Re: [ccp4bb] PyMOL now packaged as a snap on Linux

[Matic Kisovec]

Hi,

thank you very much for this. Work fine on Ubuntu 19.04.

Kind regrds,
Matic


On 17. 05. 19 20:04, Arunabh Athreya wrote:
Thanks for sharing this.

Get Outlook for Android


From: CCP4 bulletin board  
on behalf of David Schuller 
Sent: Thursday, May 16, 2019 11:41:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PyMOL now packaged as a snap on Linux

It seems to work on Fedora 30 and on Scientific Linux 7 (which means it should 
also work on RHEL7 and Centos 7)

Thank you.



On 5/16/19 10:47 AM, Darren Hart wrote:
Some more info:

https://snapcraft.io/pymol-oss

It seems to work exactly as expected.

Darren


On 16/05/2019 16:05, Folmer Fredslund wrote:
Hi Darren,

That's brilliant!

I'll give it a spin and see how it works.

Best regards
Folmer


tor. 16. maj 2019 13.02 skrev Darren Hart 
mailto:darren.h...@ibs.fr>>:
Since yesterday, PyMOL (open source version v2.3) has been packaged as a
distro-independent "snap" that can be installed easily on linux
platforms - no more cloning from gitlab and compiling after installing
the dependencies.

On Ubuntu, install from software centre or:

sudo snap install pymol-oss

Many distros have the snap architecture already installed. If not, you
just need to install snapd in the regular way first (e.g. on Debian:
sudo apt install snapd).

Hope this is useful for some folks.

Best regards,

Darren



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Re: [ccp4bb] 3D stereo and pymol

[Matic Kisovec]

Dear all,

in case anybody is interested in a used 3D setup for crystallography one is 
still available:
See here for more details: 
https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg41144.html

Kind regards,
Matic.


On 12. 12. 2017 08:39, Jim Fairman wrote:
Reporting in a setup that we just made: Quadro P4000 + 3 pin stereo bracket + 
3d vision 2 kit + ASUS VG248QE.

Running System76's PoPOS Ubuntu 17.10 distro - you'll have to install a desktop 
environment that supports non-compositing (ie: XFCE).

Works beautifully.



--
Jim Fairman
C: 1-240-479-6575

On Tue, Nov 28, 2017 at 6:40 AM, mesters 
> wrote:
Hi,

yes, consumer cards do have OpenGL implemented on a chip but the Nvidia driver 
did not allow OpenGL 3D to work until February 2013. As of Nvidia driver 
version 314.07, Nvidia added OpenGL quad buffered 3D Stereo for GeForce cards 
(at least under MS Windows 7/8). However, this was never officially announced 
and officially supported and only works if the monitor is preset to run at 120 
Hz and the software automatically switches into full-screen mode. Sadly, 
windowed applications will not work. Under MS Windows 10, it does not seem to 
work anymore.

We have a monitor with a build in emitter and that one works with the 
smaller/cheaper Quadro cards without the 3-pin connector but, it is virtually 
impossible nowadays to get such a monitor in order to avoid needing to buy an 
expensive Nvidia card with a 3-pin connector.

To enjoy OpenGL quad buffered 3D Stereo, you will at least need a Quadro 
K4000/P4000/4000 with separate 3-pin bracket (all-in-all very expensive 
solution) or you will need to buy an older FX model such as the FX3700 with 
build-in 3-pin connector.

At the Bay in the USA, unused / brand-new FX3700s are being offered right now 
for about 90-110 US$. That's the cheapest way out and 512 MB memory is 
sufficient unless you are trying work with VERY big PDB files. If so, try to 
get your hands on a "new, see details" Quadro 4000 and a separate PNY 3-pin 
mini DIN stereo bracket (930-50764--000 C for about 20 US$) or a "new, see 
details" Quadro 5000 with build-in emitter.

Good luck

Jeroen.


Am 28.11.17 um 10:50 schrieb Johannes Cramer:
Hi Christine,

as far as I know, it does not work at all with Geforce cards. The Nvidia 
drivers do not support windowed quad buffered GL, which you need for 
coot/pymol. It does not matter whether you use Windows or Linux.
But this is based on my personal experience from around Oct. 2016. Maybe 
something changed quietly since then. Again, as far as I know, you need a 
Quadro card.

Cheers,
Johannes

2017-11-06 21:24 GMT+01:00 Christine Gee 
>:
Hi,

I have looked in the archive for posts about this, but there hasn't been one 
for about a year. Can anyone comment on whether they have managed to get a 
linux flavor and GeForce cards to work with pymol and/or coot 3D stereo? 
Geforce cards supposedly support openGL, but posts from October last year on 
the BB suggests that it only works in windows unless you have a monitor with a 
built in emitter. I would appreciate any feedback.

Regards
Christine




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[ccp4bb] Off-topic: 3D display (VG278HR) + graphics card (Quadro K600) available

[Matic Kisovec]

Dear all,

in case anybody is looking for a used but solid 3D capable display together 
with Nvidia glasses and a suitable graphics card you can contact me.
We have a 27" ASUS 
VG278HR + Pny Quadro 
K600
 setup in a working condition and would like to give it a new home. We are very 
happy with the system but it has only been used sporadically and even less in 
the last year.
The combination has been discussed multiple times on CCP4BB and is compatible 
with more or less every crystallographic software.

The items are located in Slovenia, EU.

Kind regards,
Matic


<>

Re: [ccp4bb] relative domain motion calculation...

