subject:"\[PyMOL\] PyMOL 1.6 pre\-release announcement"

Re: [PyMOL] PyMOL 1.6 pre-release announcement

2013-06-20 Thread Jason Vertrees

Bob,

Sure, feel free to send those to Thomas.

Cheers,

-- Jason


On Thu, Jun 20, 2013 at 9:06 AM, Robert Hanson  wrote:

> (yes, I meant "forward compatibility" there)
>
> Jason, in our 100+ PyMOL session files that we can now read into Jmol we
> have a few files that don't seem to have backward compatibility to PyMOL
> 1.3 from the open source version 1.6.0.0. Mostly it has to do with CGOs and
> measurements. Should I just send them to you and/or Thomas?
>
> Bob
>
>
>
> On Thu, Jun 20, 2013 at 7:36 AM, Jason Vertrees <
> jason.vertr...@schrodinger.com> wrote:
>
>> Hi David,
>>
>> If you save a session file in the latest version of PyMOL there is never
>> the expectation that prior versions can read that file. Such "forward
>> compatibility" (of the older versions) is not supported. We do support,
>> however, "backward compatibility" which is when newer versions of PyMOL
>> read older session files.
>>
>> Cheers,
>>
>> -- Jason
>>
>>
>> On Wed, Jun 19, 2013 at 4:18 PM, David Hall wrote:
>>
>>> I still have this problem:
>>> session saved in 1.6 with a black background; opens in 1.5 (and earlier)
>>> with a red background
>>>
>>> Many of my collaborators use old versions of pymol, frequently installed
>>> onto their machines when they were bought X years ago, and this essentially
>>> makes it so I cannot use pymol 1.6 as I cannot share sessions with them (at
>>> least not without getting weird e-mails asking why I have a sudden affinity
>>> for the color red).
>>>
>>> -David
>>>
>>>
>>>
>>>
>>> On Tue, Jun 18, 2013 at 7:37 AM, Thomas Holder <
>>> thomas.hol...@schrodinger.com> wrote:
>>>
 This is fixed in SVN rev 4032.

 Cheers,
   Thomas

 Thomas Holder wrote, On 06/15/13 10:45:
 > Hi Rob,
 >
 > this has not been fixed yet, I'm really sorry. We'll look into this
 > ASAP. It only affects the open-source code, apparently we missed
 > something when syncing with the incentive codebase.
 >
 > Cheers,
 >   Thomas
 >
 > On Jun 14, 2013, at 9:23 PM, Robert Campbell <
 robert.campb...@queensu.ca> wrote:
 >> Hello Thomas and David,
 >>
 >> Was there any resolution of this?  I've just compiled the latest
 version
 >> from SVN and I have the same problem opening files created under
 version
 >> 1.5.0.  This is on Debian testing (32-bit).
 >>
 >> Cheers,
 >> Rob
 >>
 >> On Fri, 2013-04-26 19:15  EDT,  David Hall 
 >> wrote:
 >>
 >>> Hi Thomas,
 >>>
 >>> I'm running into issues with color compatibility between 1.6 and
 >>> earlier versions when opening pses
 >>> (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like:
 >>> Setting-Error: type read mismatch (color) 6
 >>> Setting-Error: type read mismatch (color) 663
 >>> Setting-Error: type read mismatch (color) 664
 >>> (b) background color disparity:
 >>> saved in 1.5 with black background; opens in 1.6 with a white
 background
 >>> saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a
 red
 >>> background
 >>>
 >>> These are run on openSUSE 12.3 with SVN rev 4028 . On a side note,
 >>> others who would like to beta test can use devel:languages:python
 repo
 >>> in openSUSE:
 >>>
 https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython
 >>>
 >>> -David

 --
 Thomas Holder
 PyMOL Developer
 Schrödinger Contractor


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>>>
>>>
>>>
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>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> Director of Core Modeling Products
>> Schrödinger, Inc.
>>
>> (e) jason.vertr...@schrodinger.com
>> (o) +1 (603) 374-7120
>>
>>
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Re: [PyMOL] PyMOL 1.6 pre-release announcement

2013-06-20 Thread Robert Hanson

(yes, I meant "forward compatibility" there)

Jason, in our 100+ PyMOL session files that we can now read into Jmol we
have a few files that don't seem to have backward compatibility to PyMOL
1.3 from the open source version 1.6.0.0. Mostly it has to do with CGOs and
measurements. Should I just send them to you and/or Thomas?

