Re: [ccp4bb] phenix.real_space_correlation vs overlapmap
This may be too late to be of use, but as one of the authors of the sfall/overlapmap system.. sfall does generate a coded map which flags every grid point with a unique ID of the nearest atom, ie one which is unique providing there are not too many atoms - it is adequate for most molecules though prob. not for the ribosome.. A grid point is assigned the ID of the nearest atom. And the default radius of an atom is indeed 2.5A, which will generate overlap between most atoms. However for a reasonable B factor and a fine grid (SFALL has a default grid spacing of 0.5A) most of the significant density is correctly assigned to a given atom. So the CC is reasonably accurate for atoms with acceptable B factors, but not very accurate for those with B 100 say.. Eleanor On 05/02/2011 07:18 PM, James M Holton wrote: The CCP4 program that makes the label map you are looking for is SFALL. It can be told to make a .map file where each grid point is still a floating-point number, but instead of the usual electron density it encodes the residue number, atom number, etc. The OVERLAPMAP program knows how to decode this, and you specify it as a third map, in addition to the two you want to correlate. However, the distance from the center of each atom that is still part of it is an interesting question. I think the default is 2.5 A or so, but this depends on the B factor, and probably grid points far from the center of an atom should count less than ones near the middle? If what you really want is the number of electrons in a region, then I would recommend occupancy refinement (which you can now do in REFMAC), and then adding up occ*Z for the atoms of interest (where Z is the atomic number). This has the nice property of being independent of F000 estimates. -James Holton MAD Scientist On May 2, 2011, at 11:44 AM, Matt Warkentinmattw...@gmail.com wrote: Hi all I'm trying to 'measure' the density in a region of my structure by integrating the electron density there (notwithstanding errors in F000). I understand that both overlapmap and phenix.real_space_correlation compute density surrounding individual atoms for their calculations. Is there any way to get that info out of either of them? Are the per-residue Fo and Fc columns in the output of phenix.real_space_correlation actually what I am looking for? If so what are the units and how is F000 handled? Thanks a bunch to anyone who can clear this up. Matt
Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
Not only do you not need a high-end graphics card, you don't even need the proper graphics drivers installed. When I went to FC13 (upgrade from FC7, I don't know why), my quadro fx1400 was no longer supported. It would not work with hardware stereo (emitters/glasses of old). I went to Zalman monitors and all is great. Frankly, stereo is not needed as much in a nice bright LCD monitor (very crisp, looks great), but if you want it, Zalman is the way to go (passive stereo - light glasses, no hardware requirements beyond the monitor) Good luck Dave On 5/10/2011 12:27 AM, Duangrudee Tanramluk wrote: Dear Yu, The graphic card I am using is Nvidia Quadro FX580. If all you want is Pymol and Coot, you don't need a high-end graphic card. Some commercial molecular viewer requires a really high-end Quadro graphic card. If you plan to use those packages on the same machine, you may want to check their websites for the high quality 3D-stereo before purchasing them. Cheers, Duangrudee ___ Duangrudee Tanramluk, Ph.D. Institute of Molecular Biosciences, Mahidol University Puttamonthon 4 Road, Salaya, Nakhon Pathom 73170 THAILAND
Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
Since the technique (of using polarised light) applied by the Zalman was invented in the 1920's, it's probably little surprising that we don't need special hardware for using it ;-) Cheers, Tim On Tue, May 10, 2011 at 07:08:10AM -0400, David Roberts wrote: Not only do you not need a high-end graphics card, you don't even need the proper graphics drivers installed. When I went to FC13 (upgrade from FC7, I don't know why), my quadro fx1400 was no longer supported. It would not work with hardware stereo (emitters/glasses of old). I went to Zalman monitors and all is great. Frankly, stereo is not needed as much in a nice bright LCD monitor (very crisp, looks great), but if you want it, Zalman is the way to go (passive stereo - light glasses, no hardware requirements beyond the monitor) Good luck Dave On 5/10/2011 12:27 AM, Duangrudee Tanramluk wrote: Dear Yu, The graphic card I am using is Nvidia Quadro FX580. If all you want is Pymol and Coot, you don't need a high-end graphic card. Some commercial molecular viewer requires a really high-end Quadro graphic card. If you plan to use those packages on the same machine, you may want to check their websites for the high quality 3D-stereo before purchasing them. Cheers, Duangrudee ___ Duangrudee Tanramluk, Ph.D. Institute of Molecular Biosciences, Mahidol University Puttamonthon 4 Road, Salaya, Nakhon Pathom 73170 THAILAND -- -- 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] Postdoctoral position - Structural Biology of Bacterial Secretion Systems
