Re: [ccp4bb] can anyone please give the link for downloading the software O
For 'O' just google for alwyn O it takes you quickly to http://xray.bmc.uu.se/alwyn/O_to_Go/O_to_Go_frameset.html which tells you how to get O. I am sure Ghostview is available for nearly all linux distributions and unless you install something like linux-from-scratch (but then you would not ask that question), you can just use your distribution's search tool to install it. For rpm-based ones try something like zypper install ghostview for debian-based ones (like ubuntu) try aptitude search ghostview Let us know which distribution you installed to get a more specific answer! If you do want to install ghostview from scratch, get the source at http://pages.cs.wisc.edu/~ghost/, but I would not recommend you to do so. Cheers, Tim P.S.: There are a lot more comforable postscript-viewers than ghostview, like okular (KDE-based) On Mon, Jan 24, 2011 at 12:12:16PM +0530, Hussain Bhukyagps wrote: Hi All, can anyone please give the link for downloading the software O and Ghostview for linux platform.? Thank you Regards Hussain -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A signature.asc Description: Digital signature
[ccp4bb] Merging statistics and systematic absences
Dear ccp4bb, I had an interesting question from a xia2 user last week for which I did not have a good answer. Here's the situation: - spacegroup is P212121, which was specified on the command-line - xia2 processes this as oP, assigns the spacegroup as P212121 before running scala - generates merging stats - truncate removes systematically absent reflections The end result is that there are fewer reflections in the output MTZ file and hence used for refinement than are reported in the merging statistics. The question is - what is correct? Clearly the effect on the merging statistics will be modest or trivial as there were only ~ 70 absent reflections, however removing them before scaling merging will also be a little fiddly. I see three (or maybe four) options - - truncate leave absent reflections in - remove the absent reflections before scaling - ignore this as situation normal (which is what xia2 currently does) - (less helpful *) refine against intensities which includes the absent reflections but matches the merging statistics If this were my project I would probably opt for #3 but I can appreciate that this is a question for the wider audience. What do others think? Many thanks in advance, Graeme * I mark this as less helpful because this is the wrong *reason* to merge against intensities. There are clearly good reasons for this.
Re: [ccp4bb] Merging statistics and systematic absences
My immediate response to this is that anyone worrying about the number of reflections should get out more. More seriously, is assessing the quality of measurements then multiple observed measurements of systematically absent reflections should agree within their error estimates and (ideally) have a mean = 0.0, thus it seems valid to include them in measures of internal consistency such as Rmerge, Rmeas (strictly they should be compared to 0 rather than their mean Ih), i suppose) On the other hand, in looking at intensity statistics (as in truncate) the observed intensities should be compared with their expectation values which will depend on the space group (but still included perhaps). However there are so few of these reflections that it won't make much difference (though it is more important to separate centric acentric reflections, as there may be quite a lot of centrics) ie situation normal (SNAFU?) - it is not going to make any difference Phil On 24 Jan 2011, at 09:13, Graeme Winter wrote: Dear ccp4bb, I had an interesting question from a xia2 user last week for which I did not have a good answer. Here's the situation: - spacegroup is P212121, which was specified on the command-line - xia2 processes this as oP, assigns the spacegroup as P212121 before running scala - generates merging stats - truncate removes systematically absent reflections The end result is that there are fewer reflections in the output MTZ file and hence used for refinement than are reported in the merging statistics. The question is - what is correct? Clearly the effect on the merging statistics will be modest or trivial as there were only ~ 70 absent reflections, however removing them before scaling merging will also be a little fiddly. I see three (or maybe four) options - - truncate leave absent reflections in - remove the absent reflections before scaling - ignore this as situation normal (which is what xia2 currently does) - (less helpful *) refine against intensities which includes the absent reflections but matches the merging statistics If this were my project I would probably opt for #3 but I can appreciate that this is a question for the wider audience. What do others think? Many thanks in advance, Graeme * I mark this as less helpful because this is the wrong *reason* to merge against intensities. There are clearly good reasons for this.
Re: [ccp4bb] Merging statistics and systematic absences
I absolutely agree with Phil. However I think it is very important NOT to remove systematic absences before scala. There are many cases of mis-assigned space groups where systematic absences are misleading - due to NC translation or bad measurement or whatever Eleanor On 01/24/2011 09:32 AM, Phil Evans wrote: My immediate response to this is that anyone worrying about the number of reflections should get out more. More seriously, is assessing the quality of measurements then multiple observed measurements of systematically absent reflections should agree within their error estimates and (ideally) have a mean = 0.0, thus it seems valid to include them in measures of internal consistency such as Rmerge, Rmeas (strictly they should be compared to 0 rather than their meanIh), i suppose) On the other hand, in looking at intensity statistics (as in truncate) the observed intensities should be compared with their expectation values which will depend on the space group (but still included perhaps). However there are so few of these reflections that it won't make much difference (though it is more important to separate centric acentric reflections, as there may be quite a lot of centrics) ie situation normal (SNAFU?) - it is not going to make any difference Phil On 24 Jan 2011, at 09:13, Graeme Winter wrote: Dear ccp4bb, I had an interesting question from a xia2 user last week for which I did not have a good answer. Here's the situation: - spacegroup is P212121, which was specified on the command-line - xia2 processes this as oP, assigns the spacegroup as P212121 before running scala - generates merging stats - truncate removes systematically absent reflections The end result is that there are fewer reflections in the output MTZ file and hence used for refinement than are reported in the merging statistics. The question is - what is correct? Clearly the effect on the merging statistics will be modest or trivial as there were only ~ 70 absent reflections, however removing them before scaling merging will also be a little fiddly. I see three (or maybe four) options - - truncate leave absent reflections in - remove the absent reflections before scaling - ignore this as situation normal (which is what xia2 currently does) - (less helpful *) refine against intensities which includes the absent reflections but matches the merging statistics If this were my project I would probably opt for #3 but I can appreciate that this is a question for the wider audience. What do others think? Many thanks in advance, Graeme * I mark this as less helpful because this is the wrong *reason* to merge against intensities. There are clearly good reasons for this.
[ccp4bb] sodium vs water near methionine sulfur
Dear All, Electron density picture is attached here. or https://docs.google.com/leaf?id=0B89uj7DSbtUWNDRmMzZhNTAtMzlkMC00MDllLTgxYmItNDI0NzUwMjdlNTlihl=en I am working on a structure at 1.45 Ang resolution. I have noticed a density that looks like water. However, it is surrounded by by six other atoms in the hexa-coordinate geometry. In addition to three coordinating waters (2.15 Ang, 2.7 ang, 2.85 Ang), side chain carbonyl oxygen atoms of an asparagine (2.5 Ang) and a glutamine (2.25 ang) and a methionine sulfur is at 3.07 Ang from this central atom. Based on this geometry we assume it is a sodium ion. This atom seems to have an occupancy of 0.8 and all the surrounding atoms are fully occupied. Do you think it is a sodium or a water molecule? I would like your help to understand if a sulfursodium interaction is possible. If there are some examples can you kindly suggest me? Thank you Chandan
Re: [ccp4bb] Full-screen stereo with Coot/PyMol/etc on 3D LCD displays?
