[Chimera-users] disulfide bonds ?

[Marek Maly]

Hellow,

I just visualized my Amber MD trajectory with protein containing
several disulfide bonds. These bonds as well as all the other bonds are
written in the given Amber topology (*.prmtop) file, which is read in
by Chimera. Moreover the distance of sulfur atoms connected by disulfide  
bond
is in all cases quite reasonable ( 2-2.1 A). In spite these facts Chimera
draws some of those bonds in "stick" and some of them in "dashed line"  
style,
even if one sets globally "stick" or "ball & stick" representation.
Please see the attached illustrations.

Why Chimera is doing such unwanted differences in graphical  
representations here ?

It is possible, to force Chimera to draw all of those bonds unanimously in  
"stick"
representation ?

    Thank you in advance for your help,

          Best wishes,

                Marek Maly
















-- 
Tato zpráva byla vytvořena převratným poštovním klientem Opery:  
http://www.opera.com/mail/
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Sbond_OK.jpg
Type: image/jpeg
Size: 42149 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20140714/e6d69d58/attachment.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Sbond_KO.jpg
Type: image/jpeg
Size: 40686 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20140714/e6d69d58/attachment-0001.jpg>