Bob



On Thu, Jun 20, 2013 at 7:36 AM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:

> Hi David,
>
> If you save a session file in the latest version of PyMOL there is never
> the expectation that prior versions can read that file. Such "forward
> compatibility" (of the older versions) is not supported. We do support,
> however, "backward compatibility" which is when newer versions of PyMOL
> read older session files.
>
> Cheers,
>
> -- Jason
>
>
> On Wed, Jun 19, 2013 at 4:18 PM, David Hall  wrote:
>
>> I still have this problem:
>> session saved in 1.6 with a black background; opens in 1.5 (and earlier)
>> with a red background
>>
>> Many of my collaborators use old versions of pymol, frequently installed
>> onto their machines when they were bought X years ago, and this essentially
>> makes it so I cannot use pymol 1.6 as I cannot share sessions with them (at
>> least not without getting weird e-mails asking why I have a sudden affinity
>> for the color red).
>>
>> -David
>>
>>
>>
>>
>> On Tue, Jun 18, 2013 at 7:37 AM, Thomas Holder <
>> thomas.hol...@schrodinger.com> wrote:
>>
>>> This is fixed in SVN rev 4032.
>>>
>>> Cheers,
>>>   Thomas
>>>
>>> Thomas Holder wrote, On 06/15/13 10:45:
>>> > Hi Rob,
>>> >
>>> > this has not been fixed yet, I'm really sorry. We'll look into this
>>> > ASAP. It only affects the open-source code, apparently we missed
>>> > something when syncing with the incentive codebase.
>>> >
>>> > Cheers,
>>> >   Thomas
>>> >
>>> > On Jun 14, 2013, at 9:23 PM, Robert Campbell <
>>> robert.campb...@queensu.ca> wrote:
>>> >> Hello Thomas and David,
>>> >>
>>> >> Was there any resolution of this?  I've just compiled the latest
>>> version
>>> >> from SVN and I have the same problem opening files created under
>>> version
>>> >> 1.5.0.  This is on Debian testing (32-bit).
>>> >>
>>> >> Cheers,
>>> >> Rob
>>> >>
>>> >> On Fri, 2013-04-26 19:15  EDT,  David Hall 
>>> >> wrote:
>>> >>
>>> >>> Hi Thomas,
>>> >>>
>>> >>> I'm running into issues with color compatibility between 1.6 and
>>> >>> earlier versions when opening pses
>>> >>> (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like:
>>> >>> Setting-Error: type read mismatch (color) 6
>>> >>> Setting-Error: type read mismatch (color) 663
>>> >>> Setting-Error: type read mismatch (color) 664
>>> >>> (b) background color disparity:
>>> >>> saved in 1.5 with black background; opens in 1.6 with a white
>>> background
>>> >>> saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a
>>> red
>>> >>> background
>>> >>>
>>> >>> These are run on openSUSE 12.3 with SVN rev 4028 . On a side note,
>>> >>> others who would like to beta test can use devel:languages:python
>>> repo
>>> >>> in openSUSE:
>>> >>>
>>> https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython
>>> >>>
>>> >>> -David
>>>
>>> --
>>> Thomas Holder
>>> PyMOL Developer
>>> Schrödinger Contractor
>>>
>>>
>>> --
>>> This SF.net email is sponsored by Windows:
>>>
>>> Build for Windows Store.
>>>
>>> http://p.sf.net/sfu/windows-dev2dev
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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
>>>
>>
>>
>>
>> --
>> This SF.net email is sponsored by Windows:
>>
>> Build for Windows Store.
>>
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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
>>
>
>
>
> --
> Jason Vertrees, PhD
> Director of Core Modeling Products
> Schrödinger, Inc.
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
>
> --
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
>
> http://p.sf.net/sfu/windows-dev2dev
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>



-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer fir

Re: [PyMOL] PyMOL 1.6 pre-release announcement

2013-06-20 Thread Jason Vertrees

Hi David,

If you save a session file in the latest version of PyMOL there is never
the expectation that prior versions can read that file. Such "forward
compatibility" (of the older versions) is not supported. We do support,
however, "backward compatibility" which is when newer versions of PyMOL
read older session files.

Cheers,

-- Jason


On Wed, Jun 19, 2013 at 4:18 PM, David Hall  wrote:

> I still have this problem:
> session saved in 1.6 with a black background; opens in 1.5 (and earlier)
> with a red background
>
> Many of my collaborators use old versions of pymol, frequently installed
> onto their machines when they were bought X years ago, and this essentially
> makes it so I cannot use pymol 1.6 as I cannot share sessions with them (at
> least not without getting weird e-mails asking why I have a sudden affinity
> for the color red).
>
> -David
>
>
>
>
> On Tue, Jun 18, 2013 at 7:37 AM, Thomas Holder <
> thomas.hol...@schrodinger.com> wrote:
>
>> This is fixed in SVN rev 4032.
>>
>> Cheers,
>>   Thomas
>>
>> Thomas Holder wrote, On 06/15/13 10:45:
>> > Hi Rob,
>> >
>> > this has not been fixed yet, I'm really sorry. We'll look into this
>> > ASAP. It only affects the open-source code, apparently we missed
>> > something when syncing with the incentive codebase.
>> >
>> > Cheers,
>> >   Thomas
>> >
>> > On Jun 14, 2013, at 9:23 PM, Robert Campbell <
>> robert.campb...@queensu.ca> wrote:
>> >> Hello Thomas and David,
>> >>
>> >> Was there any resolution of this?  I've just compiled the latest
>> version
>> >> from SVN and I have the same problem opening files created under
>> version
>> >> 1.5.0.  This is on Debian testing (32-bit).
>> >>
>> >> Cheers,
>> >> Rob
>> >>
>> >> On Fri, 2013-04-26 19:15  EDT,  David Hall 
>> >> wrote:
>> >>
>> >>> Hi Thomas,
>> >>>
>> >>> I'm running into issues with color compatibility between 1.6 and
>> >>> earlier versions when opening pses
>> >>> (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like:
>> >>> Setting-Error: type read mismatch (color) 6
>> >>> Setting-Error: type read mismatch (color) 663
>> >>> Setting-Error: type read mismatch (color) 664
>> >>> (b) background color disparity:
>> >>> saved in 1.5 with black background; opens in 1.6 with a white
>> background
>> >>> saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red
>> >>> background
>> >>>
>> >>> These are run on openSUSE 12.3 with SVN rev 4028 . On a side note,
>> >>> others who would like to beta test can use devel:languages:python repo
>> >>> in openSUSE:
>> >>>
>> https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython
>> >>>
>> >>> -David
>>
>> --
>> Thomas Holder
>> PyMOL Developer
>> Schrödinger Contractor
>>
>>
>> --
>> This SF.net email is sponsored by Windows:
>>
>> Build for Windows Store.
>>
>> http://p.sf.net/sfu/windows-dev2dev
>> ___
>> 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
>>
>
>
>
> --
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
>
> http://p.sf.net/sfu/windows-dev2dev
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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
>



-- 
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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Re: [PyMOL] PyMOL 1.6 pre-release announcement

2013-06-19 Thread Robert Hanson

That would be a problem with all programs -- unless there is a SAVE mode
that is "compatible with version  " (as, for example, MS Word has). One
cannot expect backward compatibility, I think.

Bob Hanson


On Wed, Jun 19, 2013 at 4:18 PM, David Hall  wrote:

> I still have this problem:
> session saved in 1.6 with a black background; opens in 1.5 (and earlier)
> with a red background
>
> Many of my collaborators use old versions of pymol, frequently installed
> onto their machines when they were bought X years ago, and this essentially
> makes it so I cannot use pymol 1.6 as I cannot share sessions with them (at
> least not without getting weird e-mails asking why I have a sudden affinity
> for the color red).
>
> -David
>
>
>
>
> On Tue, Jun 18, 2013 at 7:37 AM, Thomas Holder <
> thomas.hol...@schrodinger.com> wrote:
>
>> This is fixed in SVN rev 4032.
>>
>> Cheers,
>>   Thomas
>>
>> Thomas Holder wrote, On 06/15/13 10:45:
>> > Hi Rob,
>> >
>> > this has not been fixed yet, I'm really sorry. We'll look into this
>> > ASAP. It only affects the open-source code, apparently we missed
>> > something when syncing with the incentive codebase.
>> >
>> > Cheers,
>> >   Thomas
>> >
>> > On Jun 14, 2013, at 9:23 PM, Robert Campbell <
>> robert.campb...@queensu.ca> wrote:
>> >> Hello Thomas and David,
>> >>
>> >> Was there any resolution of this?  I've just compiled the latest
>> version
>> >> from SVN and I have the same problem opening files created under
>> version
>> >> 1.5.0.  This is on Debian testing (32-bit).
>> >>
>> >> Cheers,
>> >> Rob
>> >>
>> >> On Fri, 2013-04-26 19:15  EDT,  David Hall 
>> >> wrote:
>> >>
>> >>> Hi Thomas,
>> >>>
>> >>> I'm running into issues with color compatibility between 1.6 and
>> >>> earlier versions when opening pses
>> >>> (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like:
>> >>> Setting-Error: type read mismatch (color) 6
>> >>> Setting-Error: type read mismatch (color) 663
>> >>> Setting-Error: type read mismatch (color) 664
>> >>> (b) background color disparity:
>> >>> saved in 1.5 with black background; opens in 1.6 with a white
>> background
>> >>> saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red
>> >>> background
>> >>>
>> >>> These are run on openSUSE 12.3 with SVN rev 4028 . On a side note,
>> >>> others who would like to beta test can use devel:languages:python repo
>> >>> in openSUSE:
>> >>>
>> https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython
>> >>>
>> >>> -David
>>
>> --
>> Thomas Holder
>> PyMOL Developer
>> Schrödinger Contractor
>>
>>
>> --
>> This SF.net email is sponsored by Windows:
>>
>> Build for Windows Store.
>>
>> http://p.sf.net/sfu/windows-dev2dev
>> ___
>> 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
>>
>
>
>
> --
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
>
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>



-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [PyMOL] PyMOL 1.6 pre-release announcement

2013-06-19 Thread David Hall

I still have this problem:
session saved in 1.6 with a black background; opens in 1.5 (and earlier)
with a red background

Many of my collaborators use old versions of pymol, frequently installed
onto their machines when they were bought X years ago, and this essentially
makes it so I cannot use pymol 1.6 as I cannot share sessions with them (at
least not without getting weird e-mails asking why I have a sudden affinity
for the color red).

