BELGIUM office: +32-(0)9-264.51.24 ; mobile: +32-(0)472-92.85.19 Email: savvas.savvi...@ugent.be http://www.lprobe.ugent.be/xray.html From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Debajyoti Dutta Sent: Wednesday, August 19, 2009 4:42 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] cyseteine modification Dear Sir, Is there any other oxidation states of cysteine other than cysteine sulphinic acid and cysteine sulphonic acid. In my protein, the cysteine molecule is definitely overoxidized but the electron density is not corresponding to the sulphinic or the sulphonic acid. The positive density looks as if it can accomodate only one oxygen atom and not more. Thank you for reply in advance. Sincerely Debajyoti Dutta http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/sign atureline@middle? E-mail message checked by Spyware Doctor (6.1.0.447) Database version: 6.13080 http://www.pctools.com/en/spyware-doctor-antivirus/
Re: [ccp4bb] cyseteine modification
You can also have a look at Active site structural features for chemically modified forms of rhodanese. Gliubich F, Gazerro M, Zanotti G, Delbono S, Bombieri G, Berni R. J Biol Chem. 1996 Aug 30;271(35):21054-61. Best Roberto On 19 Aug 2009, at 15:41, Debajyoti Dutta wrote: Dear Sir, Is there any other oxidation states of cysteine other than cysteine sulphinic acid and cysteine sulphonic acid. In my protein, the cysteine molecule is definitely overoxidized but the electron density is not corresponding to the sulphinic or the sulphonic acid. The positive density looks as if it can accomodate only one oxygen atom and not more. Thank you for reply in advance. Sincerely Debajyoti Dutta
[ccp4bb] Bucanneer and molecular replacement
I have been trying to get my head around using bucanneer for molecular replacement. I am not sure that I have understood the specify a heavy atom or MR model and what this does or the model to be extended options. I am not sure of the difference between the two, and bucanneer will only run on certain models for reasons I do not understand. With many input PDB files cbucanneer tends to crash with child process killed. In fact I find that I can just read in the refmac map and the sequence and model building proceeds more or less as well. I have donwloaded 1.3 from Kevin site (Linux) but this does not run at all 'bucaanneer-1st-correlation-mode takes logical got ' Thanks Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G57 Office) 020-7631-6868 (Rosalind Franklin Laboratory) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
[ccp4bb] Cryoprotection in 3M ammonium sulfate
Hello! I would be grateful for suggestions on cryoprotectants for crystals growing in 3M ammonium sulfate. Thanks! Brenda Email Disclaimer: www.stjude.org/emaildisclaimer
Re: [ccp4bb] Unknown density
The density looks an awful lot like a polyatomic anion (sulfate, phosphate, etc.). It's hard to tell from the fixed images, but it appears to be tetrahedral. Is there any chance a polyatomic anion could be in the crystallization solution? Perhaps from the protein stock solution? Sampath Natarajan wrote: Dear All, Currently I'm modeling one structure with 2.6A data. I could find an unknown density which I located in the interface between the three similar subunits. This density shows very strong peak, which appears until 10 sigma level in the difference map. It seems to be a metal ion. But, already I could find two Zn ions in the active site and refined well. The aspartic acid of each subunit has very close interaction with this density. You can see the pictures, which I have attached with this mail. The crystallization condition is 0.05M CaCl_2 0.1M Bis-Tris pH 6.5, 30% (/v/v/) PEG monomethyl ether 550. Suggestion about this unknown density will be more helpful to find the molecule. thanks a lot, Regards, Sampath -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu
Re: [ccp4bb] Cryoprotection in 3M ammonium sulfate
Hi Brenda, You can try sugars like glucose, trehalose and sucrose for high AS contents. It has been succesfully used in really hard cases such at protein RNA crystals grown in AS. see Acta Cryst (2002) D58 1664-1669 Garber et al. HTH Pascal Egea
Re: [ccp4bb] Cryoprotection in 3M ammonium sulfate
Soluble possibilities include glucose, ethylene glycol, DMSO, glycerol (15-30%). You may not need much cryoprotectant at all at these salt concentrations. PEGs are not very soluble in high ammonium sulfate solutions. (I think PEG-400 can go up to only 4% or so at 2 M ammonium sulfate.) Cheers. Schulman, Brenda wrote: Hello! I would be grateful for suggestions on cryoprotectants for crystals growing in 3M ammonium sulfate. Thanks! Brenda Email Disclaimer: www.stjude.org/emaildisclaimer -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu
Re: [ccp4bb] Cryoprotection in 3M ammonium sulfate
