[COOT] backup file names
The files in the coot-backup directory incorporate the date into their name.
This caused a problem for one of our users, as the colon is a forbidden
character in the file transfer application used, which is Globus. Here is the
error message:
Error (transfer) Endpoint: Spectre (e2e2374a-5de4-11ed-8fd0-e9cb7c15c7d2)
Server: Globus Connect File:
/C/Users/usercl/OneDrive/Documents/Post-Doc/20221120/processing/coot-backup/coot-download_6nia.cif_Mon_Nov_21_01%3A01%3A20_2022_modification_0.cif.gz
Command: STOR
/C/Users/usercl/OneDrive/Documents/Post-Doc/20221120/processing/coot-backup/coot-download_6nia.cif_Mon_Nov_21_01:01:20_2022_modification_0.cif.gz
Message: Fatal FTP response --- Details: 500 Command failed. : A filename
cannot contain any of the following characters: \\ / : * ? " < > |\r\n
I suggest it would be preferable to substitute something else, such as an
underscore, for the colon in naming the files.
===
All Things Serve the Beam
===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
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[COOT] Sequence window
Coot 0.8.9.2 EL (ccp4) on Linux:
Why is the "Coot Sequence View" so big, particularly in the vertical? It
resists being squeezed smaller, and there is a lot empty wasted space at
the bottom. I have quite a few chains, and it is difficult to arrange
all the necessary windows on my desktop.
Oh, and Happy New Year.
--
===
All Things Serve the Beam
===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1
Re: [COOT] [ccp4bb] [COOT] 120hz LCDs and coot stereo
On Thu, 2009-12-17 at 18:25 -0500, Ajit Datta wrote: I just talked to the NVIDIA pre-sales people and they told me that this driver (195.22 beta) should work with 120Hz lcd monitors together with Nvidia 3D vision kit on a quadro graphics card. Ajit B. http://www.phoronix.com/scan.php?page=news_itempx=NzczOQ NVIDIA Pushes Out 195.22 Beta Linux Driver ... Other changes include... support for NVIDIA 3D Vision Stereo on Linux with Quadro GPUs... -- === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [COOT] [ccp4bb] [COOT] 120hz LCDs and coot stereo
On Thu, 2009-12-17 at 13:51 -0800, kai...@caltech.edu wrote: On this note, I recently bought a viewsonic 120hz LCD (VX2265wm) in the naïve believe it should work as it has the right refresh rate. I tried to run it with the normal setup, quadro with emitter via DIN, nuVision glasses, Linux. Here's the problem: I have stereo in the top and the bottom but not in the middle of the screen. The image is stable (no flickering or moving of the part that shows stereo). It seems that I got the right refresh rate (any way to check that?), but I don't understand at all what's going on. Any clues? Jens That monitor appears on the supported displays list: http://www.nvidia.com/object/3D_Vision_Requirements.html So the problem could be one (or more) of two things: 1) The glasses may be incompatible. You could try it out with the nVidia glasses. 2) The Linux driver may not be working properly yet. BTW, I see that some 1920x1080 monitors are listed on the above page, and should be available in January or so. -- === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[COOT] Hardware supported for 3D on MacOS?
Coot on Mac developers: What hardware is supported for Crystaleyes stereo in Coot under MacOS? Specifically, someone is asking me whether the Quadro 4800 card will be supported (with NuVision emmiter goggles and a big CRT) Thanks, - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [COOT] [PyMOL] Caution - 120 Hz LCDs: Not CRT killers yet...
