[ccp4bb] Ligand fitting in COOT and SHELX refinement
Hi I would like to know following issue for a ligand. A ligand of a long alkyl chain can have multiple conformation. In coot in order to fit any protein residues into difference Density, we can select a specific rotamer conformation and refine. For fitting ligand of above kind, how does it work out. Taking the PDB with ligand when we go to refine in SHELX, how restraints like (DFIX, DANG etc) are mentioned for such kind of ligand which can have multiple conformation (particularly for the long alkyl chain) and during refinement values can deviate a lot from a particular value taken from the literature. I appreciate suggestion and comments. Many Thanks Sam _ With Windows Live Hotmail, you can personalize your inbox with your favorite color. www.windowslive-hotmail.com/learnmore/personalize.html?locale=en-usocid=TXT_TAGLM_HMWL_reten_addcolor_0607
Re: [ccp4bb] Ligand fitting in COOT and SHELX refinement
My following question relates to the fitting and refinemt of a ligand, n-octyl-beta-D-glucopyranoside. Sam Date: Fri, 22 Jun 2007 06:27:45 + From: [EMAIL PROTECTED] Subject: [ccp4bb] Ligand fitting in COOT and SHELX refinement To: CCP4BB@JISCMAIL.AC.UK Hi I would like to know following issue for a ligand. A ligand of a long alkyl chain can have multiple conformation. In coot in order to fit any protein residues into difference Density, we can select a specific rotamer conformation and refine. For fitting ligand of above kind, how does it work out. Taking the PDB with ligand when we go to refine in SHELX, how restraints like (DFIX, DANG etc) are mentioned for such kind of ligand which can have multiple conformation (particularly for the long alkyl chain) and during refinement values can deviate a lot from a particular value taken from the literature. I appreciate suggestion and comments. Many Thanks Sam _ With Windows Live Hotmail, you can personalize your inbox with your favorite color. www.windowslive-hotmail.com/learnmore/personalize.html?locale=en-usocid=TXT_TAGLM_HMWL_reten_addcolor_0607 _ Hotmail to go? Get your Hotmail, news, sports and much more! Check out the New MSN Mobile! http://mobile.msn.com
Re: [ccp4bb] Save image in Postscript format from PYMOL
Pymol version 0.99 has the option to set the label position, similar to eg. molscript. Go to Select - Edit all - scroll down to label-offset - edit the x,y,z parameters. Pymol version 0.98 does not have this option. Julie. shi jiahai wrote: Hi, all I am drawing some stereo images with label by PYMOL. But the label interfere with protein. I try to output to Postscript format so that I can change the position of label. However, I can't output the image to Postscript format in Pymol. Is there anyboy know how to save image in Postscript format from PYMOL? Your help would be appreciated. Thank you very much! Shi Jiahai Dept of Biological Sciences National University of Singapore -- Julie Bouckaert, PhD[EMAIL PROTECTED] VIB Project leader VIB Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel Tel. 32-2-629-1988 Fax 32-2-6291963 ULTR, Building E 4.18 Vrije Universiteit Brussel Pleinlaan 2 1050 Brussel Belgium
[ccp4bb] Open position at the crystallography platform, Heidelberg University Biochemistry Center
Institution: Heidelberg University Biochemistry Center (BZH) and Cluster of Excellence (CellNetworks) Location: Heidelberg, Germany URL: www.uni-heidelberg.de/zentral/bzh/ Start: As soon as possible Duration: 4 years Salary: According to the German public service tariff scale TV-L. Description: We are establishing a medium-throughput crystallization facility for biological macromolecules as a central technology platform. We are looking for a scientific leader of the facility, to both run the platform and organize the user support. The successful candidate is an expert in protein biochemistry with a profound knowledge in recombinant protein expression, purification, and crystallization. Experience in X-ray crystallography and/or automation would be an advantage. Prerequisites: PhD or equivalent, basic knowledge in German Please submit: CV, 2 letters of reference until July 20 Contact: Prof. Dr. Irmgard Sinning Address: Heidelberg University Biochemistry Center (BZH), INF328, D-69120 Heidelberg, Germany. Email: irmi.sinning(at)bzh.uni-heidelberg.de, Phone: +49 6221 544780
Re: [ccp4bb] Ligand fitting in COOT and SHELX refinement
U Sam wrote: Hi I would like to know following issue for a ligand. A ligand of a long alkyl chain can have multiple conformation. In coot in order to fit any protein residues into difference Density, we can select a specific rotamer conformation and refine. For fitting ligand of above kind, how does it work out. For amino acids there are tens of thousands of examples from which one can derive rotomer libraries. There is no such luck with most other compounds. This is why Coot has special case code for handling amino acids that does not understand your (or my) favorite molecules. Fortunately, Coot does not require such information to run its real space refinement. You do need a cif definition that includes, amongst other things, the ideal bond lengths and bond angles. You can work with Coot to build the conformation of your molecule that fits your density. All conformations will be consistent with the same bonds and angles, unless you have a very strange molecule. Taking the PDB with ligand when we go to refine in SHELX, how restraints like (DFIX, DANG etc) are mentioned for such kind of ligand which can have multiple conformation (particularly for the long alkyl chain) and during refinement values can deviate a lot from a particular value taken from the literature. SHELXL will take whatever conformation you build and come up with a model that is consistent with the values on the DFIX and DANG statements. It should never produce a model that deviates from the literature values, if you put those values on your DFIX and DANG statements. The final model will have a configuration similar to what you built in Coot. Use Coot to make the big changes and SHELXL to fine tune. I have been refining some long chain hydrocarbons along with my protein and have had no problems, once I was able to create the proper definitions for Coot and SHELXL. SHELXL is certainly easier to create a library for, but you need both if you want to model build and refine. Building a cif with ideal geometry for Coot/Refmac is not an easy task. You need to understand your chemistry and the file format, which is not well documented. You have several options: 1) You can sit down and figure out how to create a cif definition. This is hard to do but a valuable skill to acquire. 2) You can find a compound similar to yours for which there is a definition built into Coot and modify it for your needs. You still need to understand the file format, but you can get away with less understanding because you are starting with something that works. 3) You can use web resources to find/create a file for you. A number of options are available, none of which I would trust completely. The HIC-UP website is perhaps the most popular, but the values are quite unreliable. These files can be used as a starting point but always verify... The Elbow builder in Phenix is quite reasonable, but takes a bit of study to understand, and again, don't trust it. Remember the quote from the Harry Potter books: Never trust anything you can't see where it keeps its brains. I appreciate suggestion and comments. Many Thanks Sam _ With Windows Live Hotmail, you can personalize your inbox with your favorite color. www.windowslive-hotmail.com/learnmore/personalize.html?locale=en-usocid=TXT_TAGLM_HMWL_reten_addcolor_0607
Re: [ccp4bb] Save image in Postscript format from PYMOL
Hi, Julie, Thank you very much for your kindly reply! But it seems this function can not set the individual label position. For example, one label is set at ( 2, 1,-0.5) while another label is set at (1, 2, 3). Is there a way to set the label position one by one? Your help is highly appreciated Thank you very much! Jiahai On 6/22/07, Julie Bouckaert [EMAIL PROTECTED] wrote: Pymol version 0.99 has the option to set the label position, similar to eg. molscript. Go to Select - Edit all - scroll down to label-offset - edit the x,y,z parameters. Pymol version 0.98 does not have this option. Julie. shi jiahai wrote: Hi, all I am drawing some stereo images with label by PYMOL. But the label interfere with protein. I try to output to Postscript format so that I can change the position of label. However, I can't output the image to Postscript format in Pymol. Is there anyboy know how to save image in Postscript format from PYMOL? Your help would be appreciated. Thank you very much! Shi Jiahai Dept of Biological Sciences National University of Singapore -- Julie Bouckaert, PhD[EMAIL PROTECTED] VIB Project leader VIB Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel Tel. 32-2-629-1988 Fax 32-2-6291963 ULTR, Building E 4.18 Vrije Universiteit Brussel Pleinlaan 2 1050 Brussel Belgium -- Best Regards, Shi Jiahai
