<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Grzegorz,<div class=""><br class=""></div><div class=""> Chimera doesn’t support making the transformation from 3d grid indices to physical coordinates containing an inversion. In theory it could since it just treats this transformation as a general affine transform (multiplying by an arbitrary 3x3 matrix, then shifting by a 3-vector). But to make it easy for users to control this transform it converts it into a rotation axis and angle, scale factors, and skewing, and does not include the possibility of inversion. So if you read a Chimera *.cmap file or some otther format (e.g. DX used by APBS maps), you will get an error from Chimera. In principle the file formats that allow a 3x3 matrix can handle it, but Chimera cannot. On the rare occassions when Chimera users have wanted to change the handedness of a 3d image the standard approach is to flip the z-stack of images with command "vop zflip #2” as Elaine mentioned.</div><div class=""><br class=""></div><div class=""> There are more problems with left-handed coordinate systems for maps in Chimera. Contour surface normal vectors will point inward instead of outward messing up the lighting appearance.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><div><blockquote type="cite" class=""><div class="">On Nov 22, 2016, at 4:18 AM, Grzegorz Bokota <<a href="mailto:g.bokota@cent.uw.edu.pl" class="">g.bokota@cent.uw.edu.pl</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Thanks for your response. I need some time to check it. I see thet it is realized by reversing volumetric data in z-dimesion and recalculating rotation axis and angel. it is impossible to be done by some parameters?<br class=""><div class="gmail_extra"><br class=""><br clear="all" class=""><div class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class="">Grzegorz Bokota<br class=""><br class=""></div></div></div>
<br class=""><div class="gmail_quote">2016-11-09 19:33 GMT+01:00 Elaine Meng <span dir="ltr" class=""><<a href="mailto:meng@cgl.ucsf.edu" target="_blank" class="">meng@cgl.ucsf.edu</a>></span>:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Grzegorz,<br class="">
I’m not sure if this is exactly what you mean, but when the data has been opened in Chimera you can use the “vop zflip” command to create a new data set with the Z planes in the opposite order:<br class="">
<br class="">
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zFlip" rel="noreferrer" target="_blank" class="">http://www.rbvi.ucsf.edu/<wbr class="">chimera/docs/UsersGuide/midas/<wbr class="">vop.html#zFlip</a>><br class="">
<br class="">
Best,<br class="">
Elaine<br class="">
-----<br class="">
Elaine C. Meng, Ph.D.<br class="">
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br class="">
Department of Pharmaceutical Chemistry<br class="">
University of California, San Francisco<br class="">
<div class="HOEnZb"><div class="h5"><br class="">
On Nov 8, 2016, at 9:35 AM, Grzegorz Bokota <<a href="mailto:g.bokota@cent.uw.edu.pl" class="">g.bokota@cent.uw.edu.pl</a>> wrote:<br class="">
<br class="">
> Hi,<br class="">
> I need to apply isometry and shift to volume data. In cmap file format it is possible to do rotation<br class="">
> but to have isometry I need to can do symmetric reflection. Ir is possible with any chimera format?<br class="">
> I found that there is "symmetries" parameter in cmap file format, but i do not seen any effect.<br class="">
><br class="">
> Sincerely,<br class="">
> Grzegorz Bokota<br class="">
</div></div></blockquote></div><br class=""></div></div>
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