Institute of Structural and Molecular Biology, Faculty of Science, Department of Biological Sciences, Birkbeck College Postdoctoral Research Assistant – Ref: 10541, Full time, fixed term appointment for up to three years The Institute of Structural and Molecular Biology is seeking a Post- doctoral Research Assistant to carry out structural analysis (x-ray crystallography or cryo-electron microscopy) of complexes formed during type IV secretion. The group is led by Professor Gabriel Waksman and has over the years produced numerous high profile publications in the highest impact journals (Cell, 2008, 133:640-652; Science, 2009, 323:266-268; Nature, 2009, 462:1011-1015; Nature, 2011, In Press). The research programme is funded by a grant from the Wellcome Trust to Prof Gabriel Waksman. Further details on the research group and on type IV secretion can be found at http://people.cryst.bbk.ac.uk/~ubcg54a/ . Applicants should have a PhD in Structural Molecular Biology, Biophysics or a related area, postdoctoral research experience and relevant research publications. Salary range will be from £33,804 to £38,722 on Grade 7 or from £39,796 to £46,950 on Grade 8 per annum inclusive of London Allowance. Initial salary will be dependent on the skills and experience of the successful applicant. This job is full time and fixed term. The salary quoted above is inclusive of London allowance. The appointment is subject to a probationary period of six months. Birkbeck also provides a generous final salary pension scheme, 31 days paid leave, flexible working arrangements and other great benefits. Closing date for completed applications: 15 June 2011 To apply for this position please go to www.bbk.ac.uk/jobs and search using reference number 10541. Birkbeck is an equal opportunities employer and encourages applications from all candidates irrespective of gender, race, disability, sexual orientation, age, religion and belief or another protected characteristic.
[ccp4bb] Postdoctoral positions in Structural Biology
Postdoctoral positions are available immediately in the Structural Biology Laboratory headed by Dr. C. S. Raman at the University of Maryland, Baltimore. Research in the Raman laboratory combines structural, biophysical, biochemical, and cell biological approaches to understand the molecular mechanisms underlying cellular signaling. The laboratory is equipped with state-of-the-art instrumentation for fermentation, high-throughput protein expression (Biomek FXP robot), purification, crystallization (liquid handlers for screen generation and optimization, Mosquito LCP robot, and crystal imaging systems), and X-ray diffraction. In addition, we have ready access to synchrotron facilities. For a representative example of our work, please consult Nature 455: 363-368. Applicants should hold a PhD in biochemistry, biophysics, chemistry, molecular biology, or a closely related field. Applicants should have experience in protein crystallography, as well as a good publication record. Strong background in protein expression is essential. Expertise in membrane protein purification is a plus. Furthermore, strong communication skills in oral and written English are required. To apply, please send a CV, and names of three references by e-mail to: cra...@rx.umaryland.edu
[ccp4bb] Scientific software development post at Diamond Light Source, UK
Please see below details of a software development post available within the Scientific Software Team at Diamond. For full details please go to the web pages at: http://www.diamond.ac.uk/Home/Jobs/Current/DIA0618-TH.html Job Title: Software Engineer Job Reference: DIA0618/TH Post Type: Full time / Permanent Division: Science Salary information: Circa £34k. Based on experience and qualifications; a higher salary may be available for an exceptionally experienced and qualified candidate. Application deadline: 10/06/2011 Date of interviews: TBC We are looking for a high calibre software engineer to join our dynamic scientific software team. The team have the responsibility for the provision of advanced data evaluation, analysis and visualization software applications for both internal and external users of Diamond. These applications often exploit the very latest techniques to address the challenging requirements of a broad range of scientific disciplines including macromolecular crystallography through to nanostructures and materials science. You will operate within the scientific software team of experienced software scientists and engineers and will work with our beamline scientists to identify and define requirements for data analysis and visualization applications and then ensure that they are implemented in a timely and effective way. It is important also to work with our data acquisition team to help optimize the whole scientific process at a Diamond beamline from data acquisition through to the experimenters leaving with high quality experimental results. The work will also involve enhancing and supporting the core features of a scientific data analysis workbench project at Diamond and to work with collaborators on other similar facilities in the world. Alun ___ Alun Ashton, alun.ash...@diamond.ac.uk Tel: +44 1235 778404 Scientific Software Team Leader, http://www.diamond.ac.uk/ Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.