Re: [ccp4bb] Open position at the crystallography platform, Heidelberg University Biochemistry Center
Whereas I am young, cheap and very very easy -- phwooaaarrr!! Gebhard Schertler wrote: Sorry Irmi, I am too old and expensive. All the best. good luck Gebhard On 22 Jun 2007, at 09:17, Klemens Wild wrote: Institution: Heidelberg University Biochemistry Center (BZH) and Cluster of Excellence (CellNetworks) Location: Heidelberg, Germany URL: www.uni-heidelberg.de/zentral/bzh/ http://www.uni-heidelberg.de/zentral/bzh/ Start: As soon as possible Duration: 4 years Salary: According to the German public service tariff scale TV-L. Description: We are establishing a medium-throughput crystallization facility for biological macromolecules as a central technology platform. We are looking for a scientific leader of the facility, to both run the platform and organize the user support. The successful candidate is an expert in protein biochemistry with a profound knowledge in recombinant protein expression, purification, and crystallization. Experience in X-ray crystallography and/or automation would be an advantage. Prerequisites: PhD or equivalent, basic knowledge in German Please submit: CV, 2 letters of reference until July 20 Contact: Prof. Dr. Irmgard Sinning Address: Heidelberg University Biochemistry Center (BZH), INF328, D-69120 Heidelberg, Germany. Email: irmi.sinning(at)bzh.uni-heidelberg.de, Phone: +49 6221 544780 Dr. Gebhard F. X. Schertler Senior Scientist and Group Leader MRC Laboratory of Molecular Biology Cambridge CB2 2QH tel 0044 1223 402328 e-mail [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] web http://www2.mrc-lmb.cam.ac.uk/SS/Schertler_G/
Re: [ccp4bb] Open position at the crystallography platform, Heidelberg University Biochemistry Center
Sorry Irmi, I am too old and expensive. All the best. good luck Gebhard On 22 Jun 2007, at 09:17, Klemens Wild wrote: Institution: Heidelberg University Biochemistry Center (BZH) and Cluster of Excellence (CellNetworks) Location: Heidelberg, Germany URL: www.uni-heidelberg.de/zentral/bzh/ Start: As soon as possible Duration: 4 years Salary: According to the German public service tariff scale TV-L. Description: We are establishing a medium-throughput crystallization facility for biological macromolecules as a central technology platform. We are looking for a scientific leader of the facility, to both run the platform and organize the user support. The successful candidate is an expert in protein biochemistry with a profound knowledge in recombinant protein expression, purification, and crystallization. Experience in X-ray crystallography and/or automation would be an advantage. Prerequisites: PhD or equivalent, basic knowledge in German Please submit: CV, 2 letters of reference until July 20 Contact: Prof. Dr. Irmgard Sinning Address: Heidelberg University Biochemistry Center (BZH), INF328, D-69120 Heidelberg, Germany. Email: irmi.sinning(at)bzh.uni-heidelberg.de, Phone: +49 6221 544780 Dr. Gebhard F. X. Schertler Senior Scientist and Group Leader MRC Laboratory of Molecular Biology Cambridge CB2 2QH tel 0044 1223 402328 e-mail [EMAIL PROTECTED] web http://www2.mrc-lmb.cam.ac.uk/SS/Schertler_G/
Re: [ccp4bb] Save image in Postscript format from PYMOL
Hi, Stefan Your advice is wonderful! This is the easiest way!! Thank you very much!!! Jiahai On 6/22/07, Stefan schmelz [EMAIL PROTECTED] wrote: Hi Jiahai, there is an easy way to move labels in pymol. You have to change your Mouse Mode from 3-Button Viewing to 3-Button Editing. Than your able to drag the labels by pressing CTRL and using your left mouse button (both has to be pressed). But be careful not changing your molecule :-)!! Stefan shi jiahai wrote: Hi, Julie, Thank you very much for your kindly reply! But it seems this function can not set the individual label position. For example, one label is set at ( 2, 1,-0.5) while another label is set at (1, 2, 3). Is there a way to set the label position one by one? Your help is highly appreciated Thank you very much! Jiahai On 6/22/07, *Julie Bouckaert * [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Pymol version 0.99 has the option to set the label position, similar to eg. molscript. Go to Select - Edit all - scroll down to label-offset - edit the x,y,z parameters. Pymol version 0.98 does not have this option. Julie. shi jiahai wrote: Hi, all I am drawing some stereo images with label by PYMOL. But the label interfere with protein. I try to output to Postscript format so that I can change the position of label. However, I can't output the image to Postscript format in Pymol. Is there anyboy know how to save image in Postscript format from PYMOL? Your help would be appreciated. Thank you very much! Shi Jiahai Dept of Biological Sciences National University of Singapore -- Julie Bouckaert, PhD[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] VIB Project leader VIB Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel Tel. 32-2-629-1988 Fax 32-2-6291963 ULTR, Building E 4.18 Vrije Universiteit Brussel Pleinlaan 2 1050 Brussel Belgium -- Best Regards, Shi Jiahai -- Best Regards, Shi Jiahai
