[PyMOL] APBS plugin woes

I download and install macpymol-1_2r2.tgz. I make a copy of MacPyMOL.app and rename it PyMOLX11Hybrid.app and fire it up. Load a pdb file after removing HETATM lines. Open APBS Tools and set grid: Log: Maximum number of grid points exceeded. Old grid dimensions were [129, 97, 129] Fine grid

[PyMOL] not getting a simple translation

I have a 5 similar domains (struct.pdb) aligned on another one (rcsb.pdb). I made a copy of one of them and translated it 37 angstroms to the right. translate [37, 0, 0 ]. But I did not get a simple translation. The two molecules end up having a rotation between them. Here's the script. I

Re: [PyMOL] not getting a simple translation

Ah, turn, yes that is better. thanks, Dave At 10:08 AM -0400 10/22/09, Warren DeLano wrote: Hi David, You have a rotate command in that script. Did you mean to 'turn' the camera rather than 'rotate' the atomic coordinates? Cheers, Warren -Original Message- From: David Garboczi

[PyMOL] How do I fill the png with the molecule

I get too much white space around the molecule when ray tracing and then writing a png file. How can I make the png file more like a bounding box? I use zoom complete=1 ray 1800, 1800 png dpi=600 thanks, Dave --

[PyMOL] startup options in MacPyMOL

How can I have a startup file read when I launch MacPyMOL? For example, to set the background to white or load a particular pdb. thanks, Dave --

[PyMOL] rotation

I have a homodimer. I place it at an arbitrary place on the screen, where it looks nice. Now move the monomers apart from each other in x. translate [10, 0, 0], object molA translate [-10, 0, 0], object molB Then I want to rotate each monomer 90 deg so that each monomer's contribution

[PyMOL] trouble with symexp command

I am examining packing in several space groups by issuing the command symexp foo, foo.pdb, sele, 10 If I select the whole reference molecule, I think that I should get all the symmates within 10 A displayed. But for one of the crystals that I am dealing with, CRYST1 29.24 44.19 107.67

[PyMOL] color on color

I have two subunits surface-painted with the color ramp from Protskin http://www.mcgnmr.ca/ProtSkin/intro/index.html I would like to color one of the subunits so that it can be distinguished, but without hiding the color ramp. Suggestions? Dave -- David N. Garboczi, PhD Phone: 301-496-4773

[PyