[Chimera-users] inter-atomic distances do not show in session after daily build upgrade

[Darren Weber]

Hi Boaz,

There is a recent addition to daily-builds to create a scene called 
'session'.  It can be seen in the Utilities > Animation dialog.  The 
purpose of this scene is to enable easy, quick return to the saved 
session state after making a few changes, without reloading the scene again.

There are a two potential problems with this new addition:
1.  Some of the saved session data or properties may not be supported by 
the scene facility, yet.  This might be the problem with the issue you 
raised, Boaz.  Elaine sent me an example session that is not yet 
supported by the scene facility and, indeed, it contains a 'selection 
set' that raises an exception in the scene code.
2.  Assuming everything in a session is supported by the scene facility, 
the 'session' scene should work.  That is, it will work only while all 
the data that it refers to (e.g., models) are present.  If changes 
result in removing any model data that is within the 'session' scene, 
the scene will contain 'orphaned' references and it will work only on 
the remaining model data (if any).

This new feature to scene support in save/restore sessions is 
experimental in the daily-builds.  For anyone using a daily-build for 
any mission-critical work, it may be handy to have a work around for the 
above problems.  Try making the following changes to 
$CHIMERA_INSTALL_PATH/share/Animate/Session.py:
1.  Comment out line 51 ("Animate.scenes.append('session')") and type 
'pass' beneath it (using the same tabbed indentation).  This will only 
disable the creation of a 'session' scene after restoring any session.  
All other session support remains enabled for scenes.
2.  To completely disable all session support in the Animate extension, 
comment out all the statements that start with 
"chimera.triggers.addHandler".

-- Darren

PS.  All of the above will be posted again in a new thread on the email 
list, to announce the potential issues with session support for daily 
builds of Chimera.


On 09/03/2011 01:53 PM, Boaz Shaanan wrote:
> Hi Elaine,
>
> Thanks for the quick response. I often find myself in a dilemma when coming across a problem in Chimera: is it me who doesn't know about an existing Chimera function or is it really a bug. Thanks to you guys it really does not matter eventually.
>
> As for using the production release: I switched to the daily built because of another problem that Eric pointed out to me with using of the castp data. That has solved the castp problem and I'm happy with using the daily built now but for the issue I reported today.
>
>     Thanks for your help,
>
>                                Boaz
>
>
> Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
>
> E-mail: bshaanan at bgu.ac.il
> Phone: 972-8-647-2220  Skype: boaz.shaanan
> Fax:   972-8-647-2992 or 972-8-646-1710
>
>
>
>
>
> ________________________________________
> From: Elaine Meng [meng at cgl.ucsf.edu]
> Sent: Saturday, September 03, 2011 10:36 PM
> To: בעז שאנן
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] inter-atomic distances do not show in session after daily build upgrade
>
> Hi Boaz,
> Generally it is better to use "Help... Report a Bug" and attach the session so that we have the data, but in this case you don't need to do it -- I just reproduced the problem in my own little test session with one distance.  I will report the bug and put you on the CC list.
>
> I almost always use daily builds too, but since they aren't tested, occasionally some bug will prevent you from doing what you want or need to do.  Sometimes I save more than one daily build.  Otherwise, I'm hoping you will be able to use the production release (version 1.5.3) until this is sorted out.  If you saved the session in a newer version, however, I understand that may not work.  I will put the bug at a high priority.
>
> Sorry about that,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Sep 3, 2011, at 11:53 AM, Boaz Shaanan wrote:
>
>> Hi,
>> I upgraded to the latest daily build and restored a session that had quite a few distances drawn. The dashed lines don't show while the table of distances is still there. Before the upgrade the session was restored several times and always showed the distances fine. Is there a way to resuscitate the display of distances? I sure hope so.
>>         Cheers,
>>                    Boaz
>
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