[Matic Kisovec]

Dear Mintu,

one possible option is the webserver DynDomhttp://fizz.cmp.uea.ac.uk/dyndom/.

Kind regards,
Matic

On 21. 04. 2015 09:39, Mintu Chandra wrote:

Dear All,
I am working with a protein containing tandem domains, connected with
3-4 residue linker. I want to calculate the relative
motion/orientation of one domain with respect to the hinge region as
well as with respect to the other domain. Both the domains have very
less seq. identity (20%). Please suggest some web server to calculate
the same.

Thanks,

Mintu


attachment: matic_kisovec.vcf

Re: [ccp4bb] Stereo monitors for use with Pymol and Coot

[Matic Kisovec]

Dear everybody,

to my recent experience not everything is good in the stereo world. Since I see 
that others don't have these problems (and I am happy/sad to see that the same 
exact combinations work without problems) I would just like to add my 
experience.

For the past 4 months I have been struggling to configure a stereo setup for 
viewing structures in Pymol.
I got the VG278HR and PNY Quadro K600 connected over the original DVI-D cable. 
Since then I was unable to get anything in stereo on Linux (tried Ubuntu, 
OpenSUSE, Fedora). Unfortunately I get a blank/black screen whenever I use the 
stereo option in xorg.conf. Also tried changing the motherboard and CPU but got 
the same result.

In Windows the demo stuff from Nvidia works just fine but again I have problems 
with Pymol. So far the only way to see anything connected to molecular 
structures in Windows was via DVI-to-HDMI cable but due to HDMI restrictions 
the quality isn't as good as it would be over DVI-D. If I use DVI-D that was 
shipped with the monitor the quadro card is detected in Pymol but the monitor 
doesn't switch to stereo.

I have been in contact with the company that makes Quadro cards (PNY) but they 
were unable to help me. I also contacted some very kind users of CCP4BB and 
they kindly answered a bunch of question regarding specific setup options. 
Thanks again! Still there was no success so far.

I am slowly giving up on the stereo so if anybody has any ideas/thoughts what 
could be wrong/done I would greatly appreciate any insight.

Kind regards,
Matic



On 06. 03. 2014 19:32, White, Mark wrote:
Alexy

I have the ASUS 27 stereo LCD monitors with built in emitter connected to 
Linux WS with the cheaper Quadro cards. The monitor comes with a special DVI 
cable that caries the sync signal and thus it does not need the 3-pin connector.

The new LCD stereo monitors produce superb 3D images that are much crisper than 
we used to get with CRT displays.

Best regards
Mark

Sent from my iPhone

On Mar 6, 2014, at 12:01 PM, Alexey Rozov 
alexey.ro...@gmail.commailto:alexey.ro...@gmail.com wrote:

Hello,

Sorry, if this question somewhat off-top to the actual discussion, but to my 
understanding one does need the 3-pin connector to operate 3D under Linux even 
for the monitors with the built-in emitter. It appears to be necessary to guide 
the emitter, or am I wrong about it? I'd be thankful if anyone can advise me on 
that since it looks like a big problem to acquire the commercial connectors and 
cables.

I think I have seen an older discussion on CCP4BB where the importance of the 
3-pin connector was emphasized...

Alexey


On 6 March 2014 18:30, mesters 
mest...@biochem.uni-luebeck.demailto:mest...@biochem.uni-luebeck.de wrote:
Hello Moutse,

as you noted correctly, the ASUS VG278H (HR or HE) comes in two flavours, one 
with build in emitter (120 Hz, HR model) and one without (144 Hz, HE model).

The VG278HR (ships with one pair of shutter glasses) with build in emitter can 
be used under windows and linux with a cheap nvidia quadro card (the ones 
without a 3-pin stereo connector).

With the VG278HE under windows and a cheap nvidia quadro, you will need the 
nvidia emitter that uses a usb port for driving the emitter. To operate the 
VG278HE under linux requires a truely expensive quadro card (k4000 and upwards) 
with an optional (!) 3-pin connector or, purchase an old refurbished quadro 
card with 3-pin.

Have a look at the following link 
http://www.nvidia.com/object/3d-vision-pro-requirements.html, especially the 
table at the end with the small print explanation 2 and 3

- J. -


Am 06.03.14 17:41, schrieb Mouts Ranaivoson:
Hi,

I am currently also looking for a 3D monitor, and I am particularly attentive 
to this particular discussion. My interrogation is that does the  Asus VG278HE 
model work under linux ? From previous ccp4bb discussions I understood that 
only built-in emmitter (like the  Asus VG278HR) are suitable for that, but 
maybe I misunderstood...

Thank you very much for your help,

Moutse.



Date: Thu, 6 Mar 2014 09:55:15 +0100
From: mest...@biochem.uni-luebeck.demailto:mest...@biochem.uni-luebeck.de

Subject: Re: [ccp4bb] Stereo monitors for use with Pymol and Coot
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK


Hi,

this is probaly due to the transition from old TFT style to new IPS panel based 
monitors... Several new passive 3d monitors are hitting the market such as AOC 
d2769Vh and the Philips Gioco 278G4. Both are based on 27 IPS Monitor panels.

A list of possible monitors can be found at Tridef (many are old but new models 
are listed),  https://www.tridef.com/products/pc-licensed-products.

Problem with passive stereo is, you will half the resolution in the vertical 
direction. It is a problem if you are looking at wire-models of structures in 
pymol and especially fine-wire electron density mesh and models in coot as 
those noticably loose resolution