Dear Brenda Check out malonate http://www.ncbi.nlm.nih.gov/pubmed/14646118? ordinalpos=2itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubm ed_DefaultReportPanel.Pubmed_RVDocSum Malonate: a versatile cryoprotectant and stabilizing solution for salt-grown macromolecular crystals. Holyoak T, Fenn TD, Wilson MA, Moulin AG, Ringe D, Petsko GA. Regards Christine On 19/08/2009, at 9:18 AM, Schulman, Brenda wrote: Hello! I would be grateful for suggestions on cryoprotectants for crystals growing in 3M ammonium sulfate. Thanks! Brenda Email Disclaimer: www.stjude.org/emaildisclaimer
Re: [ccp4bb] Cryoprotection in 3M ammonium sulfate
Hi Brenda Try 3M ammonium sulfate itself! We have tried that with great succes by cryo-cooling xtals grown at 3.2M AS straight out of their crystallization drops. You can consult the MM section in Kyndt J. et al Biochemistry 2007 Jan 9;46(1):95-105 for a more detailed description of what we did. Best of luck Savvas Savvas Savvides L-ProBE, Unit for Structural Biology Ghent University K.L. Ledeganckstraat 35 9000 Ghent, BELGIUM office: +32-(0)9-264.51.24 ; mobile: +32-(0)472-92.85.19 Email: savvas.savvi...@ugent.be http://www.lprobe.ugent.be/xray.html -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Schulman, Brenda Sent: Wednesday, August 19, 2009 6:19 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Cryoprotection in 3M ammonium sulfate Hello! I would be grateful for suggestions on cryoprotectants for crystals growing in 3M ammonium sulfate. Thanks! Brenda Email Disclaimer: www.stjude.org/emaildisclaimer E-mail message checked by Spyware Doctor (6.1.0.447) Database version: 6.13080 http://www.pctools.com/en/spyware-doctor-antivirus/
Re: [ccp4bb] Cryoprotection in 3M ammonium sulfate
Dear Brenda, I'd suggest using a mixture of 75% Paratone-N oil with 25% light, white mineral oil. Mix the two thoroughly with a positive displacement pipette then add a small amount next to the mother liquor (ML) drop. Remove a crystal from the ML using a matched cryo loop (the smaller the better) and then dip it completely into the oil. Gently slide the side of the loop containing the crystal against the surface beside the ML to wick off some of the oil, which will also remove some of the aqueous layer on the crystal surface. Then dip the crystal back into the oil; it usually takes 2-3 times to completely remove the aqueous layer. This works about 80% of the time for me for crystals grown from high salt conditions. Method courtesy of A. McPherson and J. Pflugrath. HTH, Jeff -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Schulman, Brenda Sent: Wednesday, August 19, 2009 12:19 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Cryoprotection in 3M ammonium sulfate Hello! I would be grateful for suggestions on cryoprotectants for crystals growing in 3M ammonium sulfate. Thanks! Brenda Email Disclaimer: www.stjude.org/emaildisclaimer
Re: [ccp4bb] Cryoprotection in 3M ammonium sulfate
Or saturated LiSO4 works too. Should work in this case. -Tom Tom J. Brett, PhD Assistant Professor of Medicine Division of Pulmonary and Critical Care Washington University School of Medicine Campus Box 8052, 660 S. Euclid Saint Louis, MO 63110 From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Savvas Savvides [savvas.savvi...@ugent.be] Sent: Wednesday, August 19, 2009 11:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Cryoprotection in 3M ammonium sulfate Hi Brenda Try 3M ammonium sulfate itself! We have tried that with great succes by cryo-cooling xtals grown at 3.2M AS straight out of their crystallization drops. You can consult the MM section in Kyndt J. et al Biochemistry 2007 Jan 9;46(1):95-105 for a more detailed description of what we did. Best of luck Savvas Savvas Savvides L-ProBE, Unit for Structural Biology Ghent University K.L. Ledeganckstraat 35 9000 Ghent, BELGIUM office: +32-(0)9-264.51.24 ; mobile: +32-(0)472-92.85.19 Email: savvas.savvi...@ugent.be http://www.lprobe.ugent.be/xray.html -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Schulman, Brenda Sent: Wednesday, August 19, 2009 6:19 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Cryoprotection in 3M ammonium sulfate Hello! I would be grateful for suggestions on cryoprotectants for crystals growing in 3M ammonium sulfate. Thanks! Brenda Email Disclaimer: www.stjude.org/emaildisclaimer E-mail message checked by Spyware Doctor (6.1.0.447) Database version: 6.13080 http://www.pctools.com/en/spyware-doctor-antivirus/
Re: [ccp4bb] Cryoprotection in 3M ammonium sulfate