Hi Amir, I have VMware WindowsXP (guest) running on Centos5 (host) running. Open GL - 3D does not work. VMware emulates the graphics board. VMware 6.5 supports only Direct X. I don't know whether a newer version will do; I doubt. Guenter Hi, Does newer 3-D hardware work using VMWare/Windows on a Mac? Thanks! Amir ___ _ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jim Fairman [fairman@gmail.com] Sent: Monday, January 24, 2011 6:17 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Full-screen stereo with Coot/PyMol/etc on 3D LCD displays? Forgot to mention that this is only for the newer 120 Hz LCDs using the Nvidia 3D Vision system. You'll have to stick with your CRT for now or switch to Linux/Win for the newer hardware. On Mon, Jan 24, 2011 at 1:10 AM, Jim Fairman fairman@gmail.commailto:fairman@gmail.com wrote: Stereoscopic 3D driven by OpenGL via an Nvidia Quadro FX card is only available on Linux and Windows. You'll have to beg the Nvidia gods for drivers for Mac. On Mon, Jan 24, 2011 at 12:56 AM, Luecke, Hartmut hu...@uci.edumailto:hu...@uci.edu wrote: My apologies if this has been discussed before. Has anyone got this to work? Preferably with a Mac? We would love to hear the configuration. Cheers, Hudel Hartmut Luecke Director, Center for Biomembrane Systems Depts. of Biochemistry, Biophysics Computer Science 3205 McGaugh Hall University of California Irvine, CA 92697-3900 hu...@uci.edumailto:hu...@uci.edu http://bass.bio.uci.edu/~hudel/ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. -- Jim Fairman, Ph D. Post-Doctoral Fellow National Institutes of Health - NIDDK The Buchanan Labhttp://www-mslmb.niddk.nih.gov/buchanan/index.html Lab: 1-301-594-9229 E-mail: fairman@gmail.commailto:fairman@gmail.com james.fair...@nih.govmailto:james.fair...@nih.gov -- Jim Fairman, Ph D. Post-Doctoral Fellow National Institutes of Health - NIDDK The Buchanan Labhttp://www-mslmb.niddk.nih.gov/buchanan/index.html Lab: 1-301-594-9229 E-mail: fairman@gmail.commailto:fairman@gmail.com james.fair...@nih.govmailto:james.fair...@nih.gov -- *** Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Universitaet Konstanz http://www.biologie.uni-konstanz.de/fritz e-mail: guenter.fr...@uni-konstanz.de e-mail: guenter.fr...@uniklinik-freiburg.de http://www.uniklinik-freiburg.de/neuropathologie/live/forschung/ag-g-fritz.html Tel.: +49 761 270 5078 Fax.: +49 761 270 5050
Re: [ccp4bb] Full-screen stereo with Coot/PyMol/etc on 3D LCD displays?
No, it requires a native system (Windows/Linux) installed. The graphics drivers installed by VMWare do not emulate the full HW capabilities of the Quadro card. Pedro Matias At 12:36 24-01-2011, Amir Khan wrote: Hi, Does newer 3-D hardware work using VMWare/Windows on a Mac? Thanks! Amir ___ _ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jim Fairman [fairman@gmail.com] Sent: Monday, January 24, 2011 6:17 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Full-screen stereo with Coot/PyMol/etc on 3D LCD displays? Forgot to mention that this is only for the newer 120 Hz LCDs using the Nvidia 3D Vision system. You'll have to stick with your CRT for now or switch to Linux/Win for the newer hardware. On Mon, Jan 24, 2011 at 1:10 AM, Jim Fairman fairman@gmail.commailto:fairman@gmail.com wrote: Stereoscopic 3D driven by OpenGL via an Nvidia Quadro FX card is only available on Linux and Windows. You'll have to beg the Nvidia gods for drivers for Mac. On Mon, Jan 24, 2011 at 12:56 AM, Luecke, Hartmut hu...@uci.edumailto:hu...@uci.edu wrote: My apologies if this has been discussed before. Has anyone got this to work? Preferably with a Mac? We would love to hear the configuration. Cheers, Hudel Hartmut Luecke Director, Center for Biomembrane Systems Depts. of Biochemistry, Biophysics Computer Science 3205 McGaugh Hall University of California Irvine, CA 92697-3900 hu...@uci.edumailto:hu...@uci.edu http://bass.bio.uci.edu/~hudel/ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. -- Jim Fairman, Ph D. Post-Doctoral Fellow National Institutes of Health - NIDDK The Buchanan Labhttp://www-mslmb.niddk.nih.gov/buchanan/index.html Lab: 1-301-594-9229 E-mail: fairman@gmail.commailto:fairman@gmail.com james.fair...@nih.govmailto:james.fair...@nih.gov -- Jim Fairman, Ph D. Post-Doctoral Fellow National Institutes of Health - NIDDK The Buchanan Labhttp://www-mslmb.niddk.nih.gov/buchanan/index.html Lab: 1-301-594-9229 E-mail: fairman@gmail.commailto:fairman@gmail.com james.fair...@nih.govmailto:james.fair...@nih.gov 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 : mat...@itqb.unl.pt http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit Mailing address : Instituto de Tecnologia Quimica e Biologica Apartado 127 2781-901 OEIRAS Portugal
