[PyMOL] spectral coloring

Hi there, i am trying to map b factors on a surface representation. I am using spectrum b,blue_white_red,mymol and the colors are fine. Is there a way to fine tune the color spectrum, such as with the Midpoint and Offset sliders in vmd? Best Martin

[PyMOL] Sticks and distances with individual transparencies

Dear All, I'm trying to write a Pymol script with which produces a mixture of both solid and transparent sticks I'm using the current 1.0 incentive release of MacPymol. After drawing all my sticks I issue following commands, but nothing changes although the log output suggests the change is

[PyMOL] coloring based on sequence identity

Hi, I'd like to color a molecule based on its sequence similarity to another molecule. Can this be done in Pymol? Thanks in advance. - Eva

Re: [PyMOL] coloring based on sequence identity

Am Dienstag, 26. Juni 2007 schrieb Eva Vanamee: Hi, I'd like to color a molecule based on its sequence similarity to another molecule. Can this be done in Pymol? If you can quantify similarity in a number you can write it into the b-factors of the atoms and then color it by them. Best

Re: [PyMOL] rotate about an abitrary axis

Minh, This type of use is now covered under the rotate command in the official documentation for PyMOL 1.0 ( http://delsci.info/dsc ) as well as in the current open-source code. Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL

Re: [PyMOL] Sticks and distances with individual transparencies - repost

Mark, Your confusion arises from the new set_bond command, which must be used when setting bond-specific properties. Please see the official docs on set_bond. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want

[PyMOL] PyMOL 1.0 and Official Docs

Greetings! As some of you have noticed, PyMOL 1.0 is out (at last!). Though it lacks many of the features and enhancements I had hoped to deliver in the big 1.0, we were long overdue for a major release and so the line was drawn. For those of you new to PyMOL within the past year or so, our

Re: [PyMOL] Sticks and distances with individual transparencies

Hi Mark, You could've found this one in the archives of this list. Settings work on objects, not on selections. The solution is to make an object for the solid sticks and one for the transparent sticks, using create. Cheers, Tsjerk On 6/26/07, Dr. Mark Mayer may...@mail.nih.gov wrote: Dear