Re: [COOT] Coot 1

2022-04-01 Thread Pedro Matias 

Hi Paul,

The new Coot does have a nice depth of field and that certainly helps to 
provide a 3D feeling to the image. Still, I hope you can manage to bring 
it back at some future date. Old habits die hard...


Best,

Pedro

Em 01/04/2022 12:03, Paul Emsley escreveu:


Hi Pedro,

Stereo is not available because I didn't have access to stereo at home 
and I have not been keen on touching communal equipment at the lab. My 
guess is that it needs only 100 lines or so - many of those are in 
Coot 0.9.x. I would like a chance to revisit the view matrices though 
- during a recent test of new 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 developers to *pretty please* keep coot 
0.9 as a legacy option for us users who cannot live without stereo.






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Re: [COOT] Coot 1

2022-04-01 Thread Pedro Matias 

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 years after the release of Coot 0 it's time that I actually 
released Coot 1.


Coot 1 is a major change beyond Coot 0. It has required a lot of 
writing and rewriting [1]
and has been the preponderance of my work since 2017. I have had to 
learn how to program
graphics from scratch using the new style. Much of the GUI internals 
has been

rewritten [2].

My experience with 0.9 was that I sat on it, bug-fixing for a long 
time, releasing it
too late. I don't want to repeat that mistake. So here we are, there's 
a lot of good new

stuff in Coot 1, but it's not as slick as it might be (or will become).

  o Update graphics to use OpenGL 3.3
  o Update Python to use version 3.9
  o Update GTK+ to use version 3

While many of the features that were available in 0.9.x have been 
reworked or
re-implemented, there are some gaps. Dropped features include 
Cross-hairs, Stereo, Pisa
interface, built-in key-bindings, NCS Ghosts, Edit Phi/Psi, 
anti-aliasing, Kleywegt
plots, the clipping dialog, Chemical Feature Clustering, 
Dynamically-Transformed/NCS
Maps, LSQ plane distances, dynamic distances, CABLAM-markup, the test 
suite,
user-defined colour schemes, anisotropic atoms, CURLEW, Scheme GUI 
scripting,

Skeletonization and Baton-Building.

"So, is there anything that _does_ work?" - you might ask...

The GUI has been updated, I have tried to cut down on the number of 
dialogs, the Real
Space Refinement in particular has seen quite a lot of work. The GUI 
now uses dark mode
if the theme is installed [3]. Several menu items have been relocated. 
More menus are now

alphabetically ordered [4].

The graphics is, by default, now based on triangles instead of lines 
which affords a
more pleasing representation (density maps can be represented using 
both modes) and one
can have a more expeditious if not pleasant experience with a fast 
graphics card and a
big screen. The various graphics effects and filters can be tailored 
to some extent by
changing the configuration using the GUI or by editing/replacing the 
shaders.

Full-screen mode is now an option [5].

Overall, the GUI has only had light testing. At the moment, it's 
probably best to
avoid closing dialogs using the window manager. The "OK" button now 
appears after the

"Cancel" button in dialogs.

Python scripting now has uses a history from previous sessions and the 
functions need
to be used with namespaces/modules (e.g. "coot", or "coot_utils"). 
Coot (or coot) is

now a module that can be imported into python.

This build compiles with the RDKit and optionally MoleculestoTriangles 
from Martin Noble.


The map and the model can now be exported to glTF files (for use in 
Blender and other

3D modelling software).

The build script for Coot 1, called build-it-3-3 can be found in the 
"Build from Scratch"
menu on the web page (you will need to have already installed cmake 
and Gtk+). The catch
though is that (at least in my hands) Python and friends are 
frustratingly difficult to
install, so it's possible/likely that the build script won't work. 
Likewise,
the script doesn't work for Mac OS either. But it is currently the 
best method to get
binaries so I will support it if you try it [6]. (Homebrew might be 
another method.)


Bernhard Lohkamp has been working on the WinCoot version - I will 
defer WinCoot

questions to him.

Mac Coot is now native (no X11/XQuartz needed). I would be interested 
to see how a

natively-compiled [7] version works on an M1 Max processor [8,9].

Judging from previous experience, a few rapid iterations of bug-fix 
releases will be
needed. After this, the version numbers will become sane - it's my 
plan to release a new

major version every year or so.

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-1.tar.gz 



Normally I don't cross-post releases, but this one I thought I should.