[ccp4bb] Post-Doctoral Position/Scientific Programmer on PROXIMA 2
Dear Colleagues, We are seeking a motivated young scientist or engineer with excellent skills in programming and computing to join the PROXIMA 2 team at Synchrotron SOLEIL. Please forward the announcement below to any interested parties. Kind regards, Bill Post-doctoral Position - Scientific Programmer - PROXIMA 2 The position is available immediately. Deadline for submission of applications is the 15th March 2011 SOLEIL is an optimized, 3rd generation, 2.75 GeV synchrotron light source located 25 km south of Paris, France. A total of 26 beamlines, covering the whole energy range from IR to hard X-rays, provides an outstanding panel of experimental tools based on synchrotron radiation for physics, chemistry, biology and environmental sciences. The first 20 beamlines, several of which are using new concepts of undulator sources, are open to users. A permanent staff of 358 people operates the installation. The PROXIMA 2A beamline is dedicated to micro-crystallography and specifically designed to handle the fragile micro-crystals of biological macromolecules. The source is an in-vacuum U24 undulator installed on a canted section, and the X-rays will focus down to 5 µm × 5 µm over an energy range of 5 - 15 keV. The beamline will be equipped with a micro-diffractometer, focusing X-ray mirrors, an area detector and robotic sample changer. The experimental station will also be capable of measuring anomalous differences for MAD or SAD phasing experiments in the above energy range. The beamline is currently in the construction phase, and it will be opened to users in 2012. 1. Mission We are seeking a motivated young scientist or engineer with excellent skills in programming and computing, a strong interest in macromolecular crystallography and a background in its methodological basis. As a member of the PROXIMA 2A beamline team, your principle mission will be to develop and integrate software at the client-level to communicate with the device servers of the hardware level (TANGO). The software will include routines for commissioning, maintaining and operating the beamline (such as alignment procedures, data collections, and beamline calibrations). These software routines will be linked to graphical user interfaces (e.g. MXCuBE GlobalScreen). You will also be involved in research projects developing new functionalities for the instrumentation on the beamline, as well as novel analytical and computational techniques in micro-crystallography. For further information, contact william.shep...@synchrotron-soleil.fr mailto:william.shep...@synchrotron-soleil.fr . 2. Qualifications Experience Candidates should preferably hold a Ph.D. in macromolecular crystallography or the equivalent of a Masters degree in computing with at least 3 years of experience in a relevant science or engineering field. Plenty of experience in computing and excellent skills in programming is a pre-requisite. Candidates should have expertise in the programming of scripting languages, preferably in Python and Unix/Linux shells (e.g. bash), as well as other languages such as C++, Qt or Visual Basic. Experience in macromolecular X-ray crystallography methodology or synchrotron beamline instrumentation will be much appreciated. 3. General conditions The offer concerns a Post-doctoral contract for a one year-period renewable or a fixed term contract contract (CDD, Contrat de Durée Détérminé). The place of work will be at Synchrotron SOLEIL, which is located in the Paris suburbs (Saint-Aubin). Applications should include a motivation letter and Curriculum Vitae with the addresses of two referees. Please submit applications online at http://candidature.synchrotron-soleil.fr/VotreCandidature/ http://candidature.synchrotron-soleil.fr/VotreCandidature/ mentioning the reference Post-Doc-PROXIMA2.
