[Chimera-users] how to quickly delete several markers

[Thomas Goddard]

Hi Juha,

   I see, saving markers to an XML file is broken if atoms/bonds are 
deleted, for example using shortcut Da.  Ok, I've fixed this -- try 
tonight's daily build (Feb 26 build available in about 12 hours).

	http://www.cgl.ucsf.edu/chimera/alpha-downloads.html

Sorry I did not catch this earlier.  I typically save markers in Chimera 
sessions (File / Save session) which is working with shortcut Da.  But 
the XML output is of course useful when other programs will use the markers.

	Tom


Juha Huiskonen wrote:
> Hi Tom,
> 
> Thanks for your response. However, I run into a problem.. I am sending 
> this only to you, since I am attaching some example files. (I also 
> updated Chimera to 1.3.2577 linux x86_64, but the problem persists.)
> 
> My original markers are in (the file.cmm) If I use "Volume 
> Tracer->Delete markers" and then save the marker set (file 
> file_sel.cmm), everything is fine. If I then delete more markers, now 
> with the "sc" and "Da" accelators, I get an error:
> 
> Invoked accelerator sc - Select connected atoms/bonds
> Invoked accelerator Da - Delete atoms and bonds
> <type 'exceptions.ValueError'> Exception in Tk callback
>   Function: <bound method Volume_Path_Dialog.save_marker_set_as_cb of 
> <VolumePath.gui.Volume_Path_Dialog instance at 0x2190fc8>> (type: <type 
> 'instancemethod'>)
>   Args: ()
> Traceback (innermost last):
>   File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", 
> line 1747, in __call__
>     None
>   File "CHIMERA/share/VolumePath/gui.py", line 294, in 
> save_marker_set_as_cb
>     None
>   File "CHIMERA/share/VolumePath/gui.py", line 325, in save_marker_sets
>     None
>   File "CHIMERA/share/VolumePath/markerset.py", line 707, in 
> save_marker_sets
>     None
>   File "CHIMERA/share/VolumePath/markerset.py", line 222, in save_as_xml
>     None
>   File "CHIMERA/share/VolumePath/markerset.py", line 339, in xyz
>     None
> <type 'exceptions.ValueError'>: underlying C++ Atom object is missing
> 
> 
> I can still save the marker file, but it has not links (file_sel2.cmm).
> 
> 
> Juha
> 
>




> Tom Goddard wrote:
>> Hi Juha,
>>
>>  There are always tricks!  I use keyboard shortcuts to do this.  You 
>> have to turn on keyboard shortcuts to use them (menu Tools / General 
>> Controls / Keyboard Shortcuts, then click Enable keyboard shortcuts).  
>> The shortcuts are 2-key sequences (no return key) typed in the 
>> graphics window and the relevant ones for your task are:
>>
>>    Da     - deletes selected markers/atoms
>>    sc       - select all markers/atoms connected to the already 
>> selected ones by links/bonds
>>
>> So the typical use to delete a chain of markers is to select one with 
>> the mouse then type sc, then
>> Da.  The uppercase D is important.  Upper case in shortcuts is used if 
>> the action has serious irreversible consequences.
>>
>>  If you use the Chimera command-line that overrides the shortcuts.  To 
>> get back to using shortcuts use the Chimera command "ac" and press 
>> return (that's a command not a shortcut, stands for accelerators).
>>
>>  Here's a full list of shortcuts.
>>
>>    
>> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/alist.html 
>>
>>
>>  Your mouse mode would be nice.  We need better support for alternate 
>> mouse modes in Chimera like a palette of modes as in paint programs.
>>
>>  Tom
>>
>>
>> Juha Huiskonen wrote:
>>> Dear Chimera developers & users,
>>>
>>> I am visualizing template matching results of volume data in Chimera, 
>>> and I have to discard hundreds of false positives matches, 
>>> represented as markers.
>>>
>>> Now I select some markers and then delete the selected markers from 
>>> the Volume Path Tracer menu. This is quite slow, and for me it would 
>>> be really handy, if I could delete (all linked) markers just by 
>>> clicking (one of them) them.
>>>
>>> Maybe "delete markers with mouse" feature could be added to Volume 
>>> Path Tracer module?
>>>
>>> Or is there already a faster way to do this?
>>>
>>> Thanks a lot in advance for your suggestions!
>>>
>>> Juha
>>>
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>   
> 



Tom Goddard wrote:
> Hi Juha,
> 
>   There are always tricks!  I use keyboard shortcuts to do this.  You 
> have to turn on keyboard shortcuts to use them (menu Tools / General 
> Controls / Keyboard Shortcuts, then click Enable keyboard shortcuts).  
> The shortcuts are 2-key sequences (no return key) typed in the graphics 
> window and the relevant ones for your task are:
> 
>     Da     - deletes selected markers/atoms
>     sc       - select all markers/atoms connected to the already 
> selected ones by links/bonds
> 
> So the typical use to delete a chain of markers is to select one with 
> the mouse then type sc, then
> Da.  The uppercase D is important.  Upper case in shortcuts is used if 
> the action has serious irreversible consequences.
> 
>   If you use the Chimera command-line that overrides the shortcuts.  To 
> get back to using shortcuts use the Chimera command "ac" and press 
> return (that's a command not a shortcut, stands for accelerators).
> 
>   Here's a full list of shortcuts.
> 
>     
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/alist.html
> 
>   Your mouse mode would be nice.  We need better support for alternate 
> mouse modes in Chimera like a palette of modes as in paint programs.
> 
>   Tom
> 
> 
> Juha Huiskonen wrote:
>> Dear Chimera developers & users,
>>
>> I am visualizing template matching results of volume data in Chimera, 
>> and I have to discard hundreds of false positives matches, represented 
>> as markers.
>>
>> Now I select some markers and then delete the selected markers from 
>> the Volume Path Tracer menu. This is quite slow, and for me it would 
>> be really handy, if I could delete (all linked) markers just by 
>> clicking (one of them) them.
>>
>> Maybe "delete markers with mouse" feature could be added to Volume 
>> Path Tracer module?
>>
>> Or is there already a faster way to do this?
>>
>> Thanks a lot in advance for your suggestions!
>>
>> Juha
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>   
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users