[Chimera-users] MD plots

[Elaine Meng]

Hi Luis,
This is a new feature added after the 1.5.3 release --- you would need to use a Chimera daily build to try this feature.  Daily build download:
<http://www.cgl.ucsf.edu/chimera/download.html#daily>

List of new features since the 1.5 release series:
<http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html>

Enjoy!
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 Dec 6, 2011, at 4:33 PM, lecan wrote:

> Hi Elaine.
> I was following this item that George asked about the plotting of distances in a MD and I got interest in plotting distances as well. But I can not find the plot button in Chimera 1.5.3. Could you please tell where is the plot button in this version? In the MD movie window at the analysis pull down only appear "Calculate occupancy", "Cluster" and "RMSD map".
> 
> Thank you in advance,
> 
> Luis L.
> 
> 
> On Mon, 5 Dec 2011 13:18:09 -0800, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> Hi George,
>> The distance command is for showing the distance monitor (dashed line
>> and angstrom label).  For MD movie plotting,  you need only select the
>> two atoms and then click the Plot button on the dialog.  In the image
>> you sent, the dialog is showing an error message that suggests you do
>> not have exactly two atoms selected (i.e. either fewer or more atoms
>> than two seem to be selected).   Try clearing the selection before you
>> select the two atoms.  Also make sure your selection is really getting
>> only two atoms.
>> 
>> For example, realize ":124 at H" could select more than one atom.  There
>> might be residue 124 in both chain A and chain B, and/or in model 0
>> and model 1, etc.
>> 
>> You can see how many atoms are selected, for example by clicking the
>> green magnifying glass on the lower right corner of the Chimera window
>> to open the Selection Inspector.
>> I hope this helps,
>> Elaine
>> ----------
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> 
>> 
>> 
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>