[1] new as in OpenGL 3.3 or later - using shaders - I don't mean 
Vulkan (that's for the

    future)
[2] the patch from the 0.9.x version is 285k lines
[3] I recommend it
[4] rather than chronologically
[5] double-tap Esc key (the first time) to revert to standard display
[6] I have be working with CCP4 collaborators to use their system to 
build Coot binaries.
    Hopefully the binaries will be available stand-alone, as well as 
integrated into

    the CCP4 Suite via that method
[7] so that's a different meaning of "native"
[8] the little testing I have done on a recent intel MacBook Pro shows 
unimpressive

    performance (Iris graphics, retina display)
[9] Thanks to my Mac-using colleagues for their feedback.



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Re: [COOT] Coot Stereo Issue

2022-03-02 Thread Pedro Matias 

Hi Jeroen,


Thanks for the update on Windows. I am glad this issue has finally been 
fixed (albeit indirectly). Still, we have now moved entirely to Linux 
systems and we keep praying for the continued good health of our 3D 
Vision emitters and glasses...



By "specs" I meant a note in the product sheet "3D Vision support - yes" 
that could be found on several Quadro cards.



Best regards,


Pedro


Em 02/03/2022 12:45, mesters escreveu:

Hi Pedro,

Zhuang's problem was finally solved by installation of the latest 
nvidia graphics card driver 511.79.


WinCoot works on windows 10, no doubt: Nvidia however stopped 
supporting the 3D Vision kit from within (professional) graphics 
drivers and instead offers a stand-alone separate 3D Vision driver 
390.41 that will not be updated in the future (only in case of 
security issues). So, how long this work-around will be useful is 
unknown. For the future this means, one probably needs to purchase 
the much more expensive GPUs...


For linux, there is an absolute requirement for the 3-pin connector 
(either build-in or attachable via bracket) as the USB-based 3D Vision 
kit was never actively supported by Nvidia under linux (and that is 
indeed a commercial decision...).


"Specs" will not help to select the GPU as even the small P400 or P620 
offers - according to specs - 3D quad-buffered openGL stereo support 
(that is, under Windows and making use of the 3D Vision kit). What you 
need under Linux is an nvidia GPU with an on-board 3-pin DIN stereo 
connector or, a GPU with a connector for the 3-pin DIN stereo bracket 
(NVIDIA 699-50764--001 or PNY 930-50764). So, for the GPU, one 
needs to pick a second hand model such as K / M /P4000, or newer 
models such as rtx 4000 or 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 
Windows 7, not on later Windows versions.



As for the Linux hardware you do need a more expensive graphics card 
- as far as I know there is no technical reason for the 3-pin 
connector requirement and it may be just a commercial decision by 
NVIDIA to require this. However, since NVIDIA discontinued the 3D 
Vision support these cards may be more difficult ro obtain. Basically 
you need a NVIDIA Quadro K4000, similar or higher specs - it should 
support 3D Vision stereo (maybe this is indicated in the specs and/or 
in the box).



Regards,


Pedro



Em 01/03/2022 14:03, Li, Zhuang escreveu:

Hi Jeroen,
Thank you so much for your response. I use a Win10 pro with Nvidia 
graphics driver 442.92 and 3D vision controller driver 390.41, and 
BenQ XL2411P 3D monitor. The IR emitter is connected to the computer 
only via USB, and together with 3D glasses, was from a 
not-so-often-heard vendor called epiphan.  It works pretty fine in 
UCSF chimera and PyMOL, so I assume the hardware and software 
configuration is correct. I did enable the stereo mode in Nvidia 
control panel.
This is the first time I setup a 3D work environment, and I used 
Win10 to make thing less complicated. Next time I would like to set 
up 3D workstation in Linux. Could you please kindly provide the 
hardware list that is guaranteed working with Linux? Could you 
please clarify what a 3-PIN connector is and how is it making things 
different?

Thank you in advance.
Zhuang


*From:* mesters 
*Sent:* Tuesday, March 1, 2022 8:42 AM
*To:* Li, Zhuang 
*Subject:* Fwd: Coot Stereo Issue
Please also check the following..

1.

On Windows 10, make sure “3D display mode” is set to “On” in
Windows settings: Settings --> Display --> Advanced

2.

Make sure OpenGL is turned on: --> Manage 3D Settings --> Global
Presets --> OpenGL rendering GPU --> 

3.

