[PyMOL] multiple h bonds

[Scott Classen]

PyMOL users,
	Is there a way to add multiple hydrogen bonds quickly and easily 
without having to type in an endless array of distance commands?


distance (/lc03A//D/1 and name NAI),(/lc03A//A/365 and name OE1)
distance (/lc03A//A/365 and name NE2),(/lc03A//L/1 and name O1G)
etc
etc..

Thanks,
Scott



==
  Scott Classen, Ph.D.
  clas...@uclink4.berkeley.edu
  University of California, Berkeley
  Department of Molecular & Cell Biology
  237 Hildebrand Hall #3206
  Berkeley, CA 94720-3206
  LAB 510.643.9491
  FAX 510.643.9290
==

Re: [PyMOL] labels again

[Evan Stein]

I label in stereo using Adobe Illustrator.

I place the labels at the same approximate position on the figure (aligning
them vertically) and then I adjust the horizontal position of the label on
the right figure until the label appears at the proper depth for the figure.

--
Evan Stein
Structural Biology Program
Skirball Institute / NYU School of Medicine
540 First Avenue Lab 3-4
New York, NY 10016

phone: (212) 263-8968
fax: (212) 263-8951
email: st...@saturn.med.nyu.edu
URL: http://saturn.med.nyu.edu/~stein


> From: Ricardo Aparicio 
> Date: Wed, 20 Nov 2002 15:37:46 +
> To: "pymol-users@lists.sourceforge.net" 
> Subject: [PyMOL] labels again
> 
> Dear colleagues:
> 
> I've been looking for a way to add labels to my figures.
> After a search in the e-mail list files, I could draw cgo labels, although it
> would be a pain to
> orient them by hand using cmd.rotate and cmd.translate (too many figures).
> So, in the case of mono, I have used photoshop to include labels (superposing
> figures from PyMOL).
> 
> The main problem, however, is that I need stereo now and I see two
> possibilities:
> to use cgo labels in both figures
> or
> to use labels (photoshop) in only one figure of the stereo par.
> 
> 
> My questions are:
> 
> 1a) are there "news" about labels within PyMOL? Any recent improvement? (last
> e-mail in this issue
> was from august/25)? Any other clue I didn't see?
> 
> 1b) are there "news" concerning automatic orientation?
> 
> 2) is there a way to change color of cgo labels?
> 
> 3) is there a way to change font of cgo labels?
> 
> 4) do you have any reference (paper published or web) where I can see
> PyMOL-made figures containing
> labels?
> 
> 
> Thank you very much for your help.
> 
> 
> Regards,
> 
> Ricardo Aparicio
> PhD Student
> Sao Paulo - BR
> 
> 
> 
> 
> 
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[PyMOL] labels again

[Ricardo Aparicio]

Dear colleagues:

I've been looking for a way to add labels to my figures.
After a search in the e-mail list files, I could draw cgo labels, although it 
would be a pain to
orient them by hand using cmd.rotate and cmd.translate (too many figures).
So, in the case of mono, I have used photoshop to include labels (superposing 
figures from PyMOL).

The main problem, however, is that I need stereo now and I see two 
possibilities:
to use cgo labels in both figures
or
to use labels (photoshop) in only one figure of the stereo par.


My questions are:

1a) are there "news" about labels within PyMOL? Any recent improvement? (last 
e-mail in this issue
was from august/25)? Any other clue I didn't see?

1b) are there "news" concerning automatic orientation?

2) is there a way to change color of cgo labels?

3) is there a way to change font of cgo labels?

4) do you have any reference (paper published or web) where I can see 
PyMOL-made figures containing
labels?


Thank you very much for your help.


Regards,

Ricardo Aparicio
PhD Student
Sao Paulo - BR