-David




On Tue, Jun 18, 2013 at 7:37 AM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:

> This is fixed in SVN rev 4032.
>
> Cheers,
>   Thomas
>
> Thomas Holder wrote, On 06/15/13 10:45:
> > Hi Rob,
> >
> > this has not been fixed yet, I'm really sorry. We'll look into this
> > ASAP. It only affects the open-source code, apparently we missed
> > something when syncing with the incentive codebase.
> >
> > Cheers,
> >   Thomas
> >
> > On Jun 14, 2013, at 9:23 PM, Robert Campbell 
> wrote:
> >> Hello Thomas and David,
> >>
> >> Was there any resolution of this?  I've just compiled the latest version
> >> from SVN and I have the same problem opening files created under version
> >> 1.5.0.  This is on Debian testing (32-bit).
> >>
> >> Cheers,
> >> Rob
> >>
> >> On Fri, 2013-04-26 19:15  EDT,  David Hall 
> >> wrote:
> >>
> >>> Hi Thomas,
> >>>
> >>> I'm running into issues with color compatibility between 1.6 and
> >>> earlier versions when opening pses
> >>> (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like:
> >>> Setting-Error: type read mismatch (color) 6
> >>> Setting-Error: type read mismatch (color) 663
> >>> Setting-Error: type read mismatch (color) 664
> >>> (b) background color disparity:
> >>> saved in 1.5 with black background; opens in 1.6 with a white
> background
> >>> saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red
> >>> background
> >>>
> >>> These are run on openSUSE 12.3 with SVN rev 4028 . On a side note,
> >>> others who would like to beta test can use devel:languages:python repo
> >>> in openSUSE:
> >>>
> https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython
> >>>
> >>> -David
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger Contractor
>
>
> --
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
>
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>
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Re: [PyMOL] PyMOL 1.6 pre-release announcement

2013-06-18 Thread Thomas Holder

This is fixed in SVN rev 4032.

Cheers,
  Thomas

Thomas Holder wrote, On 06/15/13 10:45:
> Hi Rob,
> 
> this has not been fixed yet, I'm really sorry. We'll look into this
> ASAP. It only affects the open-source code, apparently we missed
> something when syncing with the incentive codebase.
> 
> Cheers,
>   Thomas
> 
> On Jun 14, 2013, at 9:23 PM, Robert Campbell  
> wrote:
>> Hello Thomas and David,
>>
>> Was there any resolution of this?  I've just compiled the latest version
>> from SVN and I have the same problem opening files created under version
>> 1.5.0.  This is on Debian testing (32-bit).
>>
>> Cheers,
>> Rob
>>
>> On Fri, 2013-04-26 19:15  EDT,  David Hall 
>> wrote:
>>
>>> Hi Thomas,
>>>
>>> I'm running into issues with color compatibility between 1.6 and
>>> earlier versions when opening pses
>>> (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like:
>>> Setting-Error: type read mismatch (color) 6
>>> Setting-Error: type read mismatch (color) 663
>>> Setting-Error: type read mismatch (color) 664
>>> (b) background color disparity:
>>> saved in 1.5 with black background; opens in 1.6 with a white background
>>> saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red
>>> background
>>>
>>> These are run on openSUSE 12.3 with SVN rev 4028 . On a side note,
>>> others who would like to beta test can use devel:languages:python repo
>>> in openSUSE:
>>> https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython
>>>
>>> -David

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

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Re: [PyMOL] PyMOL 1.6 pre-release announcement

2013-06-15 Thread Thomas Holder

Hi Rob,

this has not been fixed yet, I'm really sorry. We'll look into this ASAP. It 
only affects the open-source code, apparently we missed something when syncing 
with the incentive codebase.

Cheers,
  Thomas

On Jun 14, 2013, at 9:23 PM, Robert Campbell  wrote:
> Hello Thomas and David,
> 
> Was there any resolution of this?  I've just compiled the latest version
> from SVN and I have the same problem opening files created under version
> 1.5.0.  This is on Debian testing (32-bit).
> 
> Cheers,
> Rob
> 
> On Fri, 2013-04-26 19:15  EDT,  David Hall 
> wrote:
> 
>> Hi Thomas,
>> 
>> I'm running into issues with color compatibility between 1.6 and
>> earlier versions when opening pses
>> (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like:
>> Setting-Error: type read mismatch (color) 6
>> Setting-Error: type read mismatch (color) 663
>> Setting-Error: type read mismatch (color) 664
>> (b) background color disparity:
>> saved in 1.5 with black background; opens in 1.6 with a white background
>> saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red
>> background
>> 
>> These are run on openSUSE 12.3 with SVN rev 4028 . On a side note,
>> others who would like to beta test can use devel:languages:python repo
>> in openSUSE:
>> https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython
>> 
>> -David

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Re: [PyMOL] PyMOL 1.6 pre-release announcement

2013-06-14 Thread Robert Campbell

Hello Thomas and David,

Was there any resolution of this?  I've just compiled the latest version
from SVN and I have the same problem opening files created under version
1.5.0.  This is on Debian testing (32-bit).

