date:20160229

Re: [PyMOL] Selections don't work on structures loaded using, 'fetch' command

2016-02-29 Thread Timofey Tyugashev

Thank you for prompt response. Now I recall that I've seen the mention 
of it in the release notes for 1.8, but paid no attention to it as I had 
no intent to install 1.8 so soon anyway being wary of probable bugs.
Probably earlier I just pedantically typed in the identifiers in capital 
letters, but yesterday was to tired to bother and got this unpleasant 
surprise.
I see that current versions already have it returned to work the old way.
Maybe it would be nice if all wiki pages with examples affected by 
case-sensitiveness get some kind of a note about it.
01.03.2016 03:54, pymol-users-requ...@lists.sourceforge.net пишет:
> Message: 7
> Date: Mon, 29 Feb 2016 08:35:13 -0500
> From: Thomas Holder
> Subject: Re: [PyMOL] Selections don't work on structures loaded using
>   'fetch' command
> To: Timofey Tyugashev
> Cc:pymol-users@lists.sourceforge.net
> Message-ID:<73c4c9d6-c6b2-44b9-b508-f7c84b592...@schrodinger.com>
> Content-Type: text/plain; charset=utf-8
>
> Hi Timofey,
>
> Seehttp://pymolwiki.org/index.php/ignorea _case
>
> Note: The wiki page mentions 1.8.0.0 (official release), but the SVN repo had 
> the change since 1.7.7.1 (https://sourceforge.net/p/pymol/code/4123/  ).
>
> Cheers,
>Thomas
>
> On 29 Feb 2016, at 06:23, Timofey Tyugashev  wrote:
>
>> >Sorry, it's actually part false alarm and part a completely different
>> >problem.
>> >
>> >For false alarm:Structure retrieved by 'fetch' simply lacked residue
>> >numbered 10, why my own file was already repaired and had it fine.
>> >
>> >For different problem: For some reason it turns out that 'select' is
>> >case-sensitive and it's not actually mentioned anywhere on the wiki, so
>> >selectors like 'resn' and 'name' simply silently failed.
>> >Is there a way to disable it?
>> >
>> >29.02.2016 17:10, Timofey Tyugashev ?:
>>> >>If I load my own pdb file and issue a simple select command like
>>> >>'select resi 10' it works fine, producing something like 'selection
>>> >>"sele" defined with 6 atoms'.
>>> >>However if I load the same structure using fetch command selections
>>> >>stop working,  'select resi 10'  results in 'selection "sele" defined
>>> >>with 0 atoms'.
>>> >>System is Linux. PyMOL is 1.7.7.2 version from svn.
> -- Thomas Holder PyMOL Principal Developer Schr?dinger, Inc.


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[PyMOL] Cannot save movie as MPEG

2016-02-29 Thread Ioannis Michalopoulos

Dear PyMOL users,

I run 64-bit Windows 10. I have installed the latest PyMOL (and all other
programs that are required) from:

http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol

PyMOL works fine. I make movies which look fine on PyMOL. Nevertheless,
when I try:

Menu > Save Movie As > MPEG...

a pop-up error message appears:

MPEG encoder missing.
The FreeMOL add-ons may not be installed.

Interestingly, in: "C:\Python27" where PyMOL.exe is installed,
mpeg_encode.exe and mpeg_encode-x64.exe are also found. This directory is
set to PATH.

Have I not set PyMOL properly?

Thank you in advance.

Best Regards,

Dr Ioannis Michalopoulos
-- 
Dr Ioannis Michalopoulos
Staff Research Scientist - Associate Professor Level
Centre of Systems Biology

Tel: +30 210 6597 127
Fax: +30 210 6597 545
Email: imicha...@bioacademy.gr
_
Biomedical Research Foundation, Academy of Athens
Soranou tou Efessiou 4, 115 27 Athens, Greece


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Re: [PyMOL] Selections don't work on structures loaded using 'fetch' command

2016-02-29 Thread Thomas Holder

Hi Timofey,

See http://pymolwiki.org/index.php/ignore_case

Note: The wiki page mentions 1.8.0.0 (official release), but the SVN repo had 
the change since 1.7.7.1 (https://sourceforge.net/p/pymol/code/4123/ ).

Cheers,
  Thomas

On 29 Feb 2016, at 06:23, Timofey Tyugashev  wrote:

> Sorry, it's actually part false alarm and part a completely different 
> problem.
> 
> For false alarm:Structure retrieved by 'fetch' simply lacked residue 
> numbered 10, why my own file was already repaired and had it fine.
> 
> For different problem: For some reason it turns out that 'select' is 
> case-sensitive and it's not actually mentioned anywhere on the wiki, so 
> selectors like 'resn' and 'name' simply silently failed.
> Is there a way to disable it?
> 
> 29.02.2016 17:10, Timofey Tyugashev пишет:
>> If I load my own pdb file and issue a simple select command like 
>> 'select resi 10' it works fine, producing something like 'selection 
>> "sele" defined with 6 atoms'.
>> However if I load the same structure using fetch command selections 
>> stop working,  'select resi 10'  results in 'selection "sele" defined 
>> with 0 atoms'.
>> System is Linux. PyMOL is 1.7.7.2 version from svn.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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[PyMOL] Selections don't work on structures loaded using 'fetch' command

2016-02-29 Thread Timofey Tyugashev

If I load my own pdb file and issue a simple select command like 'select 
resi 10' it works fine, producing something like 'selection "sele" 
defined with 6 atoms'.
However if I load the same structure using fetch command selections stop 
working,  'select resi 10'  results in 'selection "sele" defined with 0 
atoms'.
System is Linux. PyMOL is 1.7.7.2 version from svn.


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Re: [PyMOL] Selections don't work on structures loaded using 'fetch' command

2016-02-29 Thread Timofey Tyugashev

Sorry, it's actually part false alarm and part a completely different 
problem.

For false alarm:Structure retrieved by 'fetch' simply lacked residue 
numbered 10, why my own file was already repaired and had it fine.

For different problem: For some reason it turns out that 'select' is 
case-sensitive and it's not actually mentioned anywhere on the wiki, so 
selectors like 'resn' and 'name' simply silently failed.
Is there a way to disable it?

29.02.2016 17:10, Timofey Tyugashev пишет:
> If I load my own pdb file and issue a simple select command like 
> 'select resi 10' it works fine, producing something like 'selection 
> "sele" defined with 6 atoms'.
> However if I load the same structure using fetch command selections 
> stop working,  'select resi 10'  results in 'selection "sele" defined 
> with 0 atoms'.
> System is Linux. PyMOL is 1.7.7.2 version from svn. 


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Re: [PyMOL] Selections don't work on structures loaded using, 'fetch' command

[PyMOL] Cannot save movie as MPEG

Re: [PyMOL] Selections don't work on structures loaded using 'fetch' command

[PyMOL] Selections don't work on structures loaded using 'fetch' command

Re: [PyMOL] Selections don't work on structures loaded using 'fetch' command

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