It is my understanding that the LCD stereo monitors will be supported on Linux with the 185 driver series, not the 180 series. Open to correction. Is it really necessary to buy a new quadro card and the nVidia emitter/glasses combo? 1) Does nVidia intend to support the 120 Hz LCD monitors with existing quadro cards and emitters? 2) If a new card is necessary, I think the driver should work with GeForce cards, so that it may not be necessary to pay for Quadro. I haven't handled the equipment myself yet, but from pictures, it looks like the nVidia glasses may be more comfortable, but will not do as well fitting over eyeglasses. Cheers, - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu On Mon, 2009-06-22 at 09:54 -0700, Warren DeLano wrote: Hari Others, At this moment, the LCD flat panel to buy for use with PyMOL is the Zalman M220W (scan-line interleaved, passive stereo 3D). Unfortunately, last week's nVidia driver updates do not contain the expected support for 120 Hz LCDs from Samsung and ViewSonic. However, my personal belief and conviction is that they will be supported in the near future, and that they will work with PyMOL -- at least under Windows XP and Vista. Furthermore, having personally tested the stereo 3D capabilities of both the Samsung and ViewSonic displays with nVidia 3D Vision emitter and glasses, the Samsung 2233RZ is so much better at generating a clean, nearly ghost-free stereo 3D effect, that I plan to strongly recommend the Samsung 2233RZ over the ViewSonic VX2265wm, if (when) nVidia releases their stereo-3D-capable OpenGL drivers for 120Hz LCDs. Whereas the Samsung's 3D effect is equal to, if not better than a CRT, the ViewSonic is clearly inferior to both -- at least in my experience, using nVidia 3D Vision glasses. Hopefully ViewSonic's future 120 Hz products will be more competitive! So recap: If you need stereo 3D-capable today, then buy a Zalman M220W http://pymol.org/zalman . That display will work with Mac, Windows, and Linux, without need of any special graphics card. You give up half the vertical resolution, but hey -- it works today, and it works quite well. However, if you expect to need a stereo 3D capable LCD in the future, then plan on buying a 120Hz Samsung 2233RZ with the nVidia 3D Vision glasses and an updated Quadro graphics card. This will give you same high-quality, full-resolution 3D effect as a Crystal Eyes-based CRT setup. But please do wait until the critical drivers are released before spending any money, and realize that you may be stuck using Windows for the time being. Cheers, Warren -Original Message- From: hari jayaram [mailto:hari...@gmail.com] Sent: Monday, June 22, 2009 7:16 AM To: pymol-us...@lists.sourceforge.net; COOT@jiscmail.ac.uk Subject: Re: [PyMOL] Caution - 120 Hz LCDs: Not CRT killers yet... Hi I am wondering if there is a linux nvidia driver update or any other hack that allows Crystal Eyes 3 stereo products to work with the LCD 120Hz flat panel monitors. I should have read Warrens warning post (Dated Jan 23 , 2009 [ccp4bb] Caution - 120 Hz LCDs: Not CRT killers yet) , before purchasing the Viewsonic VX2265wm 120Hz LCD. But my CRT died last week and since I was addicted to pymol/coot-in stereo ( with Crystal Eyes 3 ) , I rushed out and bought this 120 Hz LCD monitor. Of course things dont work . And I am wondering if there is any update from nvidia or any other workaround that allows me to get stereo on this setup. Monitor : Viewsonic FuHzion VX2265wm 120Hz Graphics card: Quadro FX 4600 OS: Ubuntu Linux X86_64 - Hardy Heron 8.04 Stereo glasses: Crystal Eyes 3 with 3pin mini din connector Thanks for your help in advance Hari Jayaram Brandeis University On Tue, Feb 10, 2009 at 1:54 PM, Warren DeLano war...@delsci.com wrote: Donnie, This tripped me up for a while too, but I think the stereo DIN is an output (for projector, Z-screens, etc.) not an input. Suffice it to say that the nVidia USB dongle does not work (in my hands, with or without USB power) as a VESA-based emitter the way we apparently both hoped it would! Cheers, Warren -Original Message- From: Donnie Berkholz [mailto:dberkh...@gentoo.org] Sent: Tuesday, February 10, 2009 9:49 AM To: Warren DeLano Cc: pymol-us...@lists.sourceforge.net Subject: Re: [PyMOL] Caution - 120 Hz LCDs: Not CRT killers yet
