Hi Madhavi,
with regards to your first question:
I usually add text after rendering the stereo figures. That gives much
better control and has the advantage that label come out cleaner. Look
into Canvas, Photoshop or GIMP to do this. As an additional tip you can
control the depth of the labels this way as well. Lets say you want to
label Leu76 in the back of the figure, create one label, copy it to the
other panel and place the same part of the text on the same atom or
point of the residue you want to label. Group the labels and move them
to an unobstructive position. Repeat for the other labels.
Spheres: Tough to tell, may be you inadvertently changed the depth queue
settings and the spheres got lighter. Did the the rest of the figure
change as well?
HTH
Carsten
> -----Original Message-----
> From: Nalam, Madhavi [mailto:madhavi.na...@umassmed.edu]
> Sent: Thursday, January 20, 2011 2:36 PM
> To: 'pymol-users@lists.sourceforge.net'
> Subject: [PyMOL] colors and font size while ray tracing
>
> Hello:
> I am trying to generate stereo figures for my manuscript. When I try
to
> ray trace at higher resolution, the font size (I use label_font_id=4)
> is becoming very small. If I use any fonts from the settings tab, the
> font size doesn't change with ray tracing. If I am correct, many
> journals prefer Helvitica/Arial fonts for the publication quality
> figures. So my question is are the fonts found in the settings
> preferred by the journals? If not, can anyone please tell me what can
> be done to keep the font size from decreasing during ray tracing?
>
> Also, I have vdW spheres shown as dots in the figure. The color of the
> dots for the vdW spheres is very light after I ray trace the figure.
> Last week when I ray traced the figure from the same PyMOL session,
the
> colors are much darker!! As far as I know, I haven't changed anything
> in the session file. So can anyone please tell me how to increase the
> darkness of the vdW spheres?
>
> I use PyMOL version 1.3.x on Windows.
>
> Thanks in advance,
> Madhavi
>
>
>
-----------------------------------------------------------------------
> -------
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> Finally, a world-class log management solution at an even better
price-
> free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives:
http://www.mail-archive.com/pymol-users@lists.sourceforge.net
------------------------------------------------------------------------------
Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
Finally, a world-class log management solution at an even better price-free!
Download using promo code Free_Logger_4_Dev2Dev. Offer expires
February 28th, so secure your free ArcSight Logger TODAY!
http://p.sf.net/sfu/arcsight-sfd2d
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