Re: [ccp4bb] Full-screen stereo with Coot/PyMol/etc on 3D LCD displays?
I might be missing something here... The Zalman(s) work fine in Coot Pymol on a Mac (any Mac to be precise, from iBook to MacPro). Just add this to your coot.scm file: (add-key-binding switch to Zalman stereo z (lambda () (set-font-size 3) (set-graphics-window-size 1680 1050) (set-model-fit-refine-dialog-position 1900 0) (set-delete-dialog-position 1700 50) (set-go-to-atom-window-position 1847 67) (set-graphics-window-position 0 0) (set-graphics-window-size 1680 1050) (set-hardware-stereo-angle-factor 1.45) (set-map-line-width 2) (zalman-stereo-mode))) (add-key-binding switch to mono x (lambda () (set-map-line-width 1) (mono-mode))) and this to your Pymol alias in your .bashrc file (if running through X11) alias pymolz='pymol -S -t 6' or rename a newer flavour of Pymol according to the Pymol Wiki and just double click it Jürgen - 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/http://web.me.com/bosch_lab/ On Jan 24, 2011, at 12:56 AM, Luecke, Hartmut wrote: My apologies if this has been discussed before. Has anyone got this to work? Preferably with a Mac? We would love to hear the configuration. Cheers, Hudel Hartmut Luecke Director, Center for Biomembrane Systems Depts. of Biochemistry, Biophysics Computer Science 3205 McGaugh Hall University of California Irvine, CA 92697-3900 hu...@uci.edumailto:hu...@uci.edu http://bass.bio.uci.edu/~hudel/ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
Re: [ccp4bb] low expression and aggregation of protein
Thanks, Lin. I am sorry for being short of information. I was actually not sure what kind of information is needed. Well, the cells were grown at 27 degree in Insect-Xpress. I tried to grow cells both in shaker and stationery flask. Anything else I can try? Best, Min Date: Sat, 22 Jan 2011 21:57:02 +0100 Subject: Re: [ccp4bb] low expression and aggregation of protein From: yyb...@gmail.com To: mzhang...@hotmail.com CC: CCP4BB@jiscmail.ac.uk Actually, it is very difficult to say something just based on your simple information. You should give more informations about your work, for example, temperature, cuture, etc. Best, Lin On Fri, Jan 21, 2011 at 8:12 PM, m zhang mzhang...@hotmail.com wrote: Dear All, Recently I am trying to express a glycoprotein in Drosophila S2 cells. However, the expression yield is every low and most of the protein expressed aggregate. I was suggested making new constructs. But I am wondering if anyone here can give me some suggestions to improve it beyond that since I am new to glycoprotein? All your input will be greatly appreciated! Regards, Min
Re: [ccp4bb] Full-screen stereo with Coot/PyMol/etc on 3D LCD displays?
