Re: [COOT] duplication of the model during refinement

I believe there is a sequence of keystrokes that does that. It's happened to me occasionally as well. On 04/07/2024 11:12, Eleanor Dodson wrote: Hmmm that happened to me recently on a Mac.  I assumed I had done something silly - pushed a duplicate button or something.. Is there any way to do

Re: [COOT] Coot 1

stereo kit PyMOL was noticeably better. I wonder actually if stereo is so necessary in Coot 1 though..? - here's a side-by-side. Paul On 01/04/2022 11:32, Pedro Matias wrote: Hi Paul, Is stereo definitely off the table for Coot 1 or will you add it back later? If not, the I would ask CCP4

Re: [COOT] Coot 1

Hi Paul, Is stereo definitely off the table for Coot 1 or will you add it back later? If not, the I would ask CCP4 developers to *pretty please* keep coot 0.9 as a legacy option for us users who cannot live without stereo. Best, Pedro Em 01/04/2022 11:14, Paul Emsley escreveu: Coot 1 18

Re: [COOT] Coot Stereo Issue

rtx a4000 (a2000 will not work)... Cheers, Jeroen Am 02.03.22 um 13:07 schrieb Pedro Matias: Hi there, Coot stereo not working under Windows is a common problem. There seems to be a driver incompatibility that causes the issues you described. In our lab, we were able to use Coot stereo only under W

Re: [COOT] Coot Stereo Issue

Hi there, Coot stereo not working under Windows is a common problem. There seems to be a driver incompatibility that causes the issues you described. In our lab, we were able to use Coot stereo only under Windows 7, not on later Windows versions. As for the Linux hardware you do need a

[COOT] Simula VR SIMULA One - a Next-Gen Linux platform for COOT?

Dear COOTers, With the demise of NVIDIA 3D Vision, those of us who like to view their electron density maps in 3D stereo have very limited options, the main one being a careful nursing of the existing hardware. There is a pre-alpha COOT VR somewhere, but just today I became aware of a new

Re: [COOT] Coot 0.9.4.1 3D Hardware Stereo still does not work properly

Hi Paul, Às 13:53 de 23/02/2021, Paul Emsley escreveu: On 23/02/2021 13:42, Pedro Matias wrote: I tried both ways (coot.py and .coot) and only the latter worked for me. that should be .coot.py - presumably that's what you meant (but if not, it would explain why it didn't work) Yes. I took

Re: [COOT] Coot 0.9.4.1 3D Hardware Stereo still does not work properly

esn't work in my case, as if Coot overwrites this setting ... Cheers, Dirk. On 23.02.21 13:06, Pedro Matias wrote: Hi Dirk, I agree, but I "fixed" this by adding the line in question to my .coot file: cat ~/.coot (allow-duplicate-sequence-numbers) (set-nomenclature-errors-on-read &qu

Re: [COOT] Coot 0.9.4.1 3D Hardware Stereo still does not work properly

Hi Dirk, I agree, but I "fixed" this by adding the line in question to my .coot file: cat ~/.coot (allow-duplicate-sequence-numbers) (set-nomenclature-errors-on-read "ignore") (set-hardware-stereo-angle-factor 0.4 ) (set-display-lists-for-maps 0) HTH, Pedro Às 11:44 de 23/02/2021, Dirk

Re: [COOT] Hardware stereo mode in recent Coot versions

Hi Jean-Christophe, Is this in a Windows or Linux environment? In Linux, the problem you describe happens when maps are displayed in stereo. You can fix this by adding the line you mention to a .coot file in your user's root directory. I'm pasting below my .coot contents:

[COOT] Coot 0.9.2/3 in CCP4 - quad-buffered stereo broken?

