Re: [ccp4bb] AW: [ccp4bb] regarding Fo-Fc map in coot
Dear All, Thank you very much for your reply. I have an another doubt and I want to discuss with you. Sometimes for some structure during refinement and model building we have found a green blob (Fo-Fc and 5 sigma). If I scroll down the blue 2Fo-Fc map to a very low sigma level nearly at 0.5 a really non convincing density will appear. And from the structural point of view, it will be very difficult to put anything within it due to its position within the structure. as an example once I have found an elongated green density without any trace of blue in between a helix and a beta sheet. Is it due to noise? The structure was well refined. What should we do in such cases? Regards amlan. On Mon, Mar 10, 2014 at 4:41 PM, herman.schreu...@sanofi.com wrote: Dear Amlan, The sigma of an Fo-Fc map map depends on the residual noise in your map. In a well-refined structure, the sigma will be low, so at 3 sigma it will show very weak features. My guess is that your ligand is present in partial occupancy and that you will find it in your 2Fo-Fc map when you scroll down your contour level. If you see convincing Fo-Fc density without a ligand being fitted, the presence of the ligand must be real and you can fit it. However, I would refine a group occupancy for your ligand. Best, Herman *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von *Amlan Roychowdhury *Gesendet:* Montag, 10. März 2014 09:09 *An:* CCP4BB@JISCMAIL.AC.UK *Betreff:* [ccp4bb] regarding Fo-Fc map in coot Dear All, Some times during model building in coot we have found that at the position of ligand molecules and water, there is a good Fo-Fc map (above 3 sigma), devoid of any 2Fo-Fc map. 1.What does it physically mean and why the 2Fo-Fc map was not generated properly? 2. Can we fit ligand molecule there? Thanks in advance. Best Wishes Amlan. -- Amlan Roychowdhury. Senior Research Fellow. Protein Crystallography Lab. Dept. of Biotechnology, IIT Kharagpur. Kharagpur 721302 West Bengal. India. -- Amlan Roychowdhury. Senior Research Fellow. Protein Crystallography Lab. Dept. of Biotechnology, IIT Kharagpur. Kharagpur 721302 West Bengal. India.
[ccp4bb] positions for PhD students
Dear all: I would like to ask your kind help to distribute TIGP application announcement for 2014 on your network. The Chemical Biology and Molecular Biophysics program of Taiwan International Graduate Program is a Ph.D. program, founded by Academia Sinica, the foremost research institution of Taiwan in 2002. In cooperation with top universities in Taiwan, our CBMB program focuses on synthetic chemistry, structural biology, bioinformatics, kinetics and spectrometry and biotechnology and translational research. The TIGP-CBMB students will learn in all-English teaching and research environments, and enjoy accessing to world-class faculty and state-of-the-art research facilities at Academia Sinica and partner universities. All applicants who are admitted to TIGP will receive a fellowship from Academia Sinica. The application deadline is 31st March 2014. No application fee is required. For more information, please visit TIGP CBMB website. TIGP-CBMB: http://proj1.sinica.edu.tw/~tigpcbmb/ TIGP website: http://tigp.sinica.edu.tw/applying.html. If you have any further inquiries, please contact Ms. Elve Lin. Email: elve...@gate.sinica.edu.tw Thank you in advance for advertising TIGP program. Joseph Ho
Re: [ccp4bb] AW: [ccp4bb] regarding Fo-Fc map in coot