Zalman uses passive LCD stereo, however. From the thread of this discussion, it appears that active LCD stereo (using a 120Hz monitor, NVidia graphics card etc.) will not work on a Mac? Has anyone had a successful experience using active LCD stereo on a Mac? Padmaja On Jan 24, 2011, at 10:30 AM, Bosch, Juergen wrote: I might be missing something here... The Zalman(s) work fine in Coot Pymol on a Mac (any Mac to be precise, from iBook to MacPro). Just add this to your coot.scm file: (add-key-binding switch to Zalman stereo z (lambda () (set-font-size 3) (set-graphics-window-size 1680 1050) (set-model-fit-refine-dialog-position 1900 0) (set-delete-dialog-position 1700 50) (set-go-to-atom-window-position 1847 67) (set-graphics-window-position 0 0) (set-graphics-window-size 1680 1050) (set-hardware-stereo-angle-factor 1.45) (set-map-line-width 2) (zalman-stereo-mode))) (add-key-binding switch to mono x (lambda () (set-map-line-width 1) (mono-mode))) and this to your Pymol alias in your .bashrc file (if running through X11) alias pymolz='pymol -S -t 6' or rename a newer flavour of Pymol according to the Pymol Wiki and just double click it Jürgen - 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/ On Jan 24, 2011, at 12:56 AM, Luecke, Hartmut wrote: My apologies if this has been discussed before. Has anyone got this to work? Preferably with a Mac? We would love to hear the configuration. Cheers, Hudel Hartmut Luecke Director, Center for Biomembrane Systems Depts. of Biochemistry, Biophysics Computer Science 3205 McGaugh Hall University of California Irvine, CA 92697-3900 hu...@uci.edu http://bass.bio.uci.edu/~hudel/ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
Re: [ccp4bb] Stereo Microscope advice
Hi Kevin - 1) I can only imagine that LEDs would produce vastly less heat than halogen lamps. In general, they are small, efficient, long-lasting and don't produce a lot of heat. Here's a start for more information http://en.wikipedia.org/wiki/Light-emitting_diode . Also, a quick search got me this page http://www.tedpella.com/mscope_html/2282.htm which has what appears to be all the options you mentioned. I'm sure other manufacturers have similar models. 2) We are generally satisfied with our older model Olympus . If you will be looking at drops smaller than 1μl total volume (e.g. from a mosquito or other sub-μl liquid handler) I'd recommend at least a 2x objective lens. Some models (like the one linked above) have an option to direct the light to a camera mount instead of the eyepieces--get one of these if possible! Trying to hold a camera (or smartphone) steady in front of one of the eyepieces gets old after a while. Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center New York, NY 10016 212-263-7898 On Jan 23, 2011, at 8:35 PM, Kevin Corbett wrote: Hi everyone, I'm looking to buy a new stereo microscope for looking at crystal trays, and was wondering if anyone could help me answer a few questions: 1) Does anyone have experience with LED illumination in the microscope base? I'm worried that there might be excessive heating of the base, as this is a huge problem with integrated halogen lamps. Also, can these stands with LED's accommodate polarizers? 2) Any really good (or really bad) experiences with specific manufacturer/models? Any advice is much appreciated. Thanks very much, Kevin Kevin Corbett, Ph.D. Stephen C. Harrison Lab Harvard University Medical School corbett (at) crystal.harvard.edu (617)-432-5605 This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
Re: [ccp4bb] Stereo Microscope advice
Hi Kevin, We have 3 Olympus microscopes with three different lighting options. The three variations we have on our microscopes are: 1. a microscope with a reflective light base (internal mirror) that reflects light directed into the microscope base from an external halogen light-box. 2. a microscope with an integrated, low-power (30 watt) halogen light source (still has a mirror for the trans-illumination) 3. a microscope with an LED light source In general, the LED light source in our microscope produces very little heat so crystal trays should be safe for viewing for quite some time without heating. And, instead of a mirror, the base has a series of filters/diffusers to modulate the intensity of the light directed through the sample, or a dark-field filter. That can be helpful. However, the spectrum of light output by our LED light source is very blue (as opposed to the warmer yellow-heavy output from halogen or incandescent light sources). I don't like the cold, blue tones of the light and find that it contributes to eye fatigue. I also find that this light doesn't offer as high a contrast for viewing certain drop conditions. By that I mean that