Cheers,
Rob

 On Fri, 2013-04-26 19:15  EDT,  David Hall 
wrote:

> Hi Thomas,
> 
> I'm running into issues with color compatibility between 1.6 and
> earlier versions when opening pses
> (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like:
> Setting-Error: type read mismatch (color) 6
> Setting-Error: type read mismatch (color) 663
> Setting-Error: type read mismatch (color) 664
> (b) background color disparity:
> saved in 1.5 with black background; opens in 1.6 with a white background
> saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red
> background
> 
> These are run on openSUSE 12.3 with SVN rev 4028 . On a side note,
> others who would like to beta test can use devel:languages:python repo
> in openSUSE:
> https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython
> 
> -David
> 

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Re: [PyMOL] PyMOL 1.6 pre-release announcement

2013-04-26 Thread David Hall

Hi Thomas,

I'm running into issues with color compatibility between 1.6 and
earlier versions when opening pses
(a) when I open any 1.5 pse in 1.6, I see a bunch of errors like:
Setting-Error: type read mismatch (color) 6
Setting-Error: type read mismatch (color) 663
Setting-Error: type read mismatch (color) 664
(b) background color disparity:
saved in 1.5 with black background; opens in 1.6 with a white background
saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red
background

These are run on openSUSE 12.3 with SVN rev 4028 . On a side note,
others who would like to beta test can use devel:languages:python repo
in openSUSE:
https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython

-David


On Sun, Mar 24, 2013 at 6:02 AM, Thomas Holder
 wrote:
> Dear PyMOL users,
>
> The pre-release version of PyMOL 1.6 has been pushed to the open source 
> repository on SourceForge. Besides several minor fixes and improvements, this 
> version should complete the transition to shader-based rendering for all 
> on-screen drawing. For non-integrated chipsets this typically means higher 
> quality and quicker rendering.
>
> Please also note that the URL of the SVN repository changed due to an upgrade 
> of the SourceForge website:
>
>   svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
>
> As always, we welcome bug reports and positive feedback.
>
> Cheers,
>
> - The PyMOL Team at Schrödinger
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger Contractor
>
>
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Re: [PyMOL] PyMOL 1.6 pre-release announcement

2013-03-25 Thread Thomas Holder

Hi Christoph,

thanks a lot for the patches.

Regarding your suggestion for pymol.bat: I guess this will not work if
you install with a custom prefix, since you make assumptions where to
find pythonw.exe and the pymol module.

I suggest to discuss this off-list, since it's quite specific.

Cheers,
  Thomas

Christoph Gohlke wrote, On 03/25/13 18:11:
> On 3/24/2013 3:02 AM, Thomas Holder wrote:
>> Dear PyMOL users,
>>
>> The pre-release version of PyMOL 1.6 has been pushed to the open
>> source repository on SourceForge. Besides several minor fixes and
>> improvements, this version should complete the transition to
>> shader-based rendering for all on-screen drawing. For non-integrated
>> chipsets this typically means higher quality and quicker rendering.
>>
>> Please also note that the URL of the SVN repository changed due to an
>> upgrade of the SourceForge website:
>>
>>svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
>>
>> As always, we welcome bug reports and positive feedback.
>>
>> Cheers,
>>
>> - The PyMOL Team at Schrödinger
>>
> 
> Hello,
> 
> Please consider the attached changes for building with msvc on Windows.
> 
> Also, the latest changes to vmdir.h don't compile with msvc.
> 
> 
> 
> Opening absolute paths does not work on Windows (e.g. C:\1bna.pdb):
> 
> Index: pymol/modules/pymol/internal.py
> ===
> --- pymol/modules/pymol/internal.py(revision 4025)
> +++ pymol/modules/pymol/internal.py(working copy)
> @@ -303,7 +303,7 @@
>  try:
>  if not isinstance(finfo, basestring):
>  handle = finfo
> -elif ':' in finfo:
> +elif '://' in finfo:
>  import urllib
>  handle = urllib.urlopen(finfo)
>  else:
> 
> 
> The launch script, Scripts\pymol.bat, seems overly complicated and
> doesn't always work for binary installers. Suggestion:
> 
> Index: pymol/setup.py
> ===
> --- pymol/setup.py(revision 4025)
> +++ pymol/setup.py(working copy)
> @@ -119,9 +119,7 @@
> 
>  with open(launch_script, 'w') as out:
>  if sys.platform.startswith('win'):
> -out.write('set PYMOL_PATH=' + pymol_path + os.linesep)
> -out.write('"%s" "%s"' % (python_exe, pymol_file))
> -out.write(' %1 %2 %3 %4 %5 %6 %7 %8 %9' + os.linesep)
> +out.write(r'@%~dp0\..\pythonw.exe -m pymol.__init__ %*')
>  else:
>  out.write('#!/bin/sh' + os.linesep)
>  if sys.platform.startswith('darwin'):
> 
> 
> Thanks,
> 
> Christoph

