Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10
Xiao, If you connect the board and monitor by DisplayPort cable directly, it should work. I confirmed with Quadro M4000 and BenQ XL2420Z on CentOS 6, though not tested on Windows. Taka From: Xiao Lei [mailto:xiaolei...@gmail.com] Sent: Tuesday, January 31, 2017 10:08 AM Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10 I changed my mind, I should order the usb- powered DP to DVI dual link... On Mon, Jan 30, 2017 at 5:02 PM, Christine Gee <chr...@gmail.com<mailto:chr...@gmail.com>> wrote: Hi Xiao, I can confirm you need to buy an active adapter if you want to convert the display port on the graphics card to DVI. The one that they supply with the graphics card is passive and won't work. I was in the same boat about a year ago. I bought a USB powered active adapter which allowed 120htz. My monitor only had DVI input so I didn't try a direct display port connection. I can't comment on why that didn't work. Cheers Christine Sent from my iPhone On Jan 30, 2017, at 4:25 PM, Takaaki Fukami <fukami...@chugai-pharm.co.jp<mailto:fukami...@chugai-pharm.co.jp>> wrote: Dear Xiao, You need an active converter from DP to DVI. You can't get 120Hz if you use a passive converter, even with a DVI dual link cable. If you used an adapter come with the board, it's probably passive. Taka From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Xiao Lei Sent: Tuesday, January 31, 2017 9:10 AM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10 Dear All, I tried to make Coot and Pymol 3D working for a HP Workstation with Quadro M4000 graphics card, the card has four displayport. I also has a Asus 24 inch 3D monitor. I tried to connect the graphics card with the monitor through displayport to displayport connection and displayport to DVI-D dual link connection but failed to set the monitor run on 120Hz. It seems I have to follow the old way of using DVI-D dual link connection for both graphic card and monitor, but the problem is that the graphics card does not have a DVI-D dual link socket, it only have displayport. I appreciate any suggestions.
Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10
Dear Xiao, You need an active converter from DP to DVI. You can't get 120Hz if you use a passive converter, even with a DVI dual link cable. If you used an adapter come with the board, it's probably passive. Taka From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Xiao Lei Sent: Tuesday, January 31, 2017 9:10 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10 Dear All, I tried to make Coot and Pymol 3D working for a HP Workstation with Quadro M4000 graphics card, the card has four displayport. I also has a Asus 24 inch 3D monitor. I tried to connect the graphics card with the monitor through displayport to displayport connection and displayport to DVI-D dual link connection but failed to set the monitor run on 120Hz. It seems I have to follow the old way of using DVI-D dual link connection for both graphic card and monitor, but the problem is that the graphics card does not have a DVI-D dual link socket, it only have displayport. I appreciate any suggestions.
[ccp4bb] N-methyl-peptide bond restraints in refmac
Dear all, We have a 2 A dataset for a structure containing an N-methyl-peptide, and I want to refine the model with coot/refmac. I made a cif file for the peptide alone, with an unused het ID like VV0, without any difficulties. When I refined a model with the cif file by refmac, N-methyl-peptide bonds in trans-configuration were automatically recognized and restrained as planer, however, not those in cis-configuration. There were some N-methyl-peptide bonds in the structure, in trans and cis, and all cis-N-methyl-peptide bonds were distorted (not restrained as planer, and angles around the N atoms seemed not to be restrained). How can I make/add restraints for cis-N-methyl-peptide bonds? I'd like to integrate the restraints in the CCP4 default library file ($CLIBD_MON/list/mon_lib_list.cif ?). Is it enough to add new _chem_link and _chem_mod entries to the file? Does Coot also read it? Best regards, Takaaki Fukami - Dr. Takaaki Fukami (mailto:fukami...@chugai-pharm.co.jp) Discovery Research Dept. (Biostructure Gr.) Chugai Pharmaceutical Co.,Ltd.
Re: [ccp4bb] how to dump diffraction image header info?
Dear all,
Thank you all giving a valuable information.
I wanted to get the header info in my script, and from images not only in the
.cbf format,
though I didn’t write so. Thanks Harry for giving me a list of formats which
have a text header.
