[PyMOL] Labeling CGO objects

[Ron Jacak]

Label gurus,

I'm trying to label CGO objects with custom labels. I found the
previous posts that explain how to create CGO text and then the
"painful" way of reorienting the labels when the molecule is moved
using cmd.rotate and cmd.translate. I'm curious if an easier way has
been developed since the posts in 2002. I see that the "distance"
command draws in CGO cylinders (dashes) between two atom selections
and then labels them with the distance, meaning that it is possible
in PyMOL to have labels tied to a CGO object. I've tried to generate
a selection (since cmd.label requires a selection as the first param)
from the CGO object but I don't think it's possible and cmd.label
won't take my CGO object as the first param.

I've succeeded in getting something close to what I want by labeling
the closest atom to my CGO object with my custom label, and then
translating the label using the mouse. But this procedure is not
possible to do in a script or plugin. Is there a better way to label
CGOs?

Thanks for any ideas.

-Ron

Ron Jacak
Graduate Student
University of North Carolina - Chapel Hill

[Richard Gillilan]

I'm having trouble figuring out how to use the edit mode in PyMol. I
would like to dock an entire protein (a homodimer along with water)
into another structure by rotating and translating manually.

Is there a way to move multiple molecules like this as a group?


Thanks

Richard Gillilan
MacCHESS

[DeLano Scientific]

Ron,

CGO labels are currently insufficient and need work. Right now, the only
way to access high-quality labels (using scalable TrueType fonts) is to
create fake atoms and then label them.

Cheers,
Warren

PS. As a minor correction of fact, dashes aren't drawn with CGOs -- they're
hard-coded at the C level as measurement objects.

--
DeLano Scientific LLC
Subscriber Support Services
mailto:***@delsci.info

"Not yet a PyMOL Subscriber, but want to support the project? Email
***@delsci.com to quote your lab, school, or employer. Thank you for
sponsoring this open-source endeavor!" -WLD

-----Original Message-----
Of Ron Jacak
Sent: Monday, January 22, 2007 10:42 AM
Subject: [PyMOL] Labeling CGO objects
Label gurus,
I'm trying to label CGO objects with custom labels. I found
the previous posts that explain how to create CGO text and
then the "painful" way of reorienting the labels when the
molecule is moved using cmd.rotate and cmd.translate. I'm
curious if an easier way has been developed since the posts
in 2002. I see that the "distance"
command draws in CGO cylinders (dashes) between two atom
selections and then labels them with the distance, meaning
that it is possible in PyMOL to have labels tied to a CGO
object. I've tried to generate a selection (since cmd.label
requires a selection as the first param) from the CGO object
but I don't think it's possible and cmd.label won't take my
CGO object as the first param.
I've succeeded in getting something close to what I want by
labeling the closest atom to my CGO object with my custom
label, and then translating the label using the mouse. But
this procedure is not possible to do in a script or plugin.
Is there a better way to label CGOs?
Thanks for any ideas.
-Ron
Ron Jacak
Graduate Student
University of North Carolina - Chapel Hill
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[Terry Jones]

Hi Warren

| CGO labels are currently insufficient and need work. Right now, the only
| way to access high-quality labels (using scalable TrueType fonts) is to
| create fake atoms and then label them.

What's the recommended way to do this? Can you just put them anywhere you
like, irrespective of any underlying physical model? And then presumably
make them zero radius, or give them the background color, etc. so as not to
see them?

Terry

[DeLano Scientific]

Richard,

Probably the easiest way to do this is with the "drag" command. However,
all of the atoms to be drag must be contained within a single molecular
object. It is not currently possible to move multiple objects at once using
the mouse.

drag object-name

Then move object with shift-(left or middle or right)-click-and-drag
actions.

Cheers,
Warren

-----Original Message-----
Of Richard Gillilan
Sent: Monday, January 22, 2007 1:48 PM
Subject: [PyMOL] dock one protein into another?
I'm having trouble figuring out how to use the edit mode in
PyMol. I would like to dock an entire protein (a homodimer
along with water) into another structure by rotating and
translating manually.
Is there a way to move multiple molecules like this as a group?
Thanks
Richard Gillilan
MacCHESS
--------------------------------------------------------------
-----------
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SourceForge.net's Techsay panel and you'll get the chance to
share your opinions on IT & business topics through brief
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[DeLano Scientific]

Post by Terry Jones
| CGO labels are currently insufficient and need work. Right
now, the
| only way to access high-quality labels (using scalable
TrueType fonts)
| is to create fake atoms and then label them.
What's the recommended way to do this? Can you just put them
anywhere you like, irrespective of any underlying physical
model?

Yes. The open-source code & sponsor-only 1.x beta builds have a new
"pseudoatom" command that makes this particularly convenient.

pseudoatom my_lab, pos=[3.0,4.0,5.0], label=Custom Label Text

You can even drag the label around with the mouse (ctrl-left-click & drag).

Post by Terry Jones
And then presumably make them zero radius, or give
them the background color, etc. so as not to see them?

No need -- simply:

as label, object-name

to hide any atomic representation.

Cheers,
Warren