I second that one. Ammonium sulfate is one of my favorite cryos. I recommend making up a saturated solution of ammonium sulfate, as it is actually a very good cryo all by itself, and then dilute it by adding the rest of the stuff in your condition (buffers, etc. and a little bit of water). You want to be a little below saturation so that the salt does not grow crystals of its own while you are soaking. This is especially important if your protein crystals are hexagonal rods! -James Holton MAD Scientist Savvas Savvides wrote: Hi Brenda Try 3M ammonium sulfate itself! We have tried that with great succes by cryo-cooling xtals grown at 3.2M AS straight out of their crystallization drops. You can consult the MM section in Kyndt J. et al Biochemistry 2007 Jan 9;46(1):95-105 for a more detailed description of what we did. Best of luck Savvas Savvas Savvides L-ProBE, Unit for Structural Biology Ghent University K.L. Ledeganckstraat 35 9000 Ghent, BELGIUM office: +32-(0)9-264.51.24 ; mobile: +32-(0)472-92.85.19 Email: savvas.savvi...@ugent.be http://www.lprobe.ugent.be/xray.html -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Schulman, Brenda Sent: Wednesday, August 19, 2009 6:19 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Cryoprotection in 3M ammonium sulfate Hello! I would be grateful for suggestions on cryoprotectants for crystals growing in 3M ammonium sulfate. Thanks! Brenda Email Disclaimer: www.stjude.org/emaildisclaimer E-mail message checked by Spyware Doctor (6.1.0.447) Database version: 6.13080 http://www.pctools.com/en/spyware-doctor-antivirus/
[ccp4bb] strange pattersons
Hi All Im receiving some strange patterns in my pattersons. Space group is C222 with no confidence (due to resolution) of systematic absences to transform to C2221. Thanks! FR pattersonmap.pdf Description: Adobe PDF document - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Re: [ccp4bb] Histogram matching in DM - question
Hi Peter, You can specify in DM the mean density of the protein region in the SOLC keyword. However I am not sure this will affect the density distribution used for histogram matching. All the best, Adam.
Re: [ccp4bb] strange pattersons
Hi Francis, The space group will not influence the Patterson, as both C222 and C2221 will become Pmmm in Patterson space. (Aside: You can change the packing pattern from one into the other by shifting the origin by x+0.5, I think, equivalent to adding 0.5 to the x-coordinate. However, you haven't got there yet!). The pattern you show is probably due to the dominance of one or a few reflections that is/are unusually large relative to the others. My guess, from the plot, is H=18, K=20. In a native Patterson, this would be highly unusual, but possible with translational NCS. If this map is some kind of difference Patterson, say anomalous, it is very easy to get such individual reflections that dominate (poor resolution, according to your hint). You have to be careful in selecting the refelctions with these low accuracy measurements. SCALEIT of the data set for analysis would give you a number of measures to select reliable data with: Highest index in each direction, highest and lowest I/sigma (or whatever the coefficient relates to), maximum and minimum numerical values, etc. If all these fail to weed out the erroneous data, you can still exclude specific reflections, provided you know which ones they are. Good Luck. Pierre Rizkallah ** Dr. Pierre Rizkallah, Senior Lecturer in Structural Biology, WHRI, School of Medicine, Academic Avenue, Heath Park, Cardiff CF14 4XN email: rizkall...@cf.ac.uk phone + 44 29 2074 2248 Francis E Reyes francis.re...@colorado.edu 19/08/09 8:40 PM Hi All Im receiving some strange patterns in my pattersons. Space group is C222 with no confidence (due to resolution) of systematic absences to transform to C2221. Thanks! FR
Re: [ccp4bb] hardware stereo in Coot on Mac
Dear David: I don't know if anyone answered this, but I think for #1 you need to issue the command defaults write com.apple.x11 enable_stereo -bool true For #2, I think the latest X11 from here works ok, but I don't actually have a way to check it: http://xquartz.macosforge.org/trac/wiki HTH, Bill On Mon, Aug 10, 2009 at 3:10 PM, David Bruce McKay david.mc...@colorado.edu wrote: Two questions RE hardware (dual images on CRT monitor, 3-D with stereo glasses) stereo on a Macintosh. 1 We have a configuration: Mac dual Intel processors OS 10.4.11 NVIDIA Quadro FX 4500 graphics card X11 version 1.1.3 It runs hardware stereo in O and Pymol , which don't require an X-window terminal, and will do side-by-side stereo in Coot run from an X11 window, but when we try to do hardware stereo, we get message, This computer appears not to be able to do hardware stereo. This must have a simple fix, but I haven't found it. 2. Is there a combination of Mac OS 10.5.x and Xquartz 2.x.x that does hardware stereo reliably? Dave McKay Department of Chemistry Biochemistry University of Colorado, Boulder -- - William G. Scott contact info: http://chemistry.ucsc.edu/~wgscott Please reply to: wgsc...@chemistry.ucsc.edu