You dont say what resolution you are working at, or what the current R factor is. or how complete the model is. There are assumptions made in the refinement scaling algorithms and in their treatment of supposedly poorly ordered solvent which can generate false density (both positive and negative) on the boundaries of the model. And as well as Herman says the Sigma level is set globally whereas the actual density locally is affected by the B values. One of the strengths of COOT is that it is easy to adjust the sigma level at local regions. Eleanor On 11 March 2014 07:42, Amlan Roychowdhury amlan.iit...@gmail.com wrote: Dear All, Thank you very much for your reply. I have an another doubt and I want to discuss with you. Sometimes for some structure during refinement and model building we have found a green blob (Fo-Fc and 5 sigma). If I scroll down the blue 2Fo-Fc map to a very low sigma level nearly at 0.5 a really non convincing density will appear. And from the structural point of view, it will be very difficult to put anything within it due to its position within the structure. as an example once I have found an elongated green density without any trace of blue in between a helix and a beta sheet. Is it due to noise? The structure was well refined. What should we do in such cases? Regards amlan. On Mon, Mar 10, 2014 at 4:41 PM, herman.schreu...@sanofi.com wrote: Dear Amlan, The sigma of an Fo-Fc map map depends on the residual noise in your map. In a well-refined structure, the sigma will be low, so at 3 sigma it will show very weak features. My guess is that your ligand is present in partial occupancy and that you will find it in your 2Fo-Fc map when you scroll down your contour level. If you see convincing Fo-Fc density without a ligand being fitted, the presence of the ligand must be real and you can fit it. However, I would refine a group occupancy for your ligand. Best, Herman *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von *Amlan Roychowdhury *Gesendet:* Montag, 10. März 2014 09:09 *An:* CCP4BB@JISCMAIL.AC.UK *Betreff:* [ccp4bb] regarding Fo-Fc map in coot Dear All, Some times during model building in coot we have found that at the position of ligand molecules and water, there is a good Fo-Fc map (above 3 sigma), devoid of any 2Fo-Fc map. 1.What does it physically mean and why the 2Fo-Fc map was not generated properly? 2. Can we fit ligand molecule there? Thanks in advance. Best Wishes Amlan. -- Amlan Roychowdhury. Senior Research Fellow. Protein Crystallography Lab. Dept. of Biotechnology, IIT Kharagpur. Kharagpur 721302 West Bengal. India. -- Amlan Roychowdhury. Senior Research Fellow. Protein Crystallography Lab. Dept. of Biotechnology, IIT Kharagpur. Kharagpur 721302 West Bengal. India.
Re: [ccp4bb] AW: [ccp4bb] regarding Fo-Fc map in coot
Dear Sir May i know how to refine the group occupancy for a ligand??? Thanx in advance On Mon, Mar 10, 2014 at 2:11 PM, herman.schreu...@sanofi.com wrote: Dear Amlan, The sigma of an Fo-Fc map map depends on the residual noise in your map. In a well-refined structure, the sigma will be low, so at 3 sigma it will show very weak features. My guess is that your ligand is present in partial occupancy and that you will find it in your 2Fo-Fc map when you scroll down your contour level. If you see convincing Fo-Fc density without a ligand being fitted, the presence of the ligand must be real and you can fit it. However, I would refine a group occupancy for your ligand. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Amlan Roychowdhury Gesendet: Montag, 10. März 2014 09:09 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] regarding Fo-Fc map in coot Dear All, Some times during model building in coot we have found that at the position of ligand molecules and water, there is a good Fo-Fc map (above 3 sigma), devoid of any 2Fo-Fc map. 1.What does it physically mean and why the 2Fo-Fc map was not generated properly? 2. Can we fit ligand molecule there? Thanks in advance. Best Wishes Amlan. -- Amlan Roychowdhury. Senior Research Fellow. Protein Crystallography Lab. Dept. of Biotechnology, IIT Kharagpur. Kharagpur 721302 West Bengal. India.