[ccp4bb] How to replace 2.45M K/Na phosphate buffer
Dear list, I've crystals in a condition including 2,45 M K/Na phosphate buffer for the well condition, and 1 microl protein + 0.8 microl Na/K phosphate buffer + 0.25 microl 30% 1,6-hexanediol in the drop condition. These crystals dissolve in several cryoprotectant solutions and survive only in malonic acid, with which they give diffraction at 7-8 A. Among the several different possibilities, I'd like to try to optimize the crystals, and one possiblity among others would be to change the buffer. Any suggestions, please, about how to replace K/Na phosphate? At these concentrations it is acting as a buffer but also as a precipitant and I was wondering if anybody has experienced nice buffer-salt combinations that proved to be useful starting from a similar condition. Thanks a lot, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _ Make every IM count. Download Windows Live Messenger and join the i’m Initiative now. It’s free. http://im.live.com/messenger/im/home/?source=TAGWL_June07
Re: [ccp4bb] How to replace 2.45M K/Na phosphate buffer - 2
Dear Claudia, These crystals dissolve in several cryoprotectant solutions and survive only in malonic acid, with which they give diffraction at 7-8 A. You do not mention what the room temperature diffraction is like. If you have not tested it already, you should do so - even without malonate, you might only get 7-8A diffraction. Assuming the room-temp diffraction is OK, you could just try increasing the concentration of phosphate buffer - high salt can also act as a cryoprotectant. James Dr. James Murray Biochemistry Building Department of Biological Sciences Imperial College London London, SW7 2AZ Tel: +44 (0)20 7594 5276 -Original Message- From: CCP4 bulletin board on behalf of Claudia Scotti Sent: Fri 22/06/2007 13:42 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] How to replace 2.45M K/Na phosphate buffer - 2 Sorry: forgotten the pH: the crystals grow between pH 6.5 and 6.7. Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 Date: Fri, 22 Jun 2007 14:15:47 +0200 From: [EMAIL PROTECTED] Subject: [ccp4bb] How to replace 2.45M K/Na phosphate buffer To: CCP4BB@JISCMAIL.AC.UK Dear list, I've crystals in a condition including 2,45 M K/Na phosphate buffer for the well condition, and 1 microl protein + 0.8 microl Na/K phosphate buffer + 0.25 microl 30% 1,6-hexanediol in the drop condition. These crystals dissolve in several cryoprotectant solutions and survive only in malonic acid, with which they give diffraction at 7-8 A. Among the several different possibilities, I'd like to try to optimize the crystals, and one possiblity among others would be to change the buffer. Any suggestions, please, about how to replace K/Na phosphate? At these concentrations it is acting as a buffer but also as a precipitant and I was wondering if anybody has experienced nice buffer-salt combinations that proved to be useful starting from a similar condition. Thanks a lot, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _ Make every IM count. Download Windows Live Messenger and join the i'm Initiative now. It's free. http://im.live.com/messenger/im/home/?source=TAGWL_June07 _ Make every IM count. Download Windows Live Messenger and join the i'm Initiative now. It's free. http://im.live.com/messenger/im/home/?source=TAGWL_June07
Re: [ccp4bb] How to replace 2.45M K/Na phosphate buffer - 2