I occasionally find drop conditions for which I feel I can see differences in edge transitions or object boundaries better using the microscopes with the halogen light sources (i.e. comparing same drop with different microscope/light-source combinations). This doesn't happen often and does not dramatically affect my ability to rate the drop, but it's notable to me. In summary, I prefer alternatives to the LED light sources, but my dislike of the output spectrum is a matter of opinion. NOTE: My understanding is that the blue-heavy spectral output of white-light LEDs is a recognized property of LEDs (i.e. it's hard to achieve a true white light with LEDs). However, the ability to produce LEDs that have a more natural spectra is improving and I know at least Olympus is very close to offering such a version (more $$). With regards to polarizers, we just use screw-on polarizing filters that attach to a channel/groove near the bottom of our objective lenses. These are convenient and inexpensive (works with any light source). They won't, however, fit on all objective lenses depending on the presence of the necessary groove. -Andy Torelli -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kevin Corbett Sent: Sunday, January 23, 2011 8:35 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Stereo Microscope advice Hi everyone, I'm looking to buy a new stereo microscope for looking at crystal trays, and was wondering if anyone could help me answer a few questions: 1) Does anyone have experience with LED illumination in the microscope base? I'm worried that there might be excessive heating of the base, as this is a huge problem with integrated halogen lamps. Also, can these stands with LED's accommodate polarizers? 2) Any really good (or really bad) experiences with specific manufacturer/models? Any advice is much appreciated. Thanks very much, Kevin Kevin Corbett, Ph.D. Stephen C. Harrison Lab Harvard University Medical School corbett (at) crystal.harvard.edu (617)-432-5605
Re: [ccp4bb] Stereo Microscope advice
Just one comment on LEDs as we have them as part of an imaging system. While it is true that the LEDs themselves emit cool light, the associated electronics is hotter than I would have expected. FYI. Adrian Sent from my iPhone On 24 Jan 2011, at 19:24, Sampson, Jared jared.samp...@nyumc.org wrote: Hi Kevin - 1) I can only imagine that LEDs would produce vastly less heat than halogen lamps. In general, they are small, efficient, long-lasting and don't produce a lot of heat. Here's a start for more information http://en.wikipedia.org/wiki/Light-emitting_diode . Also, a quick search got me this page http://www.tedpella.com/mscope_html/2282.htm which has what appears to be all the options you mentioned. I'm sure other manufacturers have similar models. 2) We are generally satisfied with our older model Olympus . If you will be looking at drops smaller than 1μl total volume (e.g. from a mosquito or other sub-μl liquid handler) I'd recommend at least a 2x objective lens. Some models (like the one linked above) have an option to direct the light to a camera mount instead of the eyepieces--get one of these if possible! Trying to hold a camera (or smartphone) steady in front of one of the eyepieces gets old after a while. Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center New York, NY 10016 212-263-7898 On Jan 23, 2011, at 8:35 PM, Kevin Corbett wrote: Hi everyone, I'm looking to buy a new stereo microscope for looking at crystal trays, and was wondering if anyone could help me answer a few questions: 1) Does anyone have experience with LED illumination in the microscope base? I'm worried that there might be excessive heating of the base, as this is a huge problem with integrated halogen lamps. Also, can these stands with LED's accommodate polarizers? 2) Any really good (or really bad) experiences with specific manufacturer/models? Any advice is much appreciated. Thanks very much, Kevin Kevin Corbett, Ph.D. Stephen C. Harrison Lab Harvard University Medical School corbett (at) crystal.harvard.edu (617)-432-5605 This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
Re: [ccp4bb] Merging statistics and systematic absences