Re: [ccp4bb] AW: [ccp4bb] regarding Fo-Fc map in coot
Dear Monica, for refmac5 this is nicely explained at http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html#Occupancy Best, Tim On 03/11/2014 12:14 PM, Monica Mittal wrote: Dear Sir May i know how to refine the group occupancy for a ligand??? Thanx in advance On Mon, Mar 10, 2014 at 2:11 PM, herman.schreu...@sanofi.com wrote: Dear Amlan, The sigma of an Fo-Fc map map depends on the residual noise in your map. In a well-refined structure, the sigma will be low, so at 3 sigma it will show very weak features. My guess is that your ligand is present in partial occupancy and that you will find it in your 2Fo-Fc map when you scroll down your contour level. If you see convincing Fo-Fc density without a ligand being fitted, the presence of the ligand must be real and you can fit it. However, I would refine a group occupancy for your ligand. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Amlan Roychowdhury Gesendet: Montag, 10. März 2014 09:09 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] regarding Fo-Fc map in coot Dear All, Some times during model building in coot we have found that at the position of ligand molecules and water, there is a good Fo-Fc map (above 3 sigma), devoid of any 2Fo-Fc map. 1.What does it physically mean and why the 2Fo-Fc map was not generated properly? 2. Can we fit ligand molecule there? Thanks in advance. Best Wishes Amlan. -- Amlan Roychowdhury. Senior Research Fellow. Protein Crystallography Lab. Dept. of Biotechnology, IIT Kharagpur. Kharagpur 721302 West Bengal. India. -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature
Re: [ccp4bb] twinning problem ?
Sorry - hadnt finished.. The twinning tests are distorted by NC translation - usually the L test is safe, but the others are all suspect.. On 11 March 2014 14:09, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: What is the NC translation? If there is a factor of 0.5 that makes SG determination complicated.. Eleanor On 11 March 2014 14:04, Stephen Cusack cus...@embl.fr wrote: Dear All, I have 2.6 A data and unambiguous molecular replacement solution for two copies/asymmetric unit of a 80 K protein for a crystal integrated in P212121 (R-merge around 9%) with a=101.8, b=132.2, c=138.9. Refinement allowed rebuilding/completion of the model in the noraml way but the R-free does not go below 30%. The map in the model regions looks generally fine but there is a lot of extra positive density in the solvent regions (some of it looking like weak density for helices and strands) and unexpected positive peaks within the model region. Careful inspection allowed manual positioning of a completely different, overlapping solution for the dimer which fits the extra density perfectly. The two incompatible solutions are related by a 2-fold axis parallel to a. This clearly suggests some kind of twinning. However twinning analysis programmes (e.g. Phenix-Xtriage), while suggesting the potentiality of pseudo-merohedral twinning (-h, l, k) do not reveal any significant twinning fraction and proclaim the data likely to be untwinned. (NB. The programmes do however highlight a non-crystallographic translation and there are systematic intensity differences in the data). Refinement, including this twinning law made no difference since the estimated twinning fraction was 0.02. Yet the extra density is clearly there and I know exactly the real-space transformation between the two packing solutions. How can I best take into account this alternative solution (occupancy seems to be around 20-30%) in the refinement ? thanks for your suggestions Stephen -- ** Dr. Stephen Cusack, Head of Grenoble Outstation of EMBL Group leader in structural biology of protein-RNA complexes and viral proteins Joint appointment in EMBL Genome Biology Programme Director of CNRS-UJF-EMBL International Unit (UMI 3265) for Virus Host Cell Interactions (UVHCI) ** Email: cus...@embl.fr Website: http://www.embl.fr Tel:(33) 4 76 20 7238Secretary (33) 4 76 20 7123 Fax:(33) 4 76 20 7199 Postal address: EMBL Grenoble Outstation, 6 Rue Jules Horowitz, BP181, 38042 Grenoble Cedex 9, France Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 6 Rue Jules Horowitz, 38042 Grenoble, France **
[ccp4bb] Lecture in X-ray crystallography, University of Leeds