at around 4 molar P-buffer freezes clean. Best wishes Kornelius On Fri, 22 Jun 2007 14:42:00 +0200 Claudia Scotti [EMAIL PROTECTED] wrote: Sorry: forgotten the pH: the crystals grow between pH 6.5 and 6.7. Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 Date: Fri, 22 Jun 2007 14:15:47 +0200 From: [EMAIL PROTECTED] Subject: [ccp4bb] How to replace 2.45M K/Na phosphate buffer To: CCP4BB@JISCMAIL.AC.UK Dear list, I've crystals in a condition including 2,45 M K/Na phosphate buffer for the well condition, and 1 microl protein + 0.8 microl Na/K phosphate buffer + 0.25 microl 30% 1,6-hexanediol in the drop condition. These crystals dissolve in several cryoprotectant solutions and survive only in malonic acid, with which they give diffraction at 7-8 A. Among the several different possibilities, I'd like to try to optimize the crystals, and one possiblity among others would be to change the buffer. Any suggestions, please, about how to replace K/Na phosphate? At these concentrations it is acting as a buffer but also as a precipitant and I was wondering if anybody has experienced nice buffer-salt combinations that proved to be useful starting from a similar condition. Thanks a lot, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _ Make every IM count. Download Windows Live Messenger and join the i’m Initiative now. It’s free. http://im.live.com/messenger/im/home/?source=TAGWL_June07 _ Make every IM count. Download Windows Live Messenger and join the i’m Initiative now. It’s free. http://im.live.com/messenger/im/home/?source=TAGWL_June07 -- Kornelius Zeth Max Planck Institute for Developmental Biology Dept. Protein Evolution Spemannstr. 35 72076 Tuebingen, Germany [EMAIL PROTECTED] Tel -49 7071 601 323 Fax -49 7071 601 349
[ccp4bb] Molscript and symbolic label
Hi I would appreciate knowing how to make label of symbolic letters like alpha, beta, pi etc. using molscript. Thanks. Sam _ Make every IM count. Download Windows Live Messenger and join the i’m Initiative now. It’s free. http://im.live.com/messenger/im/home/?source=TAGWL_June07
[ccp4bb] [Fwd: Re: [ccp4bb] Flat Screen and Stereo]
Adding the following commands to my xorg.conf file fixed my problem: Section Extensions Option Composite Disable EndSection The screen now makes an attempt to run stereo: it will draw two sets of lines and the eDimensional glasses now work. But the flickering is unbearable to look at for any length of time even though the 3D effect is noticeable. It seems that there are several possible sources of this new problem: 1) asynchrony between the glasses and the monitor refresh rate [unlikely] 2) problems due to the way flat screens adjust (not all-at-once, as pointed out to me by another respondent) 3) simply too slow of a refresh rate. ( i can try to force maximum refresh rate) I am going to tool around with numbers 1 and 3 to see if I can get a halfway decent stereo effect. If i get anything to work I will post again. In the meantime, I'll try to avoid the slightly nauseating effects of the flickering. thank you for the many (and prompt!) responses to my problem, best zach cp ---BeginMessage--- Hi Zach, I think you need to add: Section Extensions Option Composite Disable EndSection to your xorg.conf file. The driver cannot do stereo with the composite extensions enabled. Steve Zach Powers wrote: Hello, I have been having a problem getting stereo to work on the lab's new flatsceeen ( i know, i know. CRTs = much better but i think the purchaser was overcome with flatscreen lust). I am using a Dell 3007WFP (2560x 1600, refresh rate = 60hz) attached to nVidia Quadro FX 4500 graphics card with the eDimensional stereo glasses. I am using the current drivers from livna (100.14.09-2lvn7) on a Fedora7 box with the 2.6.21_1.3228 kernel. When I try to get Pymol or Coot to use stereo, no luck: Coot tells me that the hardware does not support quad buffered stereo. To the best of my knowledge I have the xorg.conf file correctly configured (see below) and I am wondering if anyone has run into these problems before or if somehow the livna driver can detect a refresh rate that is suboptimal and therefore refuse to start stereo. Perhaps there is also the issue of the kernel? I don't know, but I would appreciate any help. Below is my xorg.conf file and you can see I have 'Option Stereo' set to 3. I have fiddled around with many of the options in the xorg.conf file - basically trying every variation that i found other people had used. However, still no luck, which makes me think there may be some driver or kernel issue. Anyhow, any suggestions would be greatly appreciated (I would like to get this monitor work before falling back on a CRT - if the flicker is terrible, there will be no choice but it seems others have been using these monitors for stereo). thank you, zach charlop-powers PhD Candidate Graduate School of Biological Sciences Mount Sinai School of Medicine New York, NY ### Xorg configuration created by livna-config-display Section ServerLayout Identifier single head configuration Screen 0 Screen0 