Make sure Stereo is turned on: --> Manage 3D Settings --> Global
Presets --> Stereo - Enabled >

4.

if steps 1-3 do not help, rollback the driver: 12/29/2016
Version 21.21.13.7654


 Weitergeleitete Nachricht 
Betreff:Re: Coot Stereo Issue
Datum:  Tue, 1 Mar 2022 14:35:59 +0100
Von: 	mesters  
<mailto:mest...@biochem.uni-luebeck.de>

An: Li, Zhuang  <mailto:li3...@purdue.edu>



More info would be good

What windows version?
What nvidia driver version?
Monitor type?
Quadro P620? This one does not have a 3-pin connector for signal 
output


Are you by any chance trying to use "Nvidia Vision" glasses with an 
usb-emitter to view the 3D output? This option is no longer 
supported with the newer nvidia drivers


J.


Am 01.03.22 um 13:19 schrieb Li, Zhuang:

Hi guys,
When I switched mono to hardware stereo, my coot window stuck. I 
tried 0

Re: [COOT] Coot Stereo Issue

2022-03-02 Thread 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 Windows 7, not on 
later Windows versions.



As for the Linux hardware you do need a more expensive graphics card - 
as far as I know there is no technical reason for the 3-pin connector 
requirement and it may be just a commercial decision by NVIDIA to 
require this. However, since NVIDIA discontinued the 3D Vision support 
these cards may be more difficult ro obtain. Basically you need a NVIDIA 
Quadro K4000, similar or higher specs - it should support 3D Vision 
stereo (maybe this is indicated in the specs and/or in the box).



Regards,


Pedro



Em 01/03/2022 14:03, Li, Zhuang escreveu:

Hi Jeroen,
Thank you so much for your response. I use a Win10 pro with Nvidia 
graphics driver 442.92 and 3D vision controller driver 390.41, and 
BenQ XL2411P 3D monitor. The IR emitter is connected to the computer 
only via USB, and together with 3D glasses, was from a 
not-so-often-heard vendor called epiphan.  It works pretty fine in 
UCSF chimera and PyMOL, so I assume the hardware and software 
configuration is correct. I did enable the stereo mode in Nvidia 
control panel.
This is the first time I setup a 3D work environment, and I used Win10 
to make thing less complicated. Next time I would like to set up 3D 
workstation in Linux. Could you please kindly provide the hardware 
list that is guaranteed working with Linux? Could you please clarify 
what a 3-PIN connector is and how is it making things different?

Thank you in advance.
Zhuang


*From:* mesters 
*Sent:* Tuesday, March 1, 2022 8:42 AM
*To:* Li, Zhuang 
*Subject:* Fwd: Coot Stereo Issue
Please also check the following..

1.

On Windows 10, make sure “3D display mode” is set to “On” in
Windows settings: Settings --> Display --> Advanced

2.

Make sure OpenGL is turned on: --> Manage 3D Settings --> Global
Presets --> OpenGL rendering GPU --> 

3.

Make sure Stereo is turned on: --> Manage 3D Settings --> Global
Presets --> Stereo - Enabled >

4.

if steps 1-3 do not help, rollback the driver: 12/29/2016 Version
21.21.13.7654


 Weitergeleitete Nachricht 
Betreff:Re: Coot Stereo Issue
Datum:  Tue, 1 Mar 2022 14:35:59 +0100
Von: 	mesters  


An: Li, Zhuang  



More info would be good

What windows version?
What nvidia driver version?
Monitor type?
Quadro P620? This one does not have a 3-pin connector for signal 
output


Are you by any chance trying to use "Nvidia Vision" glasses with an 
usb-emitter to view the 3D output? This option is no longer supported 
with the newer nvidia drivers


J.


Am 01.03.22 um 13:19 schrieb Li, Zhuang:

Hi guys,
When I switched mono to hardware stereo, my coot window stuck. I 
tried 0.9.7  0.9.6  0.8.7, they look all the same. I used an AMD CPU 
and Quadro P620 card, and the hardware setup is working for PyMOL and 
UCSF Chimera.

Please see screenshot as attached, and any input would be appreciated.

Zhuang




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Visiting Professorship (South Bohemian University 
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[COOT] Simula VR SIMULA One - a Next-Gen Linux platform for COOT?

2021-12-20 Thread Pedro Matias 

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 VR headset that may be the future for COOT in 3D or VR. It is not 
available commercially yet, but seems rather exciting.


Of course, COOT will need to be ported to that system...

More info at https://simulavr.com/

Happy Holiday Season for all,

Pedro

--

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

2021-02-23 Thread Pedro Matias 

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 out the . to inactivate the file when I saw it didn't work.