Please see the link below for an advert for a new Lectureship in Macromolecular X-Ray Crystallography at the University of Leeds. http://jobs.leeds.ac.uk/fe/tpl_universityofleeds01.asp?s=4A515F4E5A565B1Ajobid=110947,6951214874key=11037106c=612123217223pagestamp=sepwjldjailxhilecl Job Summary You will be appointed in the School of Molecular Cellular Biology, where you will join a dynamic School of around 40 academic staff with research interests that span Structural Biology, Molecular Biology, Cell Biology, Virology, Bacteriology and Computational Biology. The School has excellent research facilities including a recently upgraded X-ray facility, along with newly updated facilities for NMR, electron microscopy, mass spectrometry and high performance computing. You should have a PhD in a relevant area as well as a successful research track record in X-ray crystallography applied to important questions in the biological sciences. We are particularly keen to attract candidates who complement our recent strategic investments in chemical biology, inhibitor discovery and macromolecular recognition, but candidates with interests in any area of structural molecular biology that fit within the School’s research strengths are welcome to apply. University Grade 8 (£37,756 - £45,053 p.a.) Informal enquiries may be made to Professor David Westhead, tel +44 (0)113 343 3116, email d.r.westh...@leeds.ac.ukmailto:d.r.westh...@leeds.ac.uk Closing Date: 7 April 2014 Ed T.A.Edwards Ph.D. Deputy Director Astbury Centre for Structural Molecular Biology Ass. Professor, School of Molecular and Cellular Biology Garstang 8.53d University of Leeds, Leeds, LS2 9JT Telephone: 0113 343 3031 http://www.fbs.leeds.ac.uk/staff/tae/ http://www.astbury.leeds.ac.uk/people/staff/staffpage.php?StaffID=TE http://www.fbs.leeds.ac.uk/staff/profile.php?un=bmbtae --Science is always wrong. It never solves a problem without creating ten more. ~George Bernard Shaw
Re: [ccp4bb] Stereo monitors for use with Pymol and Coot
Matic, I am struggling with Ubuntu on this issue. The Nvidia driver needs the 'Composite' function disabled in order to function in 3D. This required the use of the Unity-2D package to disable the 3D used in the Ubuntu desktop effects. This worked fine in Ubuntu 12.04. Unfortuately the developers have decided that the eye candy is essential to their desktop and have deprecated the Unity-2D package(since 13.04). So in a more recent release of Ubuntu the 'Composite disable' in the xorg.conf with the Nvidia driver will yield a blank screen and a core dump. I'd certainly love it if someone could offer a solution aside from stepping back to an older release. Nic out On 03/10/2014 05:23 AM, Matic Kisovec wrote: Dear everybody, to my recent experience not everything is good in the stereo world. Since I see that others don't have these problems (and I am happy/sad to see that the same exact combinations work without problems) I would just like to add my experience. For the past 4 months I have been struggling to configure a stereo setup for viewing structures in Pymol. I got the VG278HR and PNY Quadro K600 connected over the original DVI-D cable. Since then I was unable to get anything in stereo on Linux (tried Ubuntu, OpenSUSE, Fedora). Unfortunately I get a blank/black screen whenever I use the stereo option in xorg.conf. Also tried changing the motherboard and CPU but got the same result. In Windows the demo stuff from Nvidia works just fine but again I have problems with Pymol. So far the only way to see anything connected to molecular structures in Windows was via DVI-to-HDMI cable but due to HDMI restrictions the quality isn't as good as it would be over DVI-D. If I use DVI-D that was shipped with the monitor the quadro card is detected in Pymol but the monitor doesn't switch to stereo. I have been in contact with the company that makes Quadro cards (PNY) but they were unable to help me. I also contacted some very kind users of CCP4BB and they kindly answered a bunch of question regarding specific setup options. Thanks again! Still there was no success so far. I am slowly giving up on the stereo so if anybody has any ideas/thoughts what could be wrong/done I would greatly appreciate any insight. Kind regards, Matic On 06. 03. 2014 19:32, White, Mark wrote: Alexy I have the ASUS 27" stereo LCD monitors with built in emitter connected to Linux WS with the cheaper Quadro cards. The monitor comes with a special DVI cable that caries the sync signal and thus it does not need the 3-pin connector. The new LCD stereo monitors produce superb 3D images that are much crisper than we used to get with CRT displays. Best regards Mark Sent from my iPhone On Mar 6, 2014, at 12:01 PM, "Alexey Rozov" alexey.ro...@gmail.com wrote: Hello, Sorry, if this question somewhat off-top to the actual discussion, but to my understanding one does need the 3-pin connector to operate 3D under Linux even for the monitors with the built-in emitter. It appears to be necessary to guide the emitter, or am I wrong about it? I'd be thankful if anyone can advise me on that since it looks like a big problem to acquire the commercial connectors and cables. I think I have seen an older discussion on CCP4BB where the importance of the 3-pin connector was emphasized... Alexey On 6 March 2014 18:30, mesters mest...@biochem.uni-luebeck.de wrote: Hello Moutse, as you noted correctly, the ASUS VG278H (HR or HE) comes in two flavours, one with build in emitter (120 Hz, HR model) and one without (144 Hz, HE model).