Maybe counting reflections is dull and boring, but doesn't it make you wonder sometimes when two programs read the same file and end up with different reflection counts? What sophisticated mathematics or logical conditions make it such that progams can't mimic adding machines? What else are these programs doing? It's sometimes quite bewildering. Ron On Mon, 24 Jan 2011, Phil Evans wrote: My immediate response to this is that anyone worrying about the number of reflections should get out more. More seriously, is assessing the quality of measurements then multiple observed measurements of systematically absent reflections should agree within their error estimates and (ideally) have a mean = 0.0, thus it seems valid to include them in measures of internal consistency such as Rmerge, Rmeas (strictly they should be compared to 0 rather than their mean Ih), i suppose) On the other hand, in looking at intensity statistics (as in truncate) the observed intensities should be compared with their expectation values which will depend on the space group (but still included perhaps). However there are so few of these reflections that it won't make much difference (though it is more important to separate centric acentric reflections, as there may be quite a lot of centrics) ie situation normal (SNAFU?) - it is not going to make any difference Phil On 24 Jan 2011, at 09:13, Graeme Winter wrote: Dear ccp4bb, I had an interesting question from a xia2 user last week for which I did not have a good answer. Here's the situation: - spacegroup is P212121, which was specified on the command-line - xia2 processes this as oP, assigns the spacegroup as P212121 before running scala - generates merging stats - truncate removes systematically absent reflections The end result is that there are fewer reflections in the output MTZ file and hence used for refinement than are reported in the merging statistics. The question is - what is correct? Clearly the effect on the merging statistics will be modest or trivial as there were only ~ 70 absent reflections, however removing them before scaling merging will also be a little fiddly. I see three (or maybe four) options - - truncate leave absent reflections in - remove the absent reflections before scaling - ignore this as situation normal (which is what xia2 currently does) - (less helpful *) refine against intensities which includes the absent reflections but matches the merging statistics If this were my project I would probably opt for #3 but I can appreciate that this is a question for the wider audience. What do others think? Many thanks in advance, Graeme * I mark this as less helpful because this is the wrong *reason* to merge against intensities. There are clearly good reasons for this.
Re: [ccp4bb] Stereo Microscope advice
'White' LED light produced by most integrated white LED packages is in fact a mixture of blue (~460nm), produced by the LED itself and a broad-band yellow (560nm), produced by a secondary phosphor, typically directly coating the semiconductor that emits the primary light. The net effect is a single-source mixed-wavelength light. The eye does not immediately notice the dip in the spectrum around the green (notably, the eye is in fact tuned into green for maximum sensitivity so the spectrum 'appears' smooth to us when in fact it's anything but). These LEDs are awesome for many applications and they indeed do not generate as much heat as incandescent lightbulbs do, but several folks I know have noted that their eyes are more tired after viewing LED-illuminated samples under a microscope. http://powerelectronics.com/power_management/led_drivers/Fig-2-white-LED-vs-RGB-LED-spectrum.jpg Other types of 'white' LED lights employ carefully balanced mixtures of three primary colors, each produced by a separate quantum well. Unfortunately these lights tend to shift colors with temperature and with age and appear different from different angles - feedback compensation is required for precision use. These tend to be much easier on the eye (at least to me), but I am not sure whether any scopes come with these composite LEDs installed. Artem On Sun, Jan 23, 2011 at 7:35 PM, Kevin Corbett corb...@crystal.harvard.eduwrote: Hi everyone, I'm looking to buy a new stereo microscope for looking at crystal trays, and was wondering if anyone could help me answer a few questions: 1) Does anyone have experience with LED illumination in the microscope base? I'm worried that there might be excessive heating of the base, as this is a huge problem with integrated halogen lamps. Also, can these stands with LED's accommodate polarizers? 2) Any really good (or really bad) experiences with specific manufacturer/models? Any advice is much appreciated. Thanks very much, Kevin Kevin Corbett, Ph.D. Stephen C. Harrison Lab Harvard University Medical School corbett (at) crystal.harvard.edu (617)-432-5605
Re: [ccp4bb] sodium vs water near methionine sulfur
Hi Chandan, The closest sodium-sulfur interaction that I know of within a protein is in entry 2BDG, Na (Atom 402, Chain A) to a CYS with a distance of 3.3 Angstroms. A couple of examples exist of sodium-sulfur interactions that involve coenzyme A (1FY7 and 1MJ9). I hope that helps. Take Care, Sean P212121 http://store.p212121.com/