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Re: [PyMOL] PyMOL 1.6 pre-release announcement

2013-03-25 Thread Stephen P. Molnar

On Mon, 25 Mar 2013 18:47:27 +0100
Michael Banck  wrote:

> Hi Stephen,
> 
> On Mon, Mar 25, 2013 at 01:33:16PM -0400, Stephen P. Molnar wrote:
> > On Sun, 24 Mar 2013 11:02:08 +0100
> > Thomas Holder  wrote:
> > > The pre-release version of PyMOL 1.6 has been pushed to the open
> > > source repository on SourceForge. Besides several minor fixes and
> > > improvements, this version should complete the transition to
> > > shader-based rendering for all on-screen drawing. For
> > > non-integrated chipsets this typically means higher quality and
> > > quicker rendering.
> > > 
> > > Please also note that the URL of the SVN repository changed due
> > > to an upgrade of the SourceForge website:
> > > 
> > >   svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
> > > 
> > > As always, we welcome bug reports and positive feedback.
> > > 
> > > Cheers,
> > > 
> > > - The PyMOL Team at Schrödinger
> > > 
> > 
> > I managed to download the source code.  There were a lot of warnings
> > during the compilation and I got the following error message:
> > 
> > usr/include/python2.7 -c layer1/TypeFace.c -o
> > build/temp.linux-x86_64-2.7/layer1/TypeFace.o -ffast-math
> > -funroll-loops -O3 -fcommon layer1/TypeFace.c:25:22: fatal error:
> > ft2build.h: No such file or directory compilation terminated.
> > 
> > I don't have the faintest idea as to what supplies ft2build.h and
> > would appreciate a point in the correct direction.
> 
> It's shipped by the libfreetype development package.
> 
> 
> Michael
> 
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Many thanks,  That solved the problem! v1.6.0 is now compiled and
installed.

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Re: [PyMOL] PyMOL 1.6 pre-release announcement

2013-03-25 Thread Michael Banck

Hi Stephen,

On Mon, Mar 25, 2013 at 01:33:16PM -0400, Stephen P. Molnar wrote:
> On Sun, 24 Mar 2013 11:02:08 +0100
> Thomas Holder  wrote:
> > The pre-release version of PyMOL 1.6 has been pushed to the open
> > source repository on SourceForge. Besides several minor fixes and
> > improvements, this version should complete the transition to
> > shader-based rendering for all on-screen drawing. For non-integrated
> > chipsets this typically means higher quality and quicker rendering.
> > 
> > Please also note that the URL of the SVN repository changed due to an
> > upgrade of the SourceForge website:
> > 
> >   svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
> > 
> > As always, we welcome bug reports and positive feedback.
> > 
> > Cheers,
> > 
> > - The PyMOL Team at Schrödinger
> > 
> 
> I managed to download the source code.  There were a lot of warnings
> during the compilation and I got the following error message:
> 
> usr/include/python2.7 -c layer1/TypeFace.c -o
> build/temp.linux-x86_64-2.7/layer1/TypeFace.o -ffast-math
> -funroll-loops -O3 -fcommon layer1/TypeFace.c:25:22: fatal error:
> ft2build.h: No such file or directory compilation terminated.
> 
> I don't have the faintest idea as to what supplies ft2build.h and would
> appreciate a point in the correct direction.

It's shipped by the libfreetype development package.


Michael

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Re: [PyMOL] PyMOL 1.6 pre-release announcement

2013-03-25 Thread Stephen P. Molnar

On Sun, 24 Mar 2013 11:02:08 +0100
Thomas Holder  wrote:

> Dear PyMOL users,
> 
> The pre-release version of PyMOL 1.6 has been pushed to the open
> source repository on SourceForge. Besides several minor fixes and
> improvements, this version should complete the transition to
> shader-based rendering for all on-screen drawing. For non-integrated
> chipsets this typically means higher quality and quicker rendering.
> 
> Please also note that the URL of the SVN repository changed due to an
> upgrade of the SourceForge website:
> 
>   svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
> 
> As always, we welcome bug reports and positive feedback.
> 
> Cheers,
> 
> - The PyMOL Team at Schrödinger
> 

I managed to download the source code.  There were a lot of warnings
during the compilation and I got the following error message:

usr/include/python2.7 -c layer1/TypeFace.c -o
build/temp.linux-x86_64-2.7/layer1/TypeFace.o -ffast-math
-funroll-loops -O3 -fcommon layer1/TypeFace.c:25:22: fatal error:
ft2build.h: No such file or directory compilation terminated.

