[ccp4bb] Offtopic - In vitro protein interaction analysis using Diazirine crosslinkers.
Apologies for an off topic question. I was hoping for some advice regarding the use of sulfo-NHS diazirine crosslinker (Pierce linkhttp://www.piercenet.com/products/Browse.cfm?fldID=DB013E61-5056-8A76-4EC4-473A6F2468A1) for in vitro protein interaction analysis. Have tried labeling the protein (9kDa, 10 to 20uM conc) with 2 primary amines using 30-40X excess Sulfo-NHS-Diazirine crosslinker in PBS (1hour at 4deg). Have tried other concentration combination as well, but this ratio yields some usable material. However, majority of the protein crashes out of solution. Was wondering if anyone has any suggestions in optimizing the yield of crosslinker labelled protein? Thanks in advance. -- Rohan Agashe
[ccp4bb] FW: Refmac5: Open failed: Unit: 7, File: /tmp/refmac-nm_temp1.21850_new.crd
Hello, I am working with refmac-nm code derived from refmac5 and I am encountering an error below [...] Open failed: Unit: 7, File: /tmp/refmac-nm_temp1.21850_new.crd (logical: /tmp/refmac-nm_temp1.21850_new.crd) BFONT COLOR=#FF!--SUMMARY_BEGIN-- Refmac_5.2.0019: Open failed: File: /tmp/refmac-nm_temp1.21850_new.crd [...] It is apparently very similar to bug#1004 reported on 14/01/2005 (see below) for which proposed solution was to make sure that there is CRYST1 line in the PDB file. In my case this line is present in the PDB file, but I am still getting this error. Any other possible reasons for this problem? Any help will be appreciated. Best regards, Ryszard Ryszard Czerminski AstraZeneca Pharmaceuticals LP 35 Gatehouse Drive Waltham, MA 02451 USA 781-839-4304 ryszard.czermin...@astrazeneca.com Refmac fails to open temporary file when generating new dictionary from PDB file Date : 14/01/2005 CCP4 Version : 5.0.2 and earlier System : all Level : minor Status : workaround Bugzilla number : #1004 Refmac may fail with an error message of the form: Open failed: Unit: 7, File: /scratch/rb84480/refmac5_temp1.36145_new.crd (logical: /scratch/rb84480/refmac5_temp1.36145_new.crd) Last system error message: No such file or directory Refmac_5.2.0005: Open failed: File: /scratch/rb84480/refmac5_temp1.36145_new.crd This can happen when the input PDB file doesn't contain cell or spacegroup information - this information is now compulsory and should be supplied on the CRYST1 line in the PDB file. To confirm whether this is the case check the Refmac output for a line of the form: === Warning: Input coordinate file does not have CRYST card If so then the workaround is to make sure that you add the cell and spacegroup information into the file. In future versions of Refmac the absence of this information will be a fatal error. -- Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.
[ccp4bb] Special position refinement
Dear all, we have seen again with the 5.5.0102 version that water O or Fe ion are not held on the crystallographic axis automatically. What should we do except using possibly the restrain keyword? Jan Dohnalek -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
[ccp4bb] Offtopic - In vitro protein interaction analysis using Diazirine crosslinkers.
Apologies for an off topic question. I was hoping for some advice regarding the use of sulfo-NHS diazirine crosslinker (Pierce linkhttp://www.piercenet.com/products/Browse.cfm?fldID=DB013E61-5056-8A76-4EC4-473A6F2468A1) for in vitro protein interaction analysis. Have tried labeling the protein (9kDa, 10 to 20uM conc) with 2 primary amines using 30-40X excess Sulfo-NHS-Diazirine crosslinker in PBS (1hour at 4deg). Have tried other concentration combination as well, but this ratio yields some usable material. However, majority of the protein crashes out of solution. Was wondering if anyone has any suggestions in optimizing the yield of crosslinker labelled protein? Thanks in advance. -- Rohan Agashe
[ccp4bb] Offtopic - In vitro protein interaction analysis using Diazirine crosslinkers.