.coot-preferences is a directory and its contents should not be 
edited by the user.


You'd think so, wouldn't you? I made a mistake about this directory 
years ago and have regretted it since.


Future Coots will have:

$HOME/.coot/

   preferences/   # these are scripts written by Coot

   startup-scripts/   # these are scripts that you write


I thought I had read this recommendation somewhere in your documentation.

If you do change the directory structure, I hope the first Coot version 
to implement it will migrate the old structure to the new one...






Both .coot and coot.py should reside in the user's home directory.


.coot.py yes.


For me, .coot in $HOME also works.





Paul.



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

2021-02-23 Thread Pedro Matias 

I tried both ways (coot.py and .coot) and only the latter worked for me.

.coot-preferences is a directory and its contents should not be edited 
by the user.


Both .coot and coot.py should reside in the user's home directory.

Às 13:02 de 23/02/2021, Dirk Kostrewa escreveu:

A few more tests:

if I set set_display_lists_for_maps(0) in my coot.py in 
.coot-preferences, switching to 3D stereo still leads to disappearing 
electron density maps, but if I set (set-display-lists-for-maps 0) in 
.coot, as suggested by Pedro, switching to 3D stereo does not lead to 
disappearing electron density maps. So, this is a work-around.


Best regards,

Dirk.

On 23.02.21 13:50, Dirk Kostrewa wrote:

Dear Paul,

no, I don't care about the error messages - it is the disappearing 
electron density maps upon switching to 3D stereo that is so annoying.


Cheers,

Dirk.

On 23.02.21 13:45, Paul Emsley wrote:
So, let me be clear. The bug is: "I get lots of annoying error 
messages on starting stereo. If I set_display_lists_for_maps(0) then 
it's OK and the messages go away. I want Coot to start up in a way 
where I don't have to type set_display_lists_for_maps(0)"


Is that right?

I don't have access to hardware stereo equipment at the moment, so 
it's practically impossible for me to debug this. Although I could 
suppress the error message.



Paul.


On 23/02/2021 12:17, Dirk Kostrewa wrote:

Hi Pedro,

yes, thank you for the suggestion. I've tried this, of course, but 
it doesn'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 "ignore")
(set-hardware-stereo-angle-factor 0.4 )
(set-display-lists-for-maps 0)


HTH,

Pedro

Às 11:44 de 23/02/2021, Dirk Kostrewa escreveu:

Dear Paul,

I've just updated CCP4 7.1 which contains the new Coot version 
0.9.4.1. Unfortunately, as for months now, 3D hardware stereo 
still does not work properly in this version. Upon switching to 
3D hardware stereo mode, any electron density map disappears, and 
the terminal from which Coot was started shows a lot of error 
messages "ERROR:: using display list 0 when main_or_secondary is 
1". I have to manually either give the guile script command 
"(set-display-lists-for-maps 0)" or the equivalent python script 
command "set_display_lists_for_maps(0)" to let the maps reappear. 
After issuing one of the two mentioned script commands, switching 
to 3D hardware stereo does not lead to disappearing density maps 
or produce any error messages in the terminal for the running 
Coot session, anymore.


Could you please fix this long-standing annoying bug? Our users 
tell me, that this bug drives them crazy.


Best regards,

Dirk.



 



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

2021-02-23 Thread Pedro Matias 

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 Kostrewa escreveu:

Dear Paul,

I've just updated CCP4 7.1 which contains the new Coot version 
0.9.4.1. Unfortunately, as for months now, 3D hardware stereo still 
does not work properly in this version. Upon switching to 3D hardware 
stereo mode, any electron density map disappears, and the terminal 
from which Coot was started shows a lot of error messages "ERROR:: 
using display list 0 when main_or_secondary is 1". I have to manually 
either give the guile script command "(set-display-lists-for-maps 0)" 
or the equivalent python script command 
"set_display_lists_for_maps(0)" to let the maps reappear. After 
issuing one of the two mentioned script commands, switching to 3D 
hardware stereo does not lead to disappearing density maps or produce 
any error messages in the terminal for the running Coot session, anymore.


Could you please fix this long-standing annoying bug? Our users tell 
me, that this bug drives them crazy.


Best regards,

Dirk.


