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 wrote: Dear All, I'm trying t

[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 s

Re: [PyMOL] spectral coloring

Martin, Unfortunately not -- you would need to use a PyMOL command script or Python program to achieve finer control over coloring. However, you can set the minimum and maximum values by passing those as arguments to "spectrum". Cheers, Warren > -Original Message- > From: pymol-users-bo

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

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 Subscrib

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. Bes

[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

[PyMOL] Sticks and distances with individual transparencies - repost

Apologies for prior post message font was nearly unreadable 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 nothi

[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 be

[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