I don't have the faintest idea as to what supplies ft2build.h and would
appreciate a point in the correct direction.

Thanks in advance.

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Re: [PyMOL] PyMOL 1.6 pre-release announcement

2013-03-25 Thread Christoph Gohlke


On 3/24/2013 3:02 AM, Thomas Holder wrote:

Dear PyMOL users,

The pre-release version of PyMOL 1.6 has been pushed to the open source 
repository on SourceForge. Besides several minor fixes and improvements, this 
version should complete the transition to shader-based rendering for all 
on-screen drawing. For non-integrated chipsets this typically means higher 
quality and quicker rendering.

Please also note that the URL of the SVN repository changed due to an upgrade 
of the SourceForge website:

   svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol

As always, we welcome bug reports and positive feedback.

Cheers,

- The PyMOL Team at Schrödinger



Hello,

Please consider the attached changes for building with msvc on Windows.

Also, the latest changes to vmdir.h don't compile with msvc.


Opening absolute paths does not work on Windows (e.g. C:\1bna.pdb):

Index: pymol/modules/pymol/internal.py
===
--- pymol/modules/pymol/internal.py (revision 4025)
+++ pymol/modules/pymol/internal.py (working copy)
@@ -303,7 +303,7 @@
 try:
 if not isinstance(finfo, basestring):
 handle = finfo
-elif ':' in finfo:
+elif '://' in finfo:
 import urllib
 handle = urllib.urlopen(finfo)
 else:


The launch script, Scripts\pymol.bat, seems overly complicated and 
doesn't always work for binary installers. Suggestion:


Index: pymol/setup.py
===
--- pymol/setup.py  (revision 4025)
+++ pymol/setup.py  (working copy)
@@ -119,9 +119,7 @@

 with open(launch_script, 'w') as out:
 if sys.platform.startswith('win'):
-out.write('set PYMOL_PATH=' + pymol_path + os.linesep)
-out.write('"%s" "%s"' % (python_exe, pymol_file))
-out.write(' %1 %2 %3 %4 %5 %6 %7 %8 %9' + os.linesep)
+out.write(r'@%~dp0\..\pythonw.exe -m pymol.__init__ %*')
 else:
 out.write('#!/bin/sh' + os.linesep)
 if sys.platform.startswith('darwin'):


Thanks,

Christoph
Index: pymol/layer0/os_predef.h
===
--- pymol/layer0/os_predef.h(revision 4025)
+++ pymol/layer0/os_predef.h(working copy)
@@ -109,6 +109,7 @@
 #endif
 
 #if defined(_WIN32) || defined(_WIN64)
+#define M_PI 3.1415926535897932384626433832795
 #define fmax max
 #define fmin min
 #pragma warning (disable:4996)
Index: pymol/layer2/RepLabel.c
===
--- pymol/layer2/RepLabel.c (revision 4025)
+++ pymol/layer2/RepLabel.c (working copy)
@@ -90,12 +90,13 @@
 }
   } else if(G->HaveGUI && G->ValidContext) {
 if(pick) {
+  Pickable *p;
+  int i;
   if (I->shaderCGO){
CGORenderGLPicking(I->shaderCGO, pick, &I->R.context, I->R.cs->Setting, 
I->R.obj->Setting);
return;
   }
-  Pickable *p = I->R.P;
-  int i;
+  p = I->R.P;
   SceneSetupGLPicking(G);
   if(c) {
 char *st;
Index: pymol/layer5/main.c
===
--- pymol/layer5/main.c (revision 4025)
+++ pymol/layer5/main.c (working copy)
@@ -23,7 +23,6 @@
 #ifdef WIN32
 #include 
 #include 
-#include 
 #endif
 
 /* END PROPRIETARY CODE SEGMENT */
@@ -1792,9 +1791,8 @@
 
 int main_exec(int argc, char **argv)
 {
-  is_shared = 0;
-
   PyMOLGlobals *G = SingletonPyMOLGlobals;
+  is_shared = 0;  
   myArgc = argc;
   myArgv = argv;
 
Index: pymol/modules/cealign/src/ccealignmodule.cpp
===
--- pymol/modules/cealign/src/ccealignmodule.cpp(revision 4025)
+++ pymol/modules/cealign/src/ccealignmodule.cpp(working copy)
@@ -631,11 +631,11 @@
   int m = (int) v.dim1();
   int n = (int) v.dim2();

-  TA2 rVal(n,m);
+  TA2 rVal((int)n,(int)m);

   for ( int i = 0; i < m; i++ )
 for ( int j = 0; j < n; j++ )
-  rVal[j][i] = v[i][j];
+  rVal[(int)j][(int)i] = v[(int)i][(int)j];

   return rVal;
 }
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Re: [PyMOL] PyMOL 1.6 pre-release announcement

2013-03-25 Thread Michael Banck

Hi,

On Sun, Mar 24, 2013 at 11:02:08AM +0100, Thomas Holder wrote:
> The pre-release version of PyMOL 1.6 has been pushed to the open
> source repository on SourceForge. Besides several minor fixes and
> improvements, this version should complete the transition to
> shader-based rendering for all on-screen drawing. For non-integrated
> chipsets this typically means higher quality and quicker rendering.
 