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

2020-12-29 Thread Pedro Matias 

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:



(allow-duplicate-sequence-numbers)
(set-nomenclature-errors-on-read "ignore")
(set-hardware-stereo-angle-factor 0.4 )
(set-display-lists-for-maps 0)


This works fine in 0.9.3 distributed with CCP4 (quad-buffered stereo was 
broken in 0.9.2 and may still be in the standalone 0.9.3 version).


Hope this is of help to you.

Regards,

Pedro

Às 14:41 de 24/12/2020, Jean-Christophe HAESSIG escreveu:

Hi,

I'm packaging Coot for our users which are keen on stereo mode (namely,
using 3D Vision hardware).

I have it working in 0.8.2, but starting from 0.8.9.1, it displays a
black screen when stereo mode is selected. Getting back to mono
displays correctly.

I have found a thread in the mailing list dating back from Feb'20 which
seemingly states the same problem with console messages like

ERROR:: using display list 0 when main_or_secondary is 1
(hardware-stereo-mode)
(stereo-mode-state)
ERROR:: using display list 0 when main_or_secondary is 1

However the suggested fix :


(set-display-lists-for-maps 0) ;; or maybe 1

does not seem to do anything, it just turns stereo mode off.

I tested this in 0.9.3.

I have a programming background so if required I can have a look but I
would be glad to have some pointers about where all that stuff happens
in the code.

Thank you,
J.C. Haessig
Systems administrator -- IGBMC




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

2020-11-25 Thread Pedro Matias 

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 0.9.1 from Paul's repository in standalone mode but 
it complains about a lot of missing libraries - which it did not in CCP4.


Best,

Pedro

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Re: [COOT] CCP4 7.1 Coot - stereo

2020-06-18 Thread Pedro Matias 
Hi Christoph,

The .coot file must reside in your root directory, not in
.coot-preferences, .i.e., ~/.coot

Also, I think you should only have either .coot or .coot.py there.

The .coot-preferences file is overwritten every time you change settings
in the program (and set-display-lists-for-maps is not one of them).

Regards,

Pedro

Às 09:02 de 18/06/2020, Christoph Parthier escreveu:
> Hi Pedro,
>
> For me (under Linux) the .coot file (placed the .coot-preferences directory) 
> seems to be ignored.
> Hardware stereo for map display in Coot 0.9 only worked for me when I added 
> (set-display-lists-for-maps 0)
> to the coot-preferences.scm (also in .coot-preferences directory) although 
> there is the following warning in the file:
>
> ; These commands are the preferences of coot.  You can evaluate them
> ; using "Calculate->Run Script...".
> ; 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 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 insisting, but I can't get the set_display_lists_for_maps(0)
>>> to work on my $HOME/.coot.py preferences file. COOT starts in mono by
>>> default and this command is ignored. It only works after I enter stereo
>>> mode, input through the scripting window.  Also, it does not seem to be
>>> saved in the 0-coot-state files so if I resume a previous COOT session I
>>> have the same problem. Am I doing something wrong? Is there a workaround
>>> for this issue?
>>>
>>> BTW, the stereo on COOT 0.9 looks great - I guest that the different
>>> approach makes a big improvement.
>>>
>>> Best,
>>>
>>> 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 stereo separation / depth in the new COOT? The
>>>>> picture is excessively deep in comparison with the previous version.
>>>> What you are mostly seeing, I think, is that the transformation
>>>> between the eyes is no longer a rotation and is now a shear. Which
>>>> means that now we don't get part of the map showing up in the left eye
>>>> but not the right (or vice versa).
>>>>
>>>> Anyway, yes there is and it's documented in Section 3.4.1
>>>>
>>>> set_hardware_stereo_angle_factor(0.5) # for the Python fans
>>>>
>>>>
>>>>> BTW, the issue with set-display-lists-for-maps in stereo is still
>>>>> present in the COOT version distributed with CCP4 7.1.
>>>>>
>>>> It might be a while before I am sitting at a stereo display so that I
>>>> can address that. It's not top priority as there is a reasonable
>>>> work-around.
>>>>
>>>>
>>>> Paul.
>>>>
>
>
> 
>
> To unsubscribe from the COOT list, click the following link:
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>
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Re: [COOT] CCP4 7.1 Coot - stereo