Re: [ccp4bb] Stereo monitors for use with Pymol and Coot
Hi Nic, There is no reason that you have to use the Unity desktop at all. I prefer using the XFCE4 desktop myself. It is easily installable from the Ubuntu repositories and then you just have to select it at login. Cheers, Rob On Tue, 2014-03-11 14:44 EDT, Nic Steussy csteu...@purdue.edu wrote: Matic, I am struggling with Ubuntu on this issue. The Nvidia driver needs the 'Composite' function disabled in order to function in 3D. This required the use of the Unity-2D package to disable the 3D used in the Ubuntu desktop effects. This worked fine in Ubuntu 12.04. Unfortuately the developers have decided that the eye candy is essential to their desktop and have deprecated the Unity-2D package(since 13.04). So in a more recent release of Ubuntu the 'Composite disable' in the xorg.conf with the Nvidia driver will yield a blank screen and a core dump. I'd certainly love it if someone could offer a solution aside from stepping back to an older release. Nic out On 03/10/2014 05:23 AM, Matic Kisovec wrote: Dear everybody, to my recent experience not everything is good in the stereo world. Since I see that others don't have these problems (and I am happy/sad to see that the same exact combinations work without problems) I would just like to add my experience. For the past 4 months I have been struggling to configure a stereo setup for viewing structures in Pymol. I got the VG278HR and PNY Quadro K600 connected over the original DVI-D cable. Since then I was unable to get anything in stereo on Linux (tried Ubuntu, OpenSUSE, Fedora). Unfortunately I get a blank/black screen whenever I use the stereo option in xorg.conf. Also tried changing the motherboard and CPU but got the same result. In Windows the demo stuff from Nvidia works just fine but again I have problems with Pymol. So far the only way to see anything connected to molecular structures in Windows was via DVI-to-HDMI cable but due to HDMI restrictions the quality isn't as good as it would be over DVI-D. If I use DVI-D that was shipped with the monitor the quadro card is detected in Pymol but the monitor doesn't switch to stereo. I have been in contact with the company that makes Quadro cards (PNY) but they were unable to help me. I also contacted some very kind users of CCP4BB and they kindly answered a bunch of question regarding specific setup options. Thanks again! Still there was no success so far. I am slowly giving up on the stereo so if anybody has any ideas/thoughts what could be wrong/done I would greatly appreciate any insight. Kind regards, Matic On 06. 03. 2014 19:32, White, Mark wrote: Alexy I have the ASUS 27 stereo LCD monitors with built in emitter connected to Linux WS with the cheaper Quadro cards. The monitor comes with a special DVI cable that caries the sync signal and thus it does not need the 3-pin connector. The new LCD stereo monitors produce superb 3D images that are much crisper than we used to get with CRT displays. Best regards Mark Sent from my iPhone On Mar 6, 2014, at 12:01 PM, Alexey Rozov alexey.ro...@gmail.com wrote: Hello, Sorry, if this question somewhat off-top to the actual discussion, but to my understanding one does need the 3-pin connector to operate 3D under Linux even for the monitors with the built-in emitter. It appears to be necessary to guide the emitter, or am I wrong about it? I'd be thankful if anyone can advise me on that since it looks like a big problem to acquire the commercial connectors and cables. I think I have seen an older discussion on CCP4BB where the importance of the 3-pin connector was emphasized... Alexey On 6 March 2014 18:30, mesters mest...