0 0 InputDeviceKeyboard0 CoreKeyboard EndSection Section Files ModulePath /usr/lib64/xorg/modules/extensions/nvidia ModulePath /usr/lib64/xorg/modules EndSection Section Module Load dbe Load extmod Load glx Load dbe Load extmod EndSection Section InputDevice Identifier Keyboard0 Driver kbd Option XkbModel pc105 Option XkbLayout us EndSection Section Monitor Identifier Monitor0 ModelNameDell 3007WFP HorizSync30.0 - 100.0 VertRefresh 56.0 - 76.0 Option dpms EndSection Section Device Identifier Videocard0 Driver nvidia Option Stereo 3 Option AllowDFPStereo 1 Option UBB True Option AddARGBGLXVisuals True Option DisableGLXRootClipping True EndSection Section Screen Identifier Screen0 Device Videocard0 MonitorMonitor0 DefaultDepth 24 SubSection Display Viewport 0 0 Depth 24 Modes2560x1600 1600x1200 1600x1024 1440x900 1400x1050 1280x1024 1280x960 1280x800 1152x864 1024x768 800x600 640x480 640x400 EndSubSection EndSection -- Steven Stayrook, Ph.D. Assistant Director Johnson Research Foundation Senior Research Investigator Department of Biochemistry and Biophysics 423 Guardian Blvd. G11 Blockley Hall University of Pennsylvania School of Medicine Philadelphia, Pa. 19104 e-mail: [EMAIL PROTECTED] Phone: 215-573-9968 fax:215-573-2503 ---End Message---
Re: [ccp4bb] Flat Screen and Stereo
Rather strangely my stereo set uses the following Option AllowDFPStereo on I look forward to hearing how you get on as all my past experience with stereo and LCD screens was less than positive Hope this helps Mike -Original Message- From: CCP4 bulletin board on behalf of James M. Vergis Sent: Fri 22/06/2007 17:10 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Flat Screen and Stereo I don't know if this will help but the NVIDIA readme says it should be a BOOLEAN after ALLOWDFPSTEREO. You have: OptionAllowDFPStereo 1 Change to:OptionAllowDFPStereo true Hope that helps. I'd be curious as to how an LCD works for stereo. Good luck, James James M. Vergis, Ph.D. University of Virginia Molecular Physiology and Biological Physics MKWEINR 438 Jordan Hall 1340 Jefferson Park Ave Charlottesville, VA 22908-0736 phone: 434-243-2730 FAX: 434-982-1616 [EMAIL PROTECTED] -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Zach Powers Sent: Friday, June 22, 2007 11:38 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Flat Screen and Stereo Hello, I have been having a problem getting stereo to work on the lab's new flatsceeen ( i know, i know. CRTs = much better but i think the purchaser was overcome with flatscreen lust). I am using a Dell 3007WFP (2560x 1600, refresh rate = 60hz) attached to nVidia Quadro FX 4500 graphics card with the eDimensional stereo glasses. I am using the current drivers from livna (100.14.09-2lvn7) on a Fedora7 box with the 2.6.21_1.3228 kernel. When I try to get Pymol or Coot to use stereo, no luck: Coot tells me that the hardware does not support quad buffered stereo. To the best of my knowledge I have the xorg.conf file correctly configured (see below) and I am wondering if anyone has run into these problems before or if somehow the livna driver can detect a refresh rate that is suboptimal and therefore refuse to start stereo. Perhaps there is also the issue of the kernel? I don't know, but I would appreciate any help. Below is my xorg.conf file and you can see I have 'Option Stereo' set to 3. I have fiddled around with many of the options in the xorg.conf file - basically trying every variation that i found other people had used. However, still no luck, which makes me think there may be some driver or kernel issue. Anyhow, any suggestions would be greatly appreciated (I would like to get this monitor work before falling back on a CRT - if the flicker is terrible, there will be no choice but it seems others have been using these monitors for stereo). thank you, zach charlop-powers PhD Candidate Graduate School of Biological Sciences Mount Sinai School of Medicine New York, NY ### Xorg configuration created by livna-config-display Section ServerLayout Identifier single head configuration Screen 0 Screen0 0 0 InputDeviceKeyboard0 CoreKeyboard EndSection Section Files ModulePath /usr/lib64/xorg/modules/extensions/nvidia ModulePath /usr/lib64/xorg/modules EndSection Section Module Load dbe Load extmod Load glx Load dbe Load extmod EndSection Section InputDevice Identifier Keyboard0 Driver kbd Option XkbModel pc105 Option XkbLayout us EndSection Section Monitor Identifier Monitor0 ModelNameDell 3007WFP HorizSync30.0 - 100.0 VertRefresh 56.0 - 76.0 Option dpms EndSection Section Device Identifier Videocard0 Driver nvidia Option Stereo 3 Option AllowDFPStereo 1 Option UBB True Option AddARGBGLXVisuals True Option DisableGLXRootClipping True EndSection Section Screen Identifier Screen0 Device Videocard0 MonitorMonitor0 DefaultDepth 24 SubSection Display Viewport 0 0 Depth 24 Modes2560x1600 1600x1200 1600x1024 1440x900 1400x1050 1280x1024 1280x960 1280x800 1152x864 1024x768 800x600 640x480 640x400 EndSubSection EndSection DIVFONT size=1 color=grayThis e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any
