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....

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@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....

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@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users