2020-06-17 Thread Pedro Matias 
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 insisting, but I can't get the set_display_lists_for_maps(0)
> to work on my $HOME/.coot.py preferences file. COOT starts in mono by
> default and this command is ignored. It only works after I enter stereo
> mode, input through the scripting window.  Also, it does not seem to be
> saved in the 0-coot-state files so if I resume a previous COOT session I
> have the same problem. Am I doing something wrong? Is there a workaround
> for this issue?
>
> BTW, the stereo on COOT 0.9 looks great - I guest that the different
> approach makes a big improvement.
>
> Best,
>
> 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 stereo separation / depth in the new COOT? The
>>> picture is excessively deep in comparison with the previous version.
>>
>> What you are mostly seeing, I think, is that the transformation
>> between the eyes is no longer a rotation and is now a shear. Which
>> means that now we don't get part of the map showing up in the left eye
>> but not the right (or vice versa).
>>
>> Anyway, yes there is and it's documented in Section 3.4.1
>>
>> set_hardware_stereo_angle_factor(0.5) # for the Python fans
>>
>>
>>> BTW, the issue with set-display-lists-for-maps in stereo is still
>>> present in the COOT version distributed with CCP4 7.1.
>>>
>> It might be a while before I am sitting at a stereo display so that I
>> can address that. It's not top priority as there is a reasonable
>> work-around.
>>
>>
>> Paul.
>>
-- 

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Re: [COOT] CCP4 7.1 Coot - stereo

2020-05-15 Thread Pedro Matias 
Hi Paul,

Sorry for insisting, but I can't get the set_display_lists_for_maps(0)
to work on my $HOME/.coot.py preferences file. COOT starts in mono by
default and this command is ignored. It only works after I enter stereo
mode, input through the scripting window.  Also, it does not seem to be
saved in the 0-coot-state files so if I resume a previous COOT session I
have the same problem. Am I doing something wrong? Is there a workaround
for this issue?

BTW, the stereo on COOT 0.9 looks great - I guest that the different
approach makes a big improvement.

Best,

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 stereo separation / depth in the new COOT? The
>> picture is excessively deep in comparison with the previous version.
>
>
> What you are mostly seeing, I think, is that the transformation
> between the eyes is no longer a rotation and is now a shear. Which
> means that now we don't get part of the map showing up in the left eye
> but not the right (or vice versa).
>
> Anyway, yes there is and it's documented in Section 3.4.1
>
> set_hardware_stereo_angle_factor(0.5) # for the Python fans
>
>
>>
>> BTW, the issue with set-display-lists-for-maps in stereo is still
>> present in the COOT version distributed with CCP4 7.1.
>>
>
> It might be a while before I am sitting at a stereo display so that I
> can address that. It's not top priority as there is a reasonable
> work-around.
>
>
> Paul.
>
-- 

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Re: [COOT] CCP4 7.1 Coot - stereo

2020-05-12 Thread Pedro Matias 
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 stereo separation / depth in the new COOT? The
>> picture is excessively deep in comparison with the previous version.
>
>
> What you are mostly seeing, I think, is that the transformation
> between the eyes is no longer a rotation and is now a shear. Which
> means that now we don't get part of the map showing up in the left eye
> but not the right (or vice versa).
>
> Anyway, yes there is and it's documented in Section 3.4.1
>
> set_hardware_stereo_angle_factor(0.5) # for the Python fans

>
>
>>
>> BTW, the issue with set-display-lists-for-maps in stereo is still
>> present in the COOT version distributed with CCP4 7.1.
>>
>
> It might be a while before I am sitting at a stereo display so that I
> can address that. It's not top priority as there is a reasonable
> work-around.
>
>
> Paul.
>
>
-- 

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[COOT] CCP4 7.1 Coot - stereo

2020-05-12 Thread Pedro Matias 
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

-- 

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

2018-09-17 Thread Pedro Matias 
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 unique, i.e., it does not exist in the
CCP4 library. If I have created and loaded a CIF dictionary with the a
code that already existis in the CCP4 library, this works fine for real
space refinement but not here, because LIDIA appears to pick the CCP4
dictionary and then there is an atom name mismatch. For protein-ligand
complexes, DRG or INH are cases in point.

Is there a way to tell LIDIA to use the loaded CIF dictionary instead of
the CCP4 one?

Best regards,

Pedro

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

2018-05-28 Thread Pedro Matias 
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 UltraVNC viewer on the W10 client, and as of Fedora 23 this began to
happen. I then installed VirtualGL and use vglrun to start the OpenGL
application (e.g., coot and PyMOL). This also required modifying the
ccp4 and PHENIX scripts for launching coot.