Unfortunately, I couldn’t find a way to print out the header information by
Mosflm.
Although dxtbx.print_header is nice, it doesn’t write a collection date/time in
the header,
which I also want to know. I can’t dig out a method to get the date/time in
dxtbx.
Clemens introduced me the ‘imginfo’ tool in autoPROC, and it gave me all what I
wanted.
Thanks again for your kind helps.
Takaaki
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Graeme
Winter
Sent: Monday, December 1, 2014 10:46 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] how to dump diffraction image header info?
Dear All,
dxtbx.print_header /path/to/image should work
Graemes-MacBook-Pro:~ graeme$ dxtbx.print_header
data/i04-BAG-training/th_8_2_0001.cbf
=== data/i04-BAG-training/th_8_2_0001.cbf ===
Using header reader: FormatCBFMiniPilatusDLS6MSN100
Beam:
wavelength: 0.97625
sample to source direction : {0,0,1}
divergence: 0
sigma divergence: 0
polarization normal: {0,1,0}
polarization fraction: 0.999
Goniometer:
Rotation axis: {1,0,0}
Fixed rotation: {1,0,0,0,1,0,0,0,1}
Setting rotation:{1,0,0,0,1,0,0,0,1}
Detector:
Panel:
pixel_size:{0.172,0.172}
image_size: {2463,2527}
trusted_range: {-1,161977}
fast_axis: {1,0,0}
slow_axis: {0,-1,0}
origin: {-210.76,205.277,-265.27}
Scan:
image range: {1,1}
oscillation: {82,0.15}
Total Counts: 1437712
Best wishes Graeme
On Mon Dec 01 2014 at 12:40:09 PM David Waterman
dgwater...@gmail.commailto:dgwater...@gmail.com wrote:
Dear Takaaki,
dxtbx provides a way to do this (see
http://journals.iucr.org/j/issues/2014/04/00/jo5001/jo5001.pdf). It is
available in ccp4-python (try 'import dxtbx'), however there is no script
currently in CCP4 that uses this to print the header information. One could
write such a script easily though, and I would be happy to provide one off-list
if you are interested. Scripts like this already exist in the DIALS project
(http://dials.sourceforge.net/ - try e.g. dials.import /my/images/*.cbf;
dials.show_models datablock.json).
Note that the dxtbx way is not giving you direct access to header values, but
will print information about experimental models constructed from the headers.
Usually this is what you want. If not, ADXV
(http://www.scripps.edu/tainer/arvai/adxv.html) is a useful tool that can
display image header values, but I don't know if this can be scripted to print
to console.
Cheers
-- David
On 1 December 2014 at 11:22, Takaaki Fukami
fukami...@chugai-pharm.co.jpmailto:fukami...@chugai-pharm.co.jp wrote:
Dear all,
I'd like to dump header information of a diffraction image file.
CCP4 diffdump is a good tool, though it outputs the same angle
for both oscillation start and end for .cbf image. (bug?)
Are there any other tools to get diffraction image header info?
Regards
-
Takaaki Fukami
(mailto:fukami...@chugai-pharm.co.jpmailto:fukami...@chugai-pharm.co.jp)
Discovery Research Dept. (Biostructure Gr.)
Chugai Pharmaceutical Co.,Ltd.
[ccp4bb] how to dump diffraction image header info?
Dear all, I'd like to dump header information of a diffraction image file. CCP4 diffdump is a good tool, though it outputs the same angle for both oscillation start and end for .cbf image. (bug?) Are there any other tools to get diffraction image header info? Regards - Takaaki Fukami (mailto:fukami...@chugai-pharm.co.jp) Discovery Research Dept. (Biostructure Gr.) 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.
Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
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. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eric Bennett Sent: Saturday, May 07, 2011 8:38 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro' We recently had issues setting up a 3D projector and have tried lots of combinations of monitors, drivers, cards, glasses, etc. The answer seems to be that interchangeability is very complicated and you won't know unless you try it. For example, with the last version of the Nvidia driver I tested, the driver refused to put out an Nvidia 3D Vision sync signal (stereo 10 in xorg.conf) unless there was a 3D capable LCD attached. I don't know of any technical reason the Nvidia 3D Vision couldn't be used with a CRT but Nvidia has apparently chosen to disable it (or at least make it hard to enable) in the Linux driver. Going the other direction, using RealD with and LCD system, it might be possible but you probably have to match your RealD emitter with RealD glasses. Older CrystalEyes glasses (CE3 and earlier) generally do not work with LCD monitors because of the polarization in the glasses. We recently got some CE4 glasses and they don't seem to have that problem although in practice we are using them with a projector, not LCD monitors. But I don't really like the CE4's, there is too much of my field of vision under the glasses that they don't cover. We've observed some really weird configurations that appear to mostly work, such as plugging in a RealD emitter and glasses when the driver is configured to output a signal for Nvidia 3D Vision (stereo 10 option under Linux). You don't say whether you are using Windows or Linux and there may be variations in the drivers, variations by card, etc. Regarding card to card variations, we've observed 3D setups in conference rooms with multiple emitters where some Nvidia cards happily drive multiple emitters with particular splitters boosters, but other Nvidia cards don't. The bottom line is if you mix hardware you might have problems and vendors are unlikely to help you. If you have CE4 glasses already, you can try it with an LCD and it may work. Otherwise, if you have to buy new glasses (ie, you have CE3 or older), you might as well get the Nvidia package with the emitter included. 3D Vision Pro uses the 2.4 GHz band instead of IR to transmit the sync signal so if you were setting up a conference room in theory the Pro version might be less likely to leave dead zones in the conference room. For a single user workstation it's very unlikely that you would get any benefit. Just to muddy the waters a bit, I have not seen a working 120 Hz stereo setup working on the Acer GD235 monitor. We have a bunch of them set up, and we put a 120 Hz mode line in xorg.conf. If you ask X11 it says it's running at 120. But if you ask the Nvidia driver or the monitor, it reports 100 Hz instead, and visually there is enough flickering that the monitor and the driver seem to have the correct number. I'm curious if anyone else here has looked in detail to make sure their Acer-based system is running at 120 and found that it is actually doing what people claim it can do. I find the 100 Hz LCD flicker annoying over long periods so I am still a neanderthal CRT user. My coworkers were convinced their LCD systems were running at 120, when they were actually only running at 100. I'm not sure if this is a driver problem or a monitor problem. -Eric On May 6, 2011, at 11:27 AM, zhang yu wrote: Dear colleagues, Sorry to present the stereo issue to the board again. Since my old SGI CRT monitor only has 75 HZ refresh rate, the flickering in stereo mode bothered me a lot. Recently, I want to update my old CRT to 120 HZ LCD. I have a Nvidia Quadro FX3800 in my workstation. I would like to make sure some issues before I make the upgrade. 1. Can I apply the previous stereo emitter (Purchased from Real D, Model #E-2) to 120HZ LCD? Although the company told me this emitter is not compatible with LCD, could some one tell me why? Is it true that the Nvidia 3D vision is the only solution for the stereo in LCD? 2. Nvidia supply two kinds of 3D emitters. One of them is 3D vision, while the other one is 3D vision pro. Which one is sufficient for crystallographier user? (3D vision pro is much more expensive than 3D
Re: [ccp4bb] Zalman LCD availability
Hi, Francois We bought it 5 months ago from a supplier in Japan. (and it has been put back in a box under a desk.) Zalman has its own web site in Japan. Model name is the same. http://www.zalman.com/jpn/product/monitors/ZM-M220W.asp You can buy it from many shops through the web. Check the most famous comparison site in Japan, kakaku.com: http://kakaku.com/item/00854312463/ HTH Takaaki Fukami -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Francois Berenger Sent: Friday, January 15, 2010 1:31 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Zalman LCD availability Hello, By the way, does anyone got this LCD in Japan? My team is interested to know the model's exact reference as well as from where you ordered it. Thanks a lot, Francois.