[ccp4bb] Experimental Postdoctoral Position in High Throughput Small Molecule Ligand Screening
Experimental Postdoctoral Position in High Throughput Small Molecule Ligand Screening Outstanding postdoctoral applicants to work jointly with Drs. Julia Kubakek, Mark Hay and Jeffrey Skolnick at the Georgia Institute of Technology are sought with the following qualifications: * Extensive experience in enzyme kinetics studies, enzyme purification or other aspects of protein biology and enzyme activity. Experience in handling multiple protein systems would be a plus. * A background in high throughput small molecule ligand screening is strongly preferred. * Experience with or a desire to learn computational biology and molecular modeling of protein-ligand interactions. * The ideal candidate is someone who gets satisfaction out of methods development and working through large data sets to see broad-scale patterns. To apply, please email your CV to : skoln...@gatech.edu
Re: [ccp4bb] Chlorine atoms in ligand during refinement
Check the PDB - looks like you defined them as C rather than Cl somehow. Check their temperature factors, I bet they're way lower than the rest of the ligand. Also the arginine residue in the top left corner seems to be mis-modeled - there's a water molecule where its end should be (and a nice negaive density peak near the wrong position). Artem On Tue, May 10, 2011 at 2:18 PM, Nalam, Madhavi madhavi.na...@umassmed.eduwrote: Hello: There are two chlorine atoms in the ligand that I modeled in the active site. When I first modeled the ligand, the density is very clear for the ligand. The chlorine atoms were seen as white (different color than carbon atoms). After one round of refinement, there seems to be positive density around the two chlorine atoms (please see the attached file) while the density around the rest of the ligand seem to be very clear. I tried to model two conformations thinking that there is some disorder but still the positive density doesn't disappear. After a closer look where I just modeled one conformation for the ligand, the 2Fo-Fc density seem to be clear for the entire ligand and the positive density that appeared could be a problem with scattering factor. One reason for me to think this way is now the chlorine atoms are of the same color as carbon atoms. I use version ccp4-6.1.13/Refmac5.5.0109 respectively. Can anyone suggest what is going on? Thanks in advance, Madhavi
Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
Nvidia lists that monitor on their list of supported hardware: http://www.nvidia.com/object/3d-vision-requirements.html They even sell some Acer monitors in their online store although they are labeled in conflicting ways. I tried upgrading the driver yesterday to the 270.41.06 version but it didn't make any difference, still only 100 Hz. Are you using Windows or Linux? We're using the 64-bit Linux driver. -Eric On May 9, 2011, at 4:26 AM, Takaaki Fukami wrote: not seen a working 120 Hz stereo setup working on the Acer GD235 monitor. if you ask the Nvidia driver or the monitor, it reports 100 Hz instead This is what I encountered on Dell Alienware OptX AW2310 with Quadro FX3800, which has been fixed by nVIDIA Linux driver update (in 256.44). I don't know if the Acer monitor is compatible or not, it seems better to ask NVIDIA directly. see: http://twitter.com/#!/NVIDIAQuadro/status/65188179753435137 Takaaki Fukami - Discovery Platform Technology Dept. Gr.5 Chugai Pharmaceutical Co.,Ltd.
Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
Hi, I tried upgrading the driver yesterday to the 270.41.06 version but it didn't make any difference, still only 100 Hz. Are you using Windows or Linux? We're using the 64-bit Linux driver. We had the same problem initially with the Asus VG236 until we went into nvidia-settings and turned off Force Full GPU Scaling for the monitor under the GPU settings. Usually this option is unchecked for standard 60 - 75Hz LCDs but I found this was checked for some reason, unchecked it and then the monitor went blank momentarily and came back. Then the refresh rate increased from 99.99Hz to 119.98Hz. The information menu in the monitor itself also showed 120Hz. This has to be applied for every user or you can copy ~/.nvidia-settings.rc to other users' directories. The system is currently using the 260.19.26 linux 64 bit driver running CentOS5. Here's the xorg.conf : # nvidia-settings: X configuration file generated by nvidia-settings # nvidia-settings: version 260.19.26 (buildmeis...@swio-display-x86-rhel47-07.nvidia.com) Mon Nov 29 01:13:18 PST 2010 Section ServerLayout Identifier Layout0 Screen 0 Screen0 0 0 InputDeviceKeyboard0 CoreKeyboard InputDeviceMouse0 CorePointer Option Xinerama 0 EndSection Section Files FontPathunix/:7100 EndSection Section Module Load dbe Load extmod Load type1 Load freetype Load glx EndSection Section InputDevice # generated from default Identifier Mouse0 Driver mouse Option Protocol auto Option Device /dev/input/mice Option Emulate3Buttons no Option ZAxisMapping 4 5 EndSection Section InputDevice # generated from data in /etc/sysconfig/keyboard Identifier Keyboard0 Driver kbd Option XkbLayout us Option XkbModel pc105 EndSection Section Monitor # HorizSync source: edid, VertRefresh source: edid Identifier Monitor0 VendorName Unknown ModelName Ancor Communications Inc ASUS VG236 HorizSync 24.0 - 140.0 VertRefresh 50.0 - 122.0 #Option ExactModeTimingsDVI TRUE # 1920x1080 @ 120.00 Hz (GTF) hsync: 138.84 kHz; pclk: 368.76 MHz Modeline 1920x1080_120 368.76 1920 2072 2288 2656 1080 1081 1084 1157 -HSync +Vsync # 1920x1080 @ 110.00 Hz (GTF) hsync: 126.61 kHz; pclk: 336.28 MHz Modeline 1920x1080_110 336.28 1920 2072 2288 2656 1080 1081 1084 1151 -HSync +Vsync # 1920x1080 @ 100.00 Hz (GTF) hsync: 114.40 kHz; pclk: 302.02 MHz Modeline 1920x1080_100 302.02 1920 2072 2280 2640 1080 1081 1084 1144 -HSync +Vsync # Monitor preferred modeline (60.0 Hz vsync, 67.5 kHz hsync, ratio 16/9, 95 dpi) #ModeLine 1920x1080 148.5 1920 2008 2052 2200 1080 1084 1089 1125 +hsync +vsync ModeLine 1920x1080 148.500 1920 2008 2052 2200 1080 1084 1089 1125 +hsync +vsync Option DPMS EndSection Section Device Identifier Device0 Driver nvidia VendorName NVIDIA Corporation BoardName Quadro FX 3700 Option Stereo 10 EndSection Section Screen Identifier Screen0 Device Device0 MonitorMonitor0 DefaultDepth24 Option TwinView 0 Option metamodes 1920x1080_120 +0+0; 1920x1080_110 +0+0; 1920x1080_100 +0+0 SubSection Display Depth 24 EndSubSection EndSection Section Extensions Option Composite disable EndSection ### I don't know if the modelines are actually necessary. The nvidia driver usually recognizes metamodes such as 1920x1080_120. HTH, Sabuj Pattanayek
Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
Turning off force full gpu scaling is indeed the solution to this problem (at least it was for me). On May 10, 2011 6:58 PM, Eric Bennett er...@pobox.com wrote: Nvidia lists that monitor on their list of supported hardware: http://www.nvidia.com/object/3d-vision-requirements.html They even sell some Acer monitors in their online store although they are labeled in conflicting ways. I tried upgrading the driver yesterday to the 270.41.06 version but it didn't make any difference, still only 100 Hz. Are you using Windows or Linux? We're using the 64-bit Linux driver. -Eric On May 9, 2011, at 4:26 AM, Takaaki Fukami wrote: not seen a working 120 Hz stereo setup working on the Acer GD235 monitor. if you ask the Nvidia driver or the monitor, it reports 100 Hz instead This is what I encountered on Dell Alienware OptX AW2310 with Quadro FX3800, which has been fixed by nVIDIA Linux driver update (in 256.44). I don't know if the Acer monitor is compatible or not, it seems better to ask NVIDIA directly. see: http://twitter.com/#!/NVIDIAQuadro/status/65188179753435137 Takaaki Fukami - Discovery Platform Technology Dept. Gr.5 Chugai Pharmaceutical Co.,Ltd.
Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
Eric, Takaaki: I just remembered that we ran into the same problem. If you are using Linux try launching 'nvidia-settings' and disable GPU scaling. That helped with some of our monitors, which exhibited the same problem. Not sure if that would be applicable to Windows though. HTH Carsten -Original Message- From: CCP4 bulletin board on behalf of Eric Bennett Sent: Tue 5/10/2011 6:58 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro' Nvidia lists that monitor on their list of supported hardware: http://www.nvidia.com/object/3d-vision-requirements.html They even sell some Acer monitors in their online store although they are labeled in conflicting ways. I tried upgrading the driver yesterday to the 270.41.06 version but it didn't make any difference, still only 100 Hz. Are you using Windows or Linux? We're using the 64-bit Linux driver. -Eric On May 9, 2011, at 4:26 AM, Takaaki Fukami wrote: not seen a working 120 Hz stereo setup working on the Acer GD235 monitor. if you ask the Nvidia driver or the monitor, it reports 100 Hz instead This is what I encountered on Dell Alienware OptX AW2310 with Quadro FX3800, which has been fixed by nVIDIA Linux driver update (in 256.44). I don't know if the Acer monitor is compatible or not, it seems better to ask NVIDIA directly. see: http://twitter.com/#!/NVIDIAQuadro/status/65188179753435137 Takaaki Fukami - Discovery Platform Technology Dept. Gr.5 Chugai Pharmaceutical Co.,Ltd.
Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
Hi, Eric and Carsten, If you are using Linux try launching 'nvidia-settings' and disable GPU scaling. My system was RedHat5 64-bit. I set the option at that time, though I forgot to mention it… nvidia-settings stores the settings into ~/.nvidia-setting-rc, therefore it is not system-wide. I also annoyed that I should launch nvidia-settings when I login. Instead launching 'nvidia-settings', I set FlatPanelProperties in xorg.conf as below. Section Device Identifier Videocard0 Driver nvidia Option Stereo 10 Option FlatPanelProperties Scaling = Native EndSection Hope it helps. Takaaki From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Schubert, Carsten [PRDUS] Sent: Wednesday, May 11, 2011 9:48 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro' Eric, Takaaki: I just remembered that we ran into the same problem. If you are using Linux try launching 'nvidia-settings' and disable GPU scaling. That helped with some of our monitors, which exhibited the same problem. Not sure if that would be applicable to Windows though. HTH Carsten -Original Message- From: CCP4 bulletin board on behalf of Eric Bennett Sent: Tue 5/10/2011 6:58 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro' Nvidia lists that monitor on their list of supported hardware: http://www.nvidia.com/object/3d-vision-requirements.html They even sell some Acer monitors in their online store although they are labeled in conflicting ways. I tried upgrading the driver yesterday to the 270.41.06 version but it didn't make any difference, still only 100 Hz. Are you using Windows or Linux? We're using the 64-bit Linux driver. -Eric On May 9, 2011, at 4:26 AM, Takaaki Fukami wrote: not seen a working 120 Hz stereo setup working on the Acer GD235 monitor. if you ask the Nvidia driver or the monitor, it reports 100 Hz instead This is what I encountered on Dell Alienware OptX AW2310 with Quadro FX3800, which has been fixed by nVIDIA Linux driver update (in 256.44). I don't know if the Acer monitor is compatible or not, it seems better to ask NVIDIA directly. see: http://twitter.com/#!/NVIDIAQuadro/status/65188179753435137 Takaaki Fukami - Discovery Platform Technology Dept. Gr.5 Chugai Pharmaceutical Co.,Ltd.