[ccp4bb] model building and hardware (tangent)
this post is is tangential to the model building/hardware thread - anything useful presented here is purely coincidental: tangible model building action shot: http://puffer.tamu.edu/cs_computer.htm [slide all the way to the right] http://www.bassictech.com/blogs/bassictech_news_blog/archive/2007/01/20/remapping-the-universe-using-this-gui.aspx [a protein model makes an appearance around 2:26] articulated model project : http://mgl.scripps.edu/projects the sensetable - for good measure: http://tangible.media.mit.edu/projects/sensetable/ -bryan
Re: [ccp4bb] Flat Screen and Stereo
I don't know if this will help but the NVIDIA readme says it should be a BOOLEAN after ALLOWDFPSTEREO. You have: OptionAllowDFPStereo 1 Change to:OptionAllowDFPStereo true Hope that helps. I'd be curious as to how an LCD works for stereo. Good luck, James James M. Vergis, Ph.D. University of Virginia Molecular Physiology and Biological Physics MKWEINR 438 Jordan Hall 1340 Jefferson Park Ave Charlottesville, VA 22908-0736 phone: 434-243-2730 FAX: 434-982-1616 [EMAIL PROTECTED] -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Zach Powers Sent: Friday, June 22, 2007 11:38 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Flat Screen and Stereo Hello, I have been having a problem getting stereo to work on the lab's new flatsceeen ( i know, i know. CRTs = much better but i think the purchaser was overcome with flatscreen lust). I am using a Dell 3007WFP (2560x 1600, refresh rate = 60hz) attached to nVidia Quadro FX 4500 graphics card with the eDimensional stereo glasses. I am using the current drivers from livna (100.14.09-2lvn7) on a Fedora7 box with the 2.6.21_1.3228 kernel. When I try to get Pymol or Coot to use stereo, no luck: Coot tells me that the hardware does not support quad buffered stereo. To the best of my knowledge I have the xorg.conf file correctly configured (see below) and I am wondering if anyone has run into these problems before or if somehow the livna driver can detect a refresh rate that is suboptimal and therefore refuse to start stereo. Perhaps there is also the issue of the kernel? I don't know, but I would appreciate any help. Below is my xorg.conf file and you can see I have 'Option Stereo' set to 3. I have fiddled around with many of the options in the xorg.conf file - basically trying every variation that i found other people had used. However, still no luck, which makes me think there may be some driver or kernel issue. Anyhow, any suggestions would be greatly appreciated (I would like to get this monitor work before falling back on a CRT - if the flicker is terrible, there will be no choice but it seems others have been using these monitors for stereo). thank you, zach charlop-powers PhD Candidate Graduate School of Biological Sciences Mount Sinai School of Medicine New York, NY ### Xorg configuration created by livna-config-display Section ServerLayout Identifier single head configuration Screen 0 Screen0 0 0 InputDeviceKeyboard0 CoreKeyboard EndSection Section Files ModulePath /usr/lib64/xorg/modules/extensions/nvidia ModulePath /usr/lib64/xorg/modules EndSection Section Module Load dbe Load extmod Load glx Load dbe Load extmod EndSection Section InputDevice Identifier Keyboard0 Driver kbd Option XkbModel pc105 Option XkbLayout us EndSection Section Monitor Identifier Monitor0 ModelNameDell 3007WFP HorizSync30.0 - 100.0 VertRefresh 56.0 - 76.0 Option dpms EndSection Section Device Identifier Videocard0 Driver nvidia Option Stereo 3 Option AllowDFPStereo 1 Option UBB True Option AddARGBGLXVisuals True Option DisableGLXRootClipping True EndSection Section Screen Identifier Screen0 Device Videocard0 MonitorMonitor0 DefaultDepth 24 SubSection Display Viewport 0 0 Depth 24 Modes2560x1600 1600x1200 1600x1024 1440x900 1400x1050 1280x1024 1280x960 1280x800 1152x864 1024x768 800x600 640x480 640x400 EndSubSection EndSection
[ccp4bb] POST DOCTORAL POSITION IN STRUCTURAL ENZYMOLOGY AND INHIBITOR DESIGN
