[Chimera-users] ViewDock compound state

Elaine Meng meng at cgl.ucsf.edu
Mon Jun 27 16:15:25 PDT 2011

Hi Magdalena,
One idea for categorizing your dock hits or poses is to define a model attribute.  This would not be shown or settable in the ViewDock dialog, so it would not be as friendly/easy as what you suggest, but it would let you specify or select subsets of the hits based on your own defined categories.

If your dock hits were opened as model #0, then the individual ones are "submodels" #0.1, 0.2, 0.3 .... You can create an attribute named whatever you want, say "rating" and assign values to the individual hits.  This could be done in a text file called an "attribute assignment file" or with the command "setattr."

The command approach can be used to assign one value at a time and would look something like:

setattr m rating 0 #0.133

... which would assign a value of rating=0 to the 133rd result in the file.  Not as convenient as checking a button, obviously, but the model specifier of the one you are viewing is shown in the ViewDock dialog, and later you could do things like

select #/rating=3
(select all hits with a rating of 3)
select #/rating>2
(select hits with a rating greater than 2)

... then save to a file or delete only the ones that are selected.  

The alternative way to assign an attribute, with an assignment file, can be used to make several assignments at once;  file contents would look something like:

#  Use this file to assign the attribute in Chimera with the 
#  Define Attribute tool or the command defattr.
attribute: rating
recipient: molecules
	#0.1	1
	#0.2	3
	#0.3	0
	#0.4	1
(etc., tab-separated columns of specifier and value)

File format description and more examples:

Perhaps this approach is not worth it for what you had in mind, but I thought I would put the idea out there!

On Jun 27, 2011, at 3:30 PM, Elaine Meng wrote:

> Hi Magdalena,
> Sorry, there is no "user interface" way to do that ... it would require programming.
> Best,
> 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 Jun 27, 2011, at 3:05 PM, S. Pea wrote:
>> Hello,
>> I was wondering if there is an option in ViewDock to create more bins
>> (flags) in the "change compound state"?
>> Currently there is an option to change the compound state from Viable,
>> to either Deleted or Purged but is there an option to put extra user
>> defined states.
>> Thanks,
>> Magdalena

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