Pedro


Às 07:19 de 28/05/2018, Kay Diederichs escreveu:
> We also see the ssh problem (but I didn't investigate thoroughly).
>
> We then use x2goclient; this runs an X server on the remote machine and 
> connects a desktop session to it.  That desktop runs coot (and anything else) 
> nicely. Easy to set up, and for some purposes better than NoMachine.
>
> HTH,
> Kay
>
> On Sun, 27 May 2018 13:35:53 -0400, David Schuller  
> wrote:
>> ...
>> We see it on some workstations 
>> with nVidia cards, but not others, because we are running different 
>> versions of the nVidia driver (legacy version for some older cards). 
>> This is the proprietary driver from nVidia (as loaded from el repo for 
>> sl6 and sl7 linux)
>>
>> The error messages show up with the "glxinfo" command.
>>
>> I do not know if a fix is on the way yet. You could try rolling back 
>> your nVidia driver.
> ...
>

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

2018-03-19 Thread Pedro Matias 
Hi Bernhard,

The error message in the Application Windows Event Log indicates an
exception 0xc005 for nvoglv32.dll (presumably the 32-bit OpenGL
NVIDIA driver) which is listed as an Access Violation.

We tried running coot-bin.exe as administrator and it didn't work. BTW,
coot 0.8.8 works perfectly in stereo on a PC with Windows 7 SP1 Home
64-bits, Quadro FX 380, 342.00 NVIDIA drivers and all applied Windows
updates. These cards are no longer manufactured, it seems, and have been
replaced by the 400 series.

Best,

Pedro


Às 14:06 de 19/03/2018, Bernhard Lohkamp escreveu:
> Have you tried running WinCoot in administrator mode? I had a report
> where this was required to run WinCoot in general. So not sure if this
> helps with the stereo. Unfortunately I dont have a Windows 10 machine
> with quad buffered stereo so it is difficult for me to test this
> issue. Another 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 14:13, Pedro Matias wrote:
>> Hi Christoph et al.,
>>
>> We have had the same problem on several machines with Windows 10. I
>> suspect this is caused by a recent update, to either Windows or the
>> NVIDIA drivers.
>>
>> Like you, we have no problems with PyMOL, only COOT.
>>
>> We have tried several fixes and none have worked.
>>
>> Best regards,
>>
>> Pedro
>>
>>
>> Às 12:48 de 19/03/2018, Christoph Parthier escreveu:
>>> I double-checked all three points. They were all set correctly.
>>> WinCoot crashes anyway as described...
>>>
>>> What pointed me to suspect WInCoot to be the culprit is the fact
>>> that NVIDIA quad-buffered stereo works in PyMOL on the same machine
>>> using these settings (also uses OpenGL).
>>>
>>> Christoph
>>>
>>
>

-- 

Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 441-1277 or 443-3644

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

2017-11-21 Thread Pedro Matias 
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 Matias escreveu:
>
> Dear all,
>
> Very recently, COOT took to crashing on startup on my W10 desktop (see
> image below).
>
> (snip)
>
> Looking at the Windows Event Log, the culprit seems to be the 32-bit
> NVIDIA OpenGL driver: C:\WINDOWS\SYSTEM32\nvoglv32.DLL
>
> Anyone else had this problem? I noticed there's been no new WinCoot
> version for quite some time.
>
> Thanks in advance,
>
> Pedro
>
>
> -- 
>
> Industry and Medicine Applied Crystallography
> Macromolecular Crystallography Unit
> ___
> Phones : (351-21) 446-9100 Ext. 1669
>  (351-21) 446-9669 (direct)
>  Fax   : (351-21) 441-1277 or 443-3644
>
> email : mat...@itqb.unl.pt
>
> http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
> http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit
>
> Mailing address :
> Instituto de Tecnologia Quimica e Biologica António Xavier
> Universidade Nova de Lisboa
> Av. da República
> 2780-157 Oeiras
> PORTUGAL
>
> ITQB NOVA, a great choice for your PhD
> https://youtu.be/de6j-aaTWNQ
>
> Master Programme in Biochemistry for Health
> https://youtu.be/UKstDCFjYI8

-- 

Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica António Xavier
Universidade Nova de Lisboa
Av. da República
2780-157 Oeiras
PORTUGAL

ITQB NOVA, a great choice for your PhD
https://youtu.be/de6j-aaTWNQ

Master Programme in Biochemistry for Health
https://youtu.be/UKstDCFjYI8

Re: [COOT] Coot crashes on Windows 10

2017-11-20 Thread Pedro Matias 
Dear Bernhard,

It didn't work. I updated WinCoot to 0.8.8 and it still didn't work.

