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.


--
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

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.


--
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

[PyMOL] ignore_case in next PyMOL version

[Thomas Holder]

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.


--
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311=/4140
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net