Re: [PyMOL] ignore_case in next PyMOL version

[Thomas Holder]

Hi Spencer,

Very good question. In short, the "ignore_case" setting affects all text 
matching in the selection language, including operators. The next official 
release and current latest SVN will exclude chain and segi from that, and 
handle them with "ignore_case_chain".

Correct, the idea is case-insensitive element symbols (that's ignore_case=on) 
and case-sensitive chains (ignore_case_chain=off). For all normal use cases, 
there should be no reason to change these settings.

In detail, these are the affected selectors:

- single-word selectors (http://pymolwiki.org/index.php/Single-word_Selectors )
- selection operators (http://pymolwiki.org/index.php/Selection_Algebra )
- object and selection names
- values of:
  - chain (up to 1.8.0)
  - segi (up to 1.8.0)
  - resn
  - resi (insertion code)
  - name
  - alt
  - element
  - ss
  - rep
- byca operator (CA name matching)
- in operator (resn, resi, name matching; up to 1.8.0 also chain and segi)
- like (resi and name matching)

Besides the selection language, case insensitive matching is hard coded for 
atom sorting (affects resi, resn, name; up to 1.7.0 also segi). I'm not sure 
yet whether we want to do anything about that. I don't see a reason why atom 
sorting should be case insensitive.

Case insensitive matching was also hardcoded for matching two selections with 
the following commands: fit, rms, rms_cur and update. Latest SVN considers 
"ignore_case" and "ignore_case_chain" with these commands.

Cheers,
  Thomas

On 10 Feb 2016, at 02:58, Spencer Bliven  wrote:

> Restoring the old ignore_case behaviour seems pragmatic.
> 
> Can you explain the difference with the new ignore_case_chain setting? Is the 
> idea that we would want case-insensitive element symbols (ignore_case=off) 
> but case-sensitive chains (ignore_case_chain=on)? Are there other places 
> where case is important in the selections or structures (e.g. insertion 
> codes)?
> 
> -Spencer
> 
> On Tue, Feb 9, 2016 at 4:18 PM, Thomas Holder  
> wrote:
> 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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Re: [PyMOL] slow pymol-v1.7.4.0-Linux-x86_64 in ubuntu 14.04 LTS

[Hena Dutta]

Hi Tubiana,
When I click the site
http://www.binarytides.com/install-nvidia-drivers-ubuntu-14-04/), I got the
following line.
Sorry, but you are looking for something that isn't here.

Could you please tell more explicitly what exactly I need to do to fix
this? I mean the exact command in a console to update the driver.
Thank you in advance,
Hena

On Wed, Feb 10, 2016 at 2:43 AM, TUBIANA Thibault CNRS <
thibault.tubi...@cea.fr> wrote:

> 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
>
>
>
>
> --
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
> --
>
> Tubiana Thibault
> PhD Student
> Institut de Biologie Intégrative de la Cellule
> CNRS UMR 9198
> CEA-Saclay, Bâtiment 532 - Pce 12A
> 91191 Gif-sur-Yvette
> 06.79.90.95.85http://www.tubiana.me
>
>
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Re: [PyMOL] slow pymol-v1.7.4.0-Linux-x86_64 in ubuntu 14.04 LTS

[TUBIANA Thibault CNRS]

Oh, I can access to the link only with google... Strange. Anyway there
are the commands : 

1 - Add the repo
sudo add-apt-repository ppa:xorg-edgers/ppa -y
sudo apt-get update

2 - Install the latest version 
sudo apt-get install nvidia-current

And if you want to remove it one day : sudo apt-get purge nvidia*

On Wed, 2016-02-10 at 12:43 -0500, Hena Dutta wrote:
> Hi Tubiana,
> 
> When I click the site
> http://www.binarytides.com/install-nvidia-drivers-ubuntu-14-04/), I
> got the following line.
> Sorry, but you are looking for something that isn't here.
> 
> 
> Could you please tell more explicitly what exactly I need to do to fix
> this? I mean the exact command in a console to update the driver.
> 
> Thank you in advance,
> 
> Hena
> 
> On Wed, Feb 10, 2016 at 2:43 AM, TUBIANA Thibault CNRS
>  wrote:
> 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 
> > 
> > 
> > 
> > 
> --
> > Site24x7 APM Insight: Get Deep Visibility into Application 
> Performance
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> > Monitor end-to-end web transactions and take corrective actions now
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> > ___
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> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: 
> http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> 
> -- 
> 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
> 
> 
> 
> 

-- 
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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