Hi Francesco, A couple of cents before the professionals respond with (very likely) better ideas: In response to 1) Black is best for contrast but uses a lot of ink and money. White should be fine. n response to 2) If you go to TOOLS=>VIEWING CONTROLS=>CAMERA, you can select various camera modes. CROSS-EYE stereo will put your chimera graphic into cross-eye stereo. You can save an image as it is displayed on the screen. But i find saving two images, stereo left eye and stereo right eye better. Place these side by side in another graphic program, (e.g Adobe illustrator) and voila, stereo viewing. With two single images you can switch them around to alternate between wall-eye and cross-eye. Also, with two images its easier to make the distance between them a certain length, as journals are usually stringent about how the stereo images are displayed. In response to 3)I'd to go TOOLS=>VIEWING CONTROLS=> SIDE VIEW and slide the back and front yellow planes. This will create a slab through your object removing other structural elements which might complicate the image. Also, try DEPTH CUEING under TOOLS=>VIEWING CONTROLS=> EFFECTS. tweak the "start ratio and yon intensity to further remove emphasis on unwanted objects. The Depth effects can make some really neat graphics Hope this helps. -Jason Quoting Francesco Pietra <chiendarret@gmail.com>:
Hi:
I would greatly appreciate advice about the following requests (between "".."") by the referees (interaction between two proteins; graphics by chimera):
1) "there is way too much wasted black space in figures".
As the complex of proteins is elongated along one axis, I found it unavoidable to have wasted space around. Perhaps using a white background in the hope that white is less offending than black? Or is it a way to tailor the background according to the shape of the object?
2) "a stereoview might be helpful for better understanding".
How to fulfill this request with chimera I have no idea.
3) "a molecular surface representation of the docking site would be useful".
I read on passing about molecular surfaces on this forum. Is that feasible for the highly complex situation of 3D perspective with so many atoms at different "layers"?
Thanks indeed for answering
francesco pietra _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.