Pedro


Às 10:39 de 20/11/2017, Bernhard Lohkamp escreveu:
> Dear Pedro,
>
> sorry, I didnt update the FAQ as I expected to have done. Please move
> everything from libexec to bin. That should 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 recently, possibly caused by a newer NVIDIA
>> driver.
>>
>> Best regards,
>>
>> Pedro
>>
>>
>> Às 10:13 de 20/11/2017, Bernhard Lohkamp escreveu:
>>>
>>>
>>> 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:
>>>> Dear all,
>>>>
>>>> Very recently, COOT took to crashing on startup on my W10 desktop
>>>> (see image below).
>>>>
>>>> Looking at the Windows Event Log, the culprit seems to be the 32-bit
>>>> NVIDIA OpenGL driver: C:\WINDOWS\SYSTEM32\nvoglv32.DLL
>>>>
>>>> Anyone else had this problem? I noticed there's been no new WinCoot
>>>> version for quite some time.
>>>>
>>>> Thanks in advance,
>>>>
>>>> Pedro
>>>>
>>>>
>>>> -- 
>>>>
>>>> Industry and Medicine Applied Crystallography
>>>> Macromolecular Crystallography Unit
>>>> ___
>>>> Phones : (351-21) 446-9100 Ext. 1669
>>>>    (351-21) 446-9669 (direct)
>>>>    Fax   : (351-21) 441-1277 or 443-3644
>>>>
>>>> email :mat...@itqb.unl.pt
>>>>
>>>> http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
>>>>
>>>>
>>>> http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit
>>>>
>>>> Mailing address :
>>>> Instituto de Tecnologia Quimica e Biologica António Xavier
>>>> Universidade Nova de Lisboa
>>>> Av. da República
>>>> 2780-157 Oeiras
>>>> PORTUGAL
>>>>
>>>> ITQB NOVA, a great choice for your PhD
>>>> https://youtu.be/de6j-aaTWNQ
>>>>
>>>> Master Programme in Biochemistry for Health
>>>> https://youtu.be/UKstDCFjYI8
>>>>
>>>
>>
>

-- 

Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica António Xavier
Universidade Nova de Lisboa
Av. da República
2780-157 Oeiras
PORTUGAL

ITQB NOVA, a great choice for your PhD
https://youtu.be/de6j-aaTWNQ

Master Programme in Biochemistry for Health
https://youtu.be/UKstDCFjYI8

Re: [COOT] Coot crashes on Windows 10

2017-11-20 Thread Pedro Matias 
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 recently, possibly caused by a newer NVIDIA driver.

Best regards,

Pedro


Às 10:13 de 20/11/2017, Bernhard Lohkamp escreveu:
>
>
> 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:
>> Dear all,
>>
>> Very recently, COOT took to crashing on startup on my W10 desktop
>> (see image below).
>>
>> Looking at the Windows Event Log, the culprit seems to be the 32-bit
>> NVIDIA OpenGL driver: C:\WINDOWS\SYSTEM32\nvoglv32.DLL
>>
>> Anyone else had this problem? I noticed there's been no new WinCoot
>> version for quite some time.
>>
>> Thanks in advance,
>>
>> Pedro
>>
>>
>> -- 
>>
>> Industry and Medicine Applied Crystallography
>> Macromolecular Crystallography Unit
>> ___
>> Phones : (351-21) 446-9100 Ext. 1669
>>   (351-21) 446-9669 (direct)
>>   Fax   : (351-21) 441-1277 or 443-3644
>>
>> email :mat...@itqb.unl.pt
>>
>> http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
>>
>> http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit
>>
>> Mailing address :
>> Instituto de Tecnologia Quimica e Biologica António Xavier
>> Universidade Nova de Lisboa
>> Av. da República
>> 2780-157 Oeiras
>> PORTUGAL
>>
>> ITQB NOVA, a great choice for your PhD
>> https://youtu.be/de6j-aaTWNQ
>>
>> Master Programme in Biochemistry for Health
>> https://youtu.be/UKstDCFjYI8
>>
>

-- 

Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica António Xavier
Universidade Nova de Lisboa
Av. da República
2780-157 Oeiras
PORTUGAL

ITQB NOVA, a great choice for your PhD
https://youtu.be/de6j-aaTWNQ

Master Programme in Biochemistry for Health
https://youtu.be/UKstDCFjYI8