@biochem.uni-luebeck.de wrote: Hello Moutse, as you noted correctly, the ASUS VG278H (HR or HE) comes in two flavours, one with build in emitter (120 Hz, HR model) and one without (144 Hz, HE model). The VG278HR (ships with one pair of shutter glasses) with build in emitter can be used under windows and linux with a cheap nvidia quadro card (the ones without a 3-pin stereo connector). With the VG278HE under windows and a cheap nvidia quadro, you will need the nvidia emitter that uses a usb port for driving the emitter. To operate the VG278HE under linux requires a truely expensive quadro card (k4000 and upwards) with an optional (!) 3-pin connector or, purchase an old refurbished quadro card with 3-pin. Have a look at the following link http://www.nvidia.com/object/3d-vision-pro-requirements.html, especially the table at the end with the small print explanation 2 and 3 - J. - Am 06.03.14 17:41, schrieb Mouts Ranaivoson: Hi, I am currently also looking for a 3D monitor, and I am particularly attentive to this particular discussion. My interrogation is that does the Asus VG278HE model work under linux ? From previous ccp4bb discussions I understood that only built-in emmitter (like the Asus
Re: [ccp4bb] Stereo monitors for use with Pymol and Coot
Hi Nic, There is no reason that you have to use the Unity desktop at all. I prefer using the XFCE4 desktop myself. It is easily installable from the Ubuntu repositories and then you just have to select it at login. In one of the xfce4 settings options (Window Manager Tweaks) you can disable display compositing. Cheers, Rob On Tue, 2014-03-11 14:44 EDT, Nic Steussy csteu...@purdue.edu wrote: Matic, I am struggling with Ubuntu on this issue. The Nvidia driver needs the 'Composite' function disabled in order to function in 3D. This required the use of the Unity-2D package to disable the 3D used in the Ubuntu desktop effects. This worked fine in Ubuntu 12.04. Unfortuately the developers have decided that the eye candy is essential to their desktop and have deprecated the Unity-2D package(since 13.04). So in a more recent release of Ubuntu the 'Composite disable' in the xorg.conf with the Nvidia driver will yield a blank screen and a core dump. I'd certainly love it if someone could offer a solution aside from stepping back to an older release. Nic out On 03/10/2014 05:23 AM, Matic Kisovec wrote: Dear everybody, to my recent experience not everything is good in the stereo world. Since I see that others don't have these problems (and I am happy/sad to see that the same exact combinations work without problems) I would just like to add my experience. For the past 4 months I have been struggling to configure a stereo setup for viewing structures in Pymol. I got the VG278HR and PNY Quadro K600 connected over the original DVI-D cable. Since then I was unable to get anything in stereo on Linux (tried Ubuntu, OpenSUSE, Fedora). Unfortunately I get a blank/black screen whenever I use the stereo option in xorg.conf. Also tried changing the motherboard and CPU but got the same result. In Windows the demo stuff from Nvidia works just fine but again I have problems with Pymol. So far the only way to see anything connected to molecular structures in Windows was via DVI-to-HDMI cable but due to HDMI restrictions the quality isn't as good as it would be over DVI-D. If I use DVI-D that was shipped with the monitor the quadro card is detected in Pymol but the monitor doesn't switch to stereo. I have been in contact with the company that makes Quadro cards (PNY) but they were unable to help me. I also contacted some very kind users of CCP4BB and they kindly answered a bunch of question regarding specific setup options. Thanks again! Still there was no success so far. I am slowly giving up on the stereo so if anybody has any ideas/thoughts what could be wrong/done I would greatly appreciate any insight. Kind regards, Matic On 06. 03. 