Re: [ccp4bb]: thickness of the stick model

[Celeste MacElrevey]

Hello Shivesh,   I find the easiest way to modify PyMol parameters is to use the pull-down menu under Setting - select Edit All - it lists all the parameters alphabetically.  If you want to adjust the thickness of the model itself, the parameter to modify is stick_radius - default is 0.2, I usually choose 0.15 or so.  If you want to change the thickness of the lines in the density the parameter is called mesh_width (default 1.0).    To save as a jpeg you will first need to save as .png file (you will probably want to ray trace for quality, type: ray, 900 900 - as you increase these numbers the size and quality of the image will increase, so will the time it takes to trace.  I generally use 1200,1200 for my final version, although it's a matter of choice. You can open that .png file with any photoshop or illustrator program - once opened there you can save and/or export  in whatever format you prefer.   As to getting rid of excess density - if you can't get the mouse controls of Slab (depth of field) and Clip (translates Z) to eliminate it, you can use Adobe Photoshop to "erase" it. (A handy tool only to be used with the most honorable of intentions).   Enjoy,   Celeste MacElrevey ----- Original Message ----- From: shivesh kumar To: ccp4bb@dl.ac.uk Sent: Saturday, October 14, 2006 7:32 AM Subject: [ccp4bb]: thickness of the stick model Dear all, How can I save the image in JPEG format and can I decrease the thickness of stick for better representation in electron density map...Thanx in advance. Shivesh