[...]

> As always, we welcome bug reports and positive feedback.

Works fine for me so far, I noticed one thing though: In Wizard -> Demo
-> Sculpting, the protein backbone mostly disappears if I rotate a bond,
I just see the angle and the spheres, while the backbone is almost
invisible.  This does not seem to happen if I rotate around a bond at
the outside of the protein.

In 1.5.0.1, the appearance does not change between dragging atoms and
rotating bonds which made it easier to rotate around bonds.

This is with a Lenovo T400 and internal Intel Graphics.


Michael

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Re: [PyMOL] PyMOL 1.6 pre-release announcement

2013-03-24 Thread Thomas Holder

Hi Michael,

I haven't tagged that commit. It's svn revision 4025. For the final 1.6.0 
version we will upload a tar.gz archive to sourceforge.

Cheers,
  Thomas

On Mar 24, 2013, at 1:18 PM, Michael Banck  wrote:
> Hi,
> 
> On Sun, Mar 24, 2013 at 11:02:08AM +0100, Thomas Holder wrote:
>> The pre-release version of PyMOL 1.6 has been pushed to the open
>> source repository on SourceForge. Besides several minor fixes and
>> improvements, this version should complete the transition to
>> shader-based rendering for all on-screen drawing. For non-integrated
>> chipsets this typically means higher quality and quicker rendering.
>> 
>> Please also note that the URL of the SVN repository changed due to an
>> upgrade of the SourceForge website:
>> 
>>  svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
>> 
>> As always, we welcome bug reports and positive feedback.
> 
> Great!  Is there some pre-release version number assigned to that
> commit, like "1.6.0pre1" or "1.6.0rc1", assuming a final 1.6.0 will
> follow at some point?
> 
> Best regards,
> 
> Michael

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Re: [PyMOL] PyMOL 1.6 pre-release announcement

2013-03-24 Thread Michael Banck

Hi,

On Sun, Mar 24, 2013 at 11:02:08AM +0100, Thomas Holder wrote:
> The pre-release version of PyMOL 1.6 has been pushed to the open
> source repository on SourceForge. Besides several minor fixes and
> improvements, this version should complete the transition to
> shader-based rendering for all on-screen drawing. For non-integrated
> chipsets this typically means higher quality and quicker rendering.
> 
> Please also note that the URL of the SVN repository changed due to an
> upgrade of the SourceForge website:
> 
>   svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
> 
> As always, we welcome bug reports and positive feedback.

Great!  Is there some pre-release version number assigned to that
commit, like "1.6.0pre1" or "1.6.0rc1", assuming a final 1.6.0 will
follow at some point?


Best regards,

Michael

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[PyMOL] PyMOL 1.6 pre-release announcement

2013-03-24 Thread Thomas Holder

Dear PyMOL users,

The pre-release version of PyMOL 1.6 has been pushed to the open source 
repository on SourceForge. Besides several minor fixes and improvements, this 
version should complete the transition to shader-based rendering for all 
on-screen drawing. For non-integrated chipsets this typically means higher 
quality and quicker rendering.

Please also note that the URL of the SVN repository changed due to an upgrade 
of the SourceForge website:

  svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol

As always, we welcome bug reports and positive feedback.

Cheers,

- The PyMOL Team at Schrödinger

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor


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Re: [PyMOL] PyMOL 1.6 pre-release announcement

Re: [PyMOL] PyMOL 1.6 pre-release announcement

Re: [PyMOL] PyMOL 1.6 pre-release announcement

Re: [PyMOL] PyMOL 1.6 pre-release announcement

Re: [PyMOL] PyMOL 1.6 pre-release announcement

Re: [PyMOL] PyMOL 1.6 pre-release announcement

Re: [PyMOL] PyMOL 1.6 pre-release announcement

Re: [PyMOL] PyMOL 1.6 pre-release announcement

Re: [PyMOL] PyMOL 1.6 pre-release announcement

Re: [PyMOL] PyMOL 1.6 pre-release announcement

Re: [PyMOL] PyMOL 1.6 pre-release announcement

Re: [PyMOL] PyMOL 1.6 pre-release announcement

Re: [PyMOL] PyMOL 1.6 pre-release announcement

Re: [PyMOL] PyMOL 1.6 pre-release announcement

Re: [PyMOL] PyMOL 1.6 pre-release announcement

Re: [PyMOL] PyMOL 1.6 pre-release announcement

Re: [PyMOL] PyMOL 1.6 pre-release announcement

[PyMOL] PyMOL 1.6 pre-release announcement

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