2014 19:32, White, Mark wrote: Alexy I have the ASUS 27 stereo LCD monitors with built in emitter connected to Linux WS with the cheaper Quadro cards. The monitor comes with a special DVI cable that caries the sync signal and thus it does not need the 3-pin connector. The new LCD stereo monitors produce superb 3D images that are much crisper than we used to get with CRT displays. Best regards Mark Sent from my iPhone On Mar 6, 2014, at 12:01 PM, Alexey Rozov alexey.ro...@gmail.com wrote: Hello, Sorry, if this question somewhat off-top to the actual discussion, but to my understanding one does need the 3-pin connector to operate 3D under Linux even for the monitors with the built-in emitter. It appears to be necessary to guide the emitter, or am I wrong about it? I'd be thankful if anyone can advise me on that since it looks like a big problem to acquire the commercial connectors and cables. I think I have seen an older discussion on CCP4BB where the importance of the 3-pin connector was emphasized... Alexey On 6 March 2014 18:30, mesters mest...@biochem.uni-luebeck.de wrote: Hello Moutse, as you noted correctly, the ASUS VG278H (HR or HE) comes in two flavours, one with build in emitter (120 Hz, HR model) and one without (144 Hz, HE model). The VG278HR (ships with one pair of shutter glasses) with build in emitter can be used under windows and linux with a cheap nvidia quadro card (the ones without a 3-pin stereo connector). With the VG278HE under windows and a cheap nvidia quadro, you will need the nvidia emitter that uses a usb port for driving the emitter. To operate the VG278HE under linux requires a truely expensive quadro card (k4000 and upwards) with an optional (!) 3-pin connector or, purchase an old refurbished quadro card with 3-pin. Have a look at the following link http://www.nvidia.com/object/3d-vision-pro-requirements.html, especially the table at the end with the small print explanation 2 and 3 - J. - Am 06.03.14 17:41, schrieb Mouts Ranaivoson: Hi, I am currently also looking for a 3D monitor, and I am particularly attentive to this particular discussion. My interrogation is that does the Asus VG278HE model work under
[ccp4bb] Research Specialist Position at UCSF
UNIVERSITY OF CALIFORNIA SAN FRANCISCO (UCSF) RESEARCH SPECIALIST, JURA LAB A research specialist position in Receptor Tyrosine Kinase Structural Biology is available immediately in the lab of Prof. Natalia Jura at the University of California, San Francisco (UCSF). The Jura Lab merges structural, biochemical, imaging and cell biology approaches to dissect the mechanism of multi-protein assemblies involved in receptor tyrosine kinase signaling at the plasma membrane. More information is available at the lab website: http://www.cvri.ucsf.edu/~jura The hired individual will carry a research project that involves protein purification, crystallization and X-ray structure determination of protein complexes in a collaborative project with two other labs. The position is currently funded for two years. We are most interested in candidates who want to spearhead independent research, and who are team players with good communication and interpersonal skills. The candidate must have at least BA/BS in Biochemistry, Molecular Biology or Chemistry or a related science, and several years of experience with protein expression, purification and structure determination through X-ray crystallography. The hired individual will benefit from both the multidisciplinary environment in the lab and the highly collaborative UCSF community. The lab has extensive crystallographic resources, including (as part of the UCSF crystallography group) two R-axis IV systems and regular access to synchrotron beamline 8.3.1 at the nearby Advanced Light Source (ALS) in Berkeley. Interested individuals should send a current CV to Prof. Natalia Jura at natalia.j...@ucsf.edumailto:natalia.j...@ucsf.edu Natalia Jura, Ph.D. Assistant Professor Cardiovascular Research Institute Department of Cellular and Molecular Pharmacology University of California San Francisco
Re: [ccp4bb] twinning problem ?