Hi All, In the latest coot update (to 0.9.2) in CCP4 the quad-buffered stereo doesn't seem to work. The NVIDIA emitter turns on but the stereo picture does not appear when the glasses are turned on. I also tried  the 0.9.3 pre-release update and it has the same problem. I tried to install

Re: [COOT] CCP4 7.1 Coot - stereo

..". > ; DO NOT ADD COMMANDS TO THIS FILE - it is generated by Coot > ; BUT feel free to edit the setting > I wounder what would be the proper way to add settings to > coot-preferences.scm? > > Christoph > > Am 6/17/20 um 3:20 PM schrieb Pedro Matias: >> As a follow-up to

Re: [COOT] CCP4 7.1 Coot - stereo

As a follow-up to this message, set_display_lists_for_maps(0) in .coot.py does not work but (set-display-lists-for-maps 0) in .coot does work. Is there some nasty little insect at work here? Regards, Pedro Às 10:09 de 15/05/2020, Pedro Matias escreveu: > Hi Paul, > > Sorry for

Re: [COOT] CCP4 7.1 Coot - stereo

/2020, Paul Emsley escreveu: > > On 12/05/2020 14:42, Pedro Matias wrote: >> Hi, > > > Hi. > > >> >> Is there a way to control stereo separation / depth in the new COOT? The >> picture is excessively deep in comparison with the previous versi

Re: [COOT] CCP4 7.1 Coot - stereo

Hi Paul, Thanks for your reply. Is set_hardware_stereo_angle_factor(0.5) the default? Thanks, Pedro Às 16:23 de 12/05/2020, Paul Emsley escreveu: > > On 12/05/2020 14:42, Pedro Matias wrote: >> Hi, > > > Hi. > > >> >> Is there a way to control st

[COOT] CCP4 7.1 Coot - stereo

Hi, Is there a way to control stereo separation / depth in the new COOT? The picture is excessively deep in comparison with the previous version. BTW, the issue with set-display-lists-for-maps in stereo is still present in the COOT version distributed with CCP4 7.1. Best, Pedro -- Industry

[COOT] Problem with FLEV in COOT 0.8.9.1 EL (ccp4)

Dear All, The Ligand -> FLEV_this_residue option doesn't seem to work - I get an error message: No set_atom_type() for this build/compiler WARNING:: failure to construct rdkit molecule However, using Extensions -> Lidia -> view in LIDIA does work, provided the 3-character residue code is

Re: [COOT] After upgrades I can no longer run coot over an ssh connection

Hi all, Another problem might be that recent X server versions do not support something called "indirect rendering" which makes possible displaying OpenGL applications on a remote desktop not directly connected to the OpenGL server. I run remote sessions using tigervnc on a Linux server and

Re: [COOT] COOT 0.89 crashes when Hardware-Stereo (Quad-buffered, NVIDIA 3Dvision2) is enabled

other issue may be 32 vs 64 bit. I suspect that the issue > lies there that somehow a 32 bit application (WinCoot) is not fully > supported by the (3D) drivers. I shall make a 64 but version (*) > > B > > (*) it will come... Too much teaching currently > > On 19/03/2018 14:

Re: [COOT] Coot crashes on Windows 10 * SOLVED

Dear All, I managed to solve the problem (at least for now) by removing and reinstalling the current NVIDIA display driver (using the "Clean Install" in the custom install menu), followed by a reboot. Latest Coot now runs OK. Best regards, Pedro Às 09:43 de 20/11/2017, Pedro Matia

Re: [COOT] Coot crashes on Windows 10

do the trick. > > Bernhard > > On 20/11/2017 11:30, Pedro Matias wrote: >> Dear Bernhard, >> >> I don't use stereo in Windows. The graphics card is a GTX 1050. Which >> item in the list are you specifically referring to? >> >> Also, this happened only recen

Re: [COOT] Coot crashes on Windows 10

: > > > Dear Pedro, > > probably related to: > > http://bernhardcl.github.io/coot/wincoot-faq.html#mozTocId910462 > > please try this. It should solve your problem. Otherwise please get > back to me. > > Bernhard > > On 20/11/2017 10:43, Pedro Matias wrote: &