[Chimera-users] Cannot save the labels in Volume trace

Thomas Goddard goddard at cgl.ucsf.edu
Tue Sep 1 11:58:31 PDT 2009

Hi Xing,

   Yes, now I see that if you select a link and use menu Actions / Label 
/ other... and type a text label such as a number for your helices then 
that label is not saved in sessions.  This is a bug, that labels on 
links or bonds are not saved in sessions.  Eric Pettersen says he will 
fix it this week (probably today).

   The marker notes only apply to the markers, not the links. I will fix 
the code so that marker labels created with Actions / Label / other... 
are saved.  Currently having an empty marker note overrides such labels. 
  I expect to fix this later in the week.  Will let you know when it is 


-------- Original Message --------
Subject: Re: [Chimera-users] Cannot save the labels in Volume trace
From: Xing Zhang
To: 'Thomas Goddard'
Date: 9/1/09 10:09 AM

> Thanks, Tom,
> I just found my mistake. I actually want to label the*_ linker_**_s_* 
> (not markers) between two makers to represent the sequence of each 
> secondary structure. So how can I do that in Chimera which could be 
> saved and restored? Thank you very much.
> Xing

-------- Original Message --------
Subject: Re: [Chimera-users] Cannot save the labels in Volume trace
From: Thomas Goddard
To: Xing Zhang
Date: 8/31/09 5:53 PM

> Hi Xing,
>    If you placed markers with the Volume Tracer dialog and use Features 
> / Marker Note in that dialog to label the markers they will be saved in 
> session files.  I see that if you use Actions / Label / other... to 
> label the markers then that is not saved in Chimera 1.3, and it is saved 
> but not restored in Chimera 1.4, because the empty Marker Note overrides 
> the label.
>    I'll try to fix this for the upcoming Chimera 1.4 release, so that 
> labels set with Actions / Label are treated the same as marker notes. 
> For now, use the Volume Tracer dialog Features / Marker Note and it will 
>   be saved and restored from sessions.
>    Thanks for reporting the problem.
> 	Tom
> -------- Original Message --------
> Subject: [Chimera-users] Cannot save the labels in Volume trace
> From: Xing Zhang
> To: 'Chimera BB' <chimera-users at cgl.ucsf.edu>
> Date: 8/31/09 10:10 AM
>> Dear All,
>> I try to put stickers and balls in my EM density to trace secondary
>> structures of protein. During this process, I put a number to label each of
>> the secondary structures. However, these labels are all lost after I save
>> this session and restore the session. Any suggestion to solve this problem
>> would be greatly appreciated. Thanks.
>> Xing

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