Shape of the diffraction spots changes in the statistical disorder -- twinning continuum. At both ends spots shape is like in diffraction from crystals without such disorder. However, in the intermediate case, electron density autocorrelation function has additional component to one resulting from ordered crystal. This additional component of autocorrelation creates characteristic non-Bragg diffraction, e.g. streaks aligned with particular unit cell axis. In the absence of such diffraction pattern, the ambiguity is binary. The description of the problem indicates statistical disorder. Zbyszek Otwinowski Hi, If there's an NCS translation, recent versions of Phaser can account for it and give moment tests that can detect twinning even in the presence of tNCS. But I agree with Eleanor that the L test is generally a good choice in these cases. However, the fact that you see density suggests that your crystal might be more on the statistical disorder side of the statistical disorder -- twinning continuum, i.e. the crystal doesn't have mosaic blocks corresponding to one twin fraction that are large compared to the coherence length of the X-rays. So you might want to try refinement with the whole structure duplicated as alternate conformers. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 11 Mar 2014, at 14:10, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Sorry - hadnt finished.. The twinning tests are distorted by NC translation - usually the L test is safe, but the others are all suspect.. On 11 March 2014 14:09, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: What is the NC translation? If there is a factor of 0.5 that makes SG determination complicated.. Eleanor On 11 March 2014 14:04, Stephen Cusack cus...@embl.fr wrote: Dear All, I have 2.6 A data and unambiguous molecular replacement solution for two copies/asymmetric unit of a 80 K protein for a crystal integrated in P212121 (R-merge around 9%) with a=101.8, b=132.2, c=138.9. Refinement allowed rebuilding/completion of the model in the noraml way but the R-free does not go below 30%. The map in the model regions looks generally fine but there is a lot of extra positive density in the solvent regions (some of it looking like weak density for helices and strands) and unexpected positive peaks within the model region. Careful inspection allowed manual positioning of a completely different, overlapping solution for the dimer which fits the extra density perfectly. The two incompatible solutions are related by a 2-fold axis parallel to a. This clearly suggests some kind of twinning. However twinning analysis programmes (e.g. Phenix-Xtriage), while suggesting the potentiality of pseudo-merohedral twinning (-h, l, k) do not reveal any significant twinning fraction and proclaim the data likely to be untwinned. (NB. The programmes do however highlight a non-crystallographic translation and there are systematic intensity differences in the data). Refinement, including this twinning law made no difference since the estimated twinning fraction was 0.02. Yet the extra density is clearly there and I know exactly the real-space transformation between the two packing solutions. How can I best take into account this alternative solution (occupancy seems to be around 20-30%) in the refinement ? thanks for your suggestions Stephen -- ** Dr. Stephen Cusack, Head of Grenoble Outstation of EMBL Group leader in structural biology of protein-RNA complexes and viral proteins Joint appointment in EMBL Genome Biology Programme Director of CNRS-UJF-EMBL International Unit (UMI 3265) for Virus Host Cell Interactions (UVHCI) ** Email: cus...@embl.fr Website: http://www.embl.fr Tel:(33) 4 76 20 7238Secretary (33) 4 76 20 7123 Fax:(33) 4 76 20 7199 Postal address: EMBL Grenoble Outstation, 6 Rue Jules Horowitz, BP181, 38042 Grenoble Cedex 9, France Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 6 Rue Jules Horowitz, 38042 Grenoble, France ** Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353
[ccp4bb] Set up ccp4 environment
Dear All: I try to run xds in linux, but have some problems. With xdsconv, it complains: f2mtz: error while loading shared libraries: libccp4f.so.0: cannot open shared object file: No such file or directory cad: error while loading shared libraries: libccp4f.so.0: cannot open shared object file: No such file or directory With xdsstat, it complains: xdsstat: Cannot open environ.def It seems that one needs to set up a CCP4 environment in order to run xds in linux. I have ccp4 (the latest vision for linux) installed. And I use Ubuntu 12.04 LTS. Thank you for your advice Uma