** POST DOCTORAL POSITION IN STRUCTURAL ENZYMOLOGY AND INHIBITOR DESIGN ** A post doctoral position is available immediately in the laboratories of Vern Schramm and Steve Almo in the Department of Biochemistry at the Albert Einstein College of Medicine. This program utilizes high resolution crystallographic analysis and kinetic isotope effects to define the fundamental chemical and physical determinants of enzymatic rate enhancement, and to design highly specific transition state analogs with affinities in the nM and pM ranges. These efforts are focused on the enzymes involved in nucleotide metabolism in bacterial, fungal and mammalian organisms and have produced a number of therapeutic leads that are currently being utilized in animal studies and clinical trials for malaria, T cell lymphoma and autoimmunity. The successful applicant must have extensive experience in all aspects of high resolution protein crystallography and a strong desire to complement these skills with mechanistic enzymology and state-of-the-art transition state analysis, with an overall goal of developing new therapeutic approaches. Representative publications describing this program include: Fedorov, et al. (2001) Transition state structure of purine nucleoside phosphorylase and principles of atomic motion in enzymatic catalysis. Biochemistry 40(4):853-60. Lewandowicz, et al. (2003) Over-the-barrier transition state analogues and crystal structure with Mycobacterium tuberculosis purine nucleoside phosphorylase. Biochemistry 42(20):6057-66. Singh, et al. (2004) Picomolar transition state analogue inhibitors of human 5'-methylthioadenosine phosphorylase and X-ray structure with MT-immucillin-A. Biochemistry 43(1):9-18. Kim, et al. (2006) Structural and kinetic characterization of Escherichia coli TadA, the wobble-specific tRNA deaminase. Biochemistry 45(20):6407-16. Singh, et al. (2006) Structure and inhibition of a quorum sensing target from Streptococcus pneumoniae. Biochemistry 45(43):12929-41. Murkin, et al. (2007) Neighboring group participation in the transition state of human purine nucleoside phosphorylase. Biochemistry 46(17):5038-49. Albert Einstein provides an outstanding scientific environment that includes considerable strengths in microbiology, immunology, cancer biology, mechanistic enzymology, biophysics, computational biology and structural genomics. Close proximity to the National Synchrotron Light Source at Brookhaven National Laboratory ensures extensive and sustained access to several bending magnet and insertion device beamlines. This position affords the successful applicant with the opportunity to exploit their expertise in structural biology within the context of a strong biological program focused on inhibitor and therapeutic development. Interested applicants should provide a CV and arrange for three letter of reference to be sent directly to [EMAIL PROTECTED]
Re: [ccp4bb] Ligand fitting in COOT and SHELX refinement
You can use SHELXPRO to generate ligand restraints, reading in the ligand from the CSD or as a SHELX file (which if necessary can be generated from a PDB file using SHELXPRO). You may have to add some extra restraints by hand (e.g. FLAT, CHIV). 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 On Fri, 22 Jun 2007, U Sam wrote: Hi I would like to know following issue for a ligand. A ligand of a long alkyl chain can have multiple conformation. In coot in order to fit any protein residues into difference Density, we can select a specific rotamer conformation and refine. For fitting ligand of above kind, how does it work out. Taking the PDB with ligand when we go to refine in SHELX, how restraints like (DFIX, DANG etc) are mentioned for such kind of ligand which can have multiple conformation (particularly for the long alkyl chain) and during refinement values can deviate a lot from a particular value taken from the literature. I appreciate suggestion and comments. Many Thanks Sam _ With Windows Live Hotmail, you can personalize your inbox with your favorite color. www.windowslive-hotmail.com/learnmore/personalize.html?locale=en-usocid=TXT_TAGLM_HMWL_reten_addcolor_0607
[ccp4bb] Suse 10.2 install problem
Hi, I installed ccp4 (along with others such as coot) on Suse 10.2. Everything seemed to go well at first. The gui pops up normally. But when I try to run a process the gui shows the process as starting and it hangs there never switching to running. And there is no log file available in the gui as well. Any ideas? Thanks, John Bruning
