Re: [PyMOL] ignore_case in next PyMOL version

[Thomas Holder]

Hi all,

Quick update on the "ignore_case" issue:

- ignore_case=on default restored in PyMOL 1.8.0.5 and latest SVN
- latest SVN introduces new "ignore_case_chain" setting

Cheers,
  Thomas

On 02 Feb 2016, at 14:38, Thomas Holder  wrote:

> Greetings,
> 
> I like to let you know that we plan another change for the "ignore_case" 
> setting behavior. We want to restore the old default (ignore_case=on) and 
> introduce a new setting "ignore_case_chain=off", which will affect the 
> "chain" and "segi" identifiers.
> 
> As you may (or should) know, we changed the default of the "ignore_case" 
> setting in PyMOL 1.8 from "on" to "off". The rationale was to have default 
> settings which properly support PDB files which mix upper and lower case 
> chain identifiers (e.g. 3a0b). Users who still prefer a case insensitive 
> selection language can put a "set ignore_case" line in their pymolrc file.
> 
> However, we now realized that this is not very practical. One reason is that 
> too many scripts and code samples use lower case resn and name selections, 
> fixing those historic resources is often not feasible or desirable. Another 
> reason is that PyMOL inconsistently stores element symbols, for example 
> chlorine is "CL" when loaded from a PDB file, but "Cl" when loaded from SDF. 
> The logical conclusion is that PyMOL should handle chain and segi different 
> from resn, name and elem.
> 
> See also: http://pymolwiki.org/index.php/ignore_case
> 
> Any kind of feedback regarding the planned change will be appreciated.
> 
> Cheers,
>  Thomas

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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[PyMOL] slow pymol-v1.7.4.0-Linux-x86_64 in ubuntu 14.04 LTS

[Hena Dutta]

Dear Pymol members,
I have a hard time to use pymol-v1.7.4.0-Linux-x86_64 in ubuntu 14.04 LTS
which I need to use very often. Although other graphics programs like COOT,
CCP4MG are running just fine.
After I load the pdb file, it just taking too much time for any operation
like zoom in or out, rotating/translating molecule or even going through
the menu when dragging the mouse. I have no clue.
My computer specifications:
Memory 5.8 GiB
Processor Intel Xenon(R) CPU W3505 @ 2.53 GHz x 2
Graphics Gallium 0.4 on NVC1 (Graphics card Quadro 600)
OS type 64-bit
DISK 978.0 GB

Can anyone tell the fix for this problem asap.
My best regards,
Hena
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Re: [PyMOL] slow pymol-v1.7.4.0-Linux-x86_64 in ubuntu 14.04 LTS

[TUBIANA Thibault CNRS]

Hi Hena,

I had the same problem once and I fixed it when I installed the Nvidia Driver 
(see how here http://www.binarytides.com/install-nvidia-drivers-ubuntu-14-04/)

"Graphics Gallium 0.4" appear when you have the default driver. With an Nvidia 
Quadro 600 it should be something like
Detected OpenGL version 2.0 or greater. Shaders available.
Detected GLSL version 4.50.
OpenGL graphics engine:
  GL_VENDOR:   NVIDIA Corporation
  GL_RENDERER: Quadro K2200/PCIe/SSE2
  GL_VERSION:  4.5.0 NVIDIA 352.39
Adapting to Quadro hardware.
Detected 24 CPU cores.  Enabled multithreaded rendering.

Kind regards,
Thibault.

On Tue, 2016-02-09 at 11:24 -0500, Hena Dutta wrote:
Dear Pymol members,

I have a hard time to use pymol-v1.7.4.0-Linux-x86_64 in ubuntu 14.04 LTS which 
I need to use very often. Although other graphics programs like COOT, CCP4MG 
are running just fine.

After I load the pdb file, it just taking too much time for any operation like 
zoom in or out, rotating/translating molecule or even going through the menu 
when dragging the mouse. I have no clue.

My computer specifications:

Memory 5.8 GiB

Processor Intel Xenon(R) CPU W3505 @ 2.53 GHz x 2

Graphics Gallium 0.4 on NVC1 (Graphics card Quadro 600)

OS type 64-bit

DISK 978.0 GB


Can anyone tell the fix for this problem asap.

My best regards,

Hena





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--


Tubiana Thibault
PhD Student
Institut de Biologie Intégrative de la Cellule
CNRS UMR 9198
CEA-Saclay, Bâtiment 532 - Pce 12A
91191 Gif-sur-Yvette
06.79.90.95.85
http://www.tubiana.me




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