Apologies for an off topic question. I was hoping for some advice regarding the use of sulfo-NHS diazirine crosslinker (Pierce - http://www.piercenet.com/products/Browse.cfm?fldID=DB013E61-5056-8A76-4EC4-473A6F2468A1) for in vitro protein interaction analysis. Have tried labeling the protein (9kDa, 10 to 20uM conc) with 2 primary amines using 30-40X excess Sulfo-NHS-Diazirine crosslinker in PBS (1hour at 4deg). Have tried other concentration combination as well, but this ratio yields some usable material. However, majority of the protein crashes out of solution. Was wondering if anyone has any suggestions in optimizing the yield of crosslinker labelled protein? Thanks in advance. regards, Rohan Agashe
[ccp4bb] Off topic - nickel magnetic beads
Hi all, I'm looking at getting some nickel magnetic beads. I've never used them before, and they seem pretty expensive. Does anyone know of a good inexpensive supplier? Thanks in advance for any replies! _ Bing brings you maps, menus, and reviews organized in one place. http://www.bing.com/search?q=restaurantsform=MFESRPpubl=WLHMTAGcrea=TEXT_MFESRP_Local_MapsMenu_Resturants_1x1
[ccp4bb] Zalman monitor on Linux and Coot
Hello everyone, Sorry for a non-CCP4 related question again. Can anyone let me know how to make stereo work on linux with Zalman monitor with Coot? Is it as simple as what we do with CRT monitors? Or do we need something else? We presently use CRT monitors on a Quadro FX 4600 graphics card. I would like to move to LCDs. Thanks for all inputs Ajit B.
Re: [ccp4bb] Zalman monitor on Linux and Coot
Hi Ajit; One of our CRT monitors broke recently, and in the context of bemoaning the loss to a friend I was told that LCD monitors will not work for stereo viewing. I understood the reason to be related to the difference in refresh rates (?), with LCD's not being fast enough so that the viewer is left seeing ghosts. The effect, which I have not seen first hand, was described to me as capable of making most hapless stereo viewers very ill, very fast. I would encourage you to plumb the depths of knowledge on this subject further, but that is my simple understanding. Best wishes~ ~Justin Quoting Ajit Datta adat...@jhmi.edu: Hello everyone, Sorry for a non-CCP4 related question again. Can anyone let me know how to make stereo work on linux with Zalman monitor with Coot? Is it as simple as what we do with CRT monitors? Or do we need something else? We presently use CRT monitors on a Quadro FX 4600 graphics card. I would like to move to LCDs. Thanks for all inputs Ajit B.
Re: [ccp4bb] Zalman monitor on Linux and Coot
Rubbish, excuse my English :-) I have four Zalman's running in stereo although I have to confess they're all running on various Macs (MacBook Pro, Mac Mini, MacPro) under 10.5 or 10.6. I have no clue if the Zalman runs under linux. Regarding the stereo effect it is superior than conventional CRT with shutter glasses. My 5 cents, Jürgen On Nov 4, 2009, at 1:26 PM, Justin Hall wrote: Hi Ajit; One of our CRT monitors broke recently, and in the context of bemoaning the loss to a friend I was told that LCD monitors will not work for stereo viewing. I understood the reason to be related to the difference in refresh rates (?), with LCD's not being fast enough so that the viewer is left seeing ghosts. The effect, which I have not seen first hand, was described to me as capable of making most hapless stereo viewers very ill, very fast. I would encourage you to plumb the depths of knowledge on this subject further, but that is my simple understanding. Best wishes~ ~Justin Quoting Ajit Datta adat...@jhmi.edu: Hello everyone, Sorry for a non-CCP4 related question again. Can anyone let me know how to make stereo work on linux with Zalman monitor with Coot? Is it as simple as what we do with CRT monitors? Or do we need something else? We presently use CRT monitors on a Quadro FX 4600 graphics card. I would like to move to LCDs. Thanks for all inputs Ajit B. - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
Re: [ccp4bb] Zalman monitor on Linux and Coot
