Re: [PyMOL] OS-X question

Hanspeter Niederstrasser wrote: Joel Tyndall wrote: I have recently installed pymol on a friends ibook and it all works fine...but there seems to be no external GUI (as seen on PC and Linux versions). Is it missing on OSX or is my install flawed? It does make it a little easier to use for the

Re: [PyMOL] reiterating a ccp4 map problem

Jacob Corn wrote: This question was posted by someone else in January, but no solution was ever described. I'm currently running up against the same problem and would very much like to know if there is a solution, or if I'm stuck in bug-land. I have several CCP4 maps that have been calculate

Re: [PyMOL] cannot save .png files

kostas wrote: Hallo I've just installed macpymol using the disk image and playing around to get familiar with the program I found that cannot save images. The error that I get is: ScenePNG-Error: error writing "/NEB/pymol.png"! Please check directory... I will appreciate any help Hi Kosta

[PyMOL] bug in resizing viewport?

Hi all - I'm noticing some odd behavior with MacPymol (v0.94) involving the "viewport" command to resize the window. This command seems like it couldn't be more straightforward: specify width and height in pixels. However, look at the following output: PyMOL>viewport 100,100 PyMOL>png test.

Re: [PyMOL] Breaking down PDB files

Tony Giannetti wrote: Hey everyone, I know I should be past this, but I can't seem to figure out how to do this. I have a couple of crystal structures that contain multiple copies in the asymmetric unit, and I would like to superimpose each copy to see what the differences are. One way is

Re: [PyMOL] True Black?

On Monday, April 26, 2004, at 04:19 PM, wrote: Hello Pymoliacs, I have been playing around with the lighting and gamma settings, but can never get a true black. The black always shows up as grey. Does anyone know how to get black to be black? Pete D. UCLA Chemistry Hi Pete - If what

[PyMOL] restoring default surface coloring

I was recently making a figure of a ligand nestled in its binding pocket, where I wanted the surface of the binding protein colored by electrostatic potential, and the surface of the ligand colored by atom type. So I read in a DelPhi map from Grasp, used ramp_new to set up the color ramp, then

Re: [PyMOL] Zoom in a movie

Jose Avalos wrote: Dear all, Is it possible to do a movie in which you start looking at the entire enzyme and then you zoom into the active site and finally alternate between different states? If so, can somebody please point me in the right direction? Thank you very much Jose Avalos It cer

Re: [PyMOL] controlling atom sphere radii

rbax...@uchicago.edu wrote: Dear All, I have some residues shown as sticks and a heteroatom shown as a sphere. I woul dlike to make the sphere a little smaller compared to the sticks. How can I control the radius of the sphere? Hi Richard - Add the following lines (suitably modified) to your

Re: [PyMOL] Ray Tracing Crash

Morri Feldman wrote: I am running pymol .93. When I try to ray trace a scene, the gui shows a white status bar that moves halfway across the screen and then freezes. After this the GUI is frozen and must be killed. No error messages are shown. The computer is running RedHat 9 and has 4 proces

[PyMOL] running pymol in command mode

Hi all - I'm trying to use pymol to render a large number of complex images in order to make a molecular movie. This already takes a long time (1-2 minutes per frame) on my Octane due to the large molecular surfaces I'm drawing, but I'm now going to need to raise the surface quality, increas