From: Chris Rife <chris.rife@va...> - 2002-05-10 15:47:16
I am making some stereo images and would like to put in some labels that
will move with the model. When I use the "label" command, the labels are
okay but they disappear with ray tracing. Is there any way around this,
other than adding in the labels in an image editing program?
Thanks to some recent and much appreciated development assistance
from PyMOL user, this is something I hope we can deliver in the next
For now, save your ray-traced images as PNG files and then annotate
manually in PowerPoint, Photoshop, or Keynote. Sorry for the inconvenience.
> -----Original Message-----
> From: pymol-users-admin@...
> [mailto:pymol-users-admin@...] On Behalf Of
> Jose Avalos
> Sent: Wednesday, February 11, 2004 1:01 PM
> To: Warren DeLano
> Cc: pymol-users@...
> Subject: [PyMOL] labels
> Dear all:
> What do I need to do avoid losing the labels when I ray trace?
> Thank you again
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I have just installed the new release of PyMol and was particularly
pleased that labels can now be rendered. Then it occured to me that I
actually don't know how to label a residue Tyr84 (or whatever) and have
the label positioned next to the residue.
Any hints would be appreciated.
Also, am I the only one who can't access the mail-list archives?
I got a odd problem with labeling:
label resi 196 and name c, "%s %s" % (resn, resi)
set label_color, black
set label_font_id, 4
To shift the label I "shift-middle-click-drag (in 3-Button-editing-mode)"
but I get a duplication of the label?=20
When I opened another pse-file there was no duplication or if I said "hide =
label" it only removed the one it hasn't moved.=20
But in the case with the more complicated stuff it either showed them doubl=
e or none?
What am I doing wrong?
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From: Robert Campbell <rlc@k2...> - 2002-05-10 15:58:35
* Chris Rife <chris.rife@...> [2002-05-10 10:47] wrote:
> I am making some stereo images and would like to put in some labels that
> will move with the model. When I use the "label" command, the labels are
> okay but they disappear with ray tracing. Is there any way around this,
> other than adding in the labels in an image editing program?
You can use the cgo text (line or cylinder versions) as I mentioned in
my reply about drawing the xyz axes, but be warned that the labels
rotate with you molecule, so getting them oriented perpendicular to the
view may be a pain (unless there is something I've missed).
Warren's example from a previous reply of his:
# draw text using cgo
from pymol import cmd
from pymol.cgo import *
from pymol.vfont import plain
cgo = 
axes = [[2.0,0.0,0.0],[0.0,2.0,0.0],[0.0,0.0,2.0]]
pos = [0.0,0.0,0.0]
pos = [0.0,-3.0,0.0]
Robert L. Campbell, Ph.D. http://biophysics.med.jhmi.edu/rlc
rlc@... phone: 410-614-6313
Research Specialist/X-ray Facility Manager
HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University
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