The Zalman defeats these with a very smart trick. We got out first one, and it's really very good, albeit not perfect in some details. Pymol and Coot worked just like that with it. Sent from my iPhone On 4 Nov 2009, at 19:26, Justin Hall hallj...@onid.orst.edu wrote: Hi Ajit; One of our CRT monitors broke recently, and in the context of bemoaning the loss to a friend I was told that LCD monitors will not work for stereo viewing. I understood the reason to be related to the difference in refresh rates (?), with LCD's not being fast enough so that the viewer is left seeing ghosts. The effect, which I have not seen first hand, was described to me as capable of making most hapless stereo viewers very ill, very fast. I would encourage you to plumb the depths of knowledge on this subject further, but that is my simple understanding. Best wishes~ ~Justin Quoting Ajit Datta adat...@jhmi.edu: Hello everyone, Sorry for a non-CCP4 related question again. Can anyone let me know how to make stereo work on linux with Zalman monitor with Coot? Is it as simple as what we do with CRT monitors? Or do we need something else? We presently use CRT monitors on a Quadro FX 4600 graphics card. I would like to move to LCDs. Thanks for all inputs Ajit B.
Re: [ccp4bb] Zalman monitor on Linux and Coot
I can personally verify that the new Nvidia 3D Vision system on 120 Hz LCD monitors and a Nvidia Quadro FX Video Card display stereo flawlessly in Pymol, Wincoot, UCSD Chimerica, and any other application that uses OpenGL or Direct3D as its display media within both Windows Vista and Windows 7 (Nvidia documentation says it will also work in Windows XP, but I have not tested this). This will not work in any Linux distributions yet (as far as I am aware), but here's to hoping they develop the drivers soon. Here are a few links: 1. Nvidia 3D Vision Webpage: http://www.nvidia.com/object/3D_Vision_Overview.html 2. Nvidia 3D Vision and QuadroFX Video Cards: http://www.nvidia.com/object/quadro_pro_graphics_boards.html Cheers, Jim On Wed, Nov 4, 2009 at 10:26 AM, Justin Hall hallj...@onid.orst.edu wrote: Hi Ajit; One of our CRT monitors broke recently, and in the context of bemoaning the loss to a friend I was told that LCD monitors will not work for stereo viewing. I understood the reason to be related to the difference in refresh rates (?), with LCD's not being fast enough so that the viewer is left seeing ghosts. The effect, which I have not seen first hand, was described to me as capable of making most hapless stereo viewers very ill, very fast. I would encourage you to plumb the depths of knowledge on this subject further, but that is my simple understanding. Best wishes~ ~Justin Quoting Ajit Datta adat...@jhmi.edu: Hello everyone, Sorry for a non-CCP4 related question again. Can anyone let me know how to make stereo work on linux with Zalman monitor with Coot? Is it as simple as what we do with CRT monitors? Or do we need something else? We presently use CRT monitors on a Quadro FX 4600 graphics card. I would like to move to LCDs. Thanks for all inputs Ajit B. -- Jim Fairman, Ph D. Post-Doctoral Fellow National Institutes of Health - NIDDK Cell: 1-866-748-8672 Lab: 1-301-594-9230 E-mail: fairman@gmail.com james.fair...@nih.gov
Re: [ccp4bb] Zalman monitor on Linux and Coot
Thanks to everyone for the info on Zalman monitors, sorry to have muddied the waters for you Ajit. Best wishes~ ~Justin Quoting Justin Hall hallj...@onid.orst.edu: Hi Ajit; One of our CRT monitors broke recently, and in the context of bemoaning the loss to a friend I was told that LCD monitors will not work for stereo viewing. I understood the reason to be related to the difference in refresh rates (?), with LCD's not being fast enough so that the viewer is left seeing ghosts. The effect, which I have not seen first hand, was described to me as capable of making most hapless stereo viewers very ill, very fast. I would encourage you to plumb the depths of knowledge on this subject further, but that is my simple understanding. Best wishes~ ~Justin Quoting Ajit Datta adat...@jhmi.edu: Hello everyone, Sorry for a non-CCP4 related question again. Can anyone let me know how to make stereo work on linux with Zalman monitor with Coot? Is it as simple as what we do with CRT monitors? Or do we need something else? We presently use CRT monitors on a Quadro FX 4600 graphics card. I would like to move to LCDs. Thanks for all inputs Ajit B.
Re: [ccp4bb] Zalman monitor on Linux and Coot
I should add that I have only seen Joel Bard's Zalman monitor briefly. We tweaked the settings a bit to improve the representation in the following way: 1) use nvidia-settings to override application anti-aliasing - crank it up to 16x if you have a good graphics card 2) add to ~/.coot file (or otherwise initialise coot with): (set-map-line-width 2) After that, it looked quite good (I thought). For the record, I do not think that Coot questions are off-topic on ccp4bb. Having said that, you might like to fine-tune your audience by posting to the Coot list (see the Coot Web page for details). Paul. Anastassis Perrakis wrote: The Zalman defeats these with a very smart trick. We got out first one, and it's really very good, albeit not perfect in some details. Pymol and Coot worked just like that with it. Sent from my iPhone On 4 Nov 2009, at 19:26, Justin Hall hallj...@onid.orst.edu wrote: Hi Ajit; One of our CRT monitors broke recently, and in the context of bemoaning the loss to a friend I was told that LCD monitors will not work for stereo viewing. I understood the reason to be related to the difference in refresh rates (?), with LCD's not being fast enough so that the viewer is left seeing ghosts. The effect, which I have not seen first hand, was described to me as capable of making most hapless stereo viewers very ill, very fast. I would encourage you to plumb the depths of knowledge on this subject further, but that is my simple understanding. Best wishes~ ~Justin Quoting Ajit Datta adat...@jhmi.edu: Hello everyone, Sorry for a non-CCP4 related question again. Can anyone let me know how to make stereo work on linux with Zalman monitor with Coot? Is it as simple as what we do with CRT monitors? Or do we need something else? We presently use CRT monitors on a Quadro FX 4600 graphics card. I would like to move to LCDs. Thanks for all inputs Ajit B.
[ccp4bb] Index, glossary and errata for BMC
Dear All, as a first step towards building the web resources for my book Biomolecular Crystallography: Principles, Practice and application to Structural Biology I have made publicly available the Index and the Glossary in searchable PDF format. I hope this might help locating contents more quickly and also one or the other definition. More to come later. http://www.ruppweb.org/Garland/ There is also a link to the Errata page for the second printing. If you find anything unclear or plain wrong, please email me. So far I found mostly poor English that escaped us at the proofing stage, so no offense is taken pointing out also unclear phrasing or other poor wording. Thank you for your help. Best, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@qedlife.com bernhardr...@sbcglobal.net http://www.ruppweb.org/ - The hard part about playing chicken is to know when to flinch -
[ccp4bb] map display in pymol
Dear Friends, I can create a mesh in pymol as follows: isomesh 2ffmesh, nov42_001_2mFo-DFc.map, 2.5, sele, carve=1.6, where the 'sele' is a particular residue and the map is created ommiting that residue from the pdb. But, I can't create the mesh in pymol when I am using Fo-Fc map as follows: isomesh ffmesh, nov42_001_mFo-DFc.map, 2.5, sele, carve=1.6 I can see both 2ff and ff maps at that residue in coot. I shall be grateful if someone can help me to solve this problem. Thanks... Raja The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/