[COOT] Troubles with torsion rotations in NAD
I have an NAD cofactor. Coordinates attached; they were generated by running libcheck on the CCP4 dictionary file NAD.cif (standard file taken from CCP4 6.1.0). I am trying to rotate various torsional angles. I am using the Edit Chi Angles feature of Coot 0.6-pre-1. Is this the best way? Behaviour seems a bit irregular. I frequently see this message (such as when attempting to rotate about var_2 NN1 -- NC1*): first atom : NN1: not found in residue WARNING:: failure to find all atom pair in residue atoms! Atom NN1 is in my file (attached). So is every other atom which appears in a torsion line with NN1 in the .cif file. If I choose the top listed bond (var_1 NC7 -- NC3), the nicotinamide ring rotates, but the rest of the dinucleotide doesn't. Attempting var_8 gives a CHI readout, but I can't see anything moving. Same for var_9. Cheers, - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu ATOM 1 NO7 NAD A 1 0.000 0.000 0.000 1.00 20.00 O ATOM 2 NC7 NAD A 1 0.986 1.010 0.066 1.00 20.00 C ATOM 3 NN7 NAD A 1 2.264 0.661 0.123 1.00 20.00 N ATOM 6 NC3 NAD A 1 0.588 2.438 0.051 1.00 20.00 C ATOM 7 NC4 NAD A 1 -0.737 2.770 0.244 1.00 20.00 C ATOM 9 NC5 NAD A 1 -1.049 4.111 0.230 1.00 20.00 C ATOM 11 NC6 NAD A 1 -0.094 5.090 0.042 1.00 20.00 C ATOM 13 NC2 NAD A 1 1.527 3.446 -0.147 1.00 20.00 C ATOM 15 NN1 NAD A 1 1.195 4.766 -0.150 1.00 20.00 N ATOM 16 NC1* NAD A 1 2.221 5.786 -0.370 1.00 20.00 C ATOM 18 NC2* NAD A 1 1.763 6.840 -1.365 1.00 20.00 C ATOM 20 NO2* NAD A 1 2.558 6.768 -2.519 1.00 20.00 O ATOM 22 NC3* NAD A 1 1.875 8.201 -0.658 1.00 20.00 C ATOM 24 NO3* NAD A 1 2.789 9.047 -1.317 1.00 20.00 O ATOM 26 NO4* NAD A 1 2.550 6.464 0.832 1.00 20.00 O ATOM 27 NC4* NAD A 1 2.438 7.884 0.733 1.00 20.00 C ATOM 29 NC5* NAD A 1 1.589 8.323 1.928 1.00 20.00 C ATOM 32 NO5* NAD A 1 0.283 7.838 1.811 1.00 20.00 O ATOM 33 NP NAD A 1 -0.861 7.976 2.917 1.00 20.00 P ATOM 34 NO1 NAD A 1 -2.086 7.327 2.393 1.00 20.00 O ATOM 35 NO2 NAD A 1 -0.343 7.583 4.244 1.00 20.00 O ATOM 36 O3 NAD A 1 -1.143 9.553 2.862 1.00 20.00 O ATOM 37 AP NAD A 1 -2.060 10.247 3.976 1.00 20.00 P ATOM 38 AO1 NAD A 1 -2.821 11.380 3.407 1.00 20.00 O ATOM 39 AO2 NAD A 1 -2.959 9.251 4.599 1.00 20.00 O ATOM 40 AO5* NAD A 1 -0.988 10.748 5.044 1.00 20.00 O ATOM 41 AC5* NAD A 1 0.055 11.614 4.702 1.00 20.00 C ATOM 44 AC4* NAD A 1 0.566 12.256 5.988 1.00 20.00 C ATOM 46 AO4* NAD A 1 1.597 13.153 5.579 1.00 20.00 O ATOM 47 AC1* NAD A 1 1.502 14.414 6.212 1.00 20.00 C ATOM 49 AC2* NAD A 1 0.221 14.422 7.029 1.00 20.00 C ATOM 51 AO2* NAD A 1 0.520 14.729 8.366 1.00 20.00 O ATOM 53 AC3* NAD A 1 -0.412 13.032 6.866 1.00 20.00 C ATOM 55 AO3* NAD A 1 -0.587 12.391 8.108 1.00 20.00 O ATOM 57 AN9 NAD A 1 1.512 15.495 5.237 1.00 20.00 N ATOM 58 AC8 NAD A 1 0.492 15.869 4.414 1.00 20.00 C ATOM 60 AN7 NAD A 1 0.920 16.921 3.701 1.00 20.00 N ATOM 61 AC5 NAD A 1 2.181 17.233 4.029 1.00 20.00 C ATOM 62 AC6 NAD A 1 3.036 18.216 3.566 1.00 20.00 C ATOM 63 AN6 NAD A 1 2.658 19.073 2.623 1.00 20.00 N ATOM 66 AC4 NAD A 1 2.580 16.341 5.009 1.00 20.00 C ATOM 67 AN3 NAD A 1 3.831 16.437 5.520 1.00 20.00 N ATOM 68 AC2 NAD A 1 4.702 17.412 5.081 1.00 20.00 C ATOM 70 AN1 NAD A 1 4.308 18.303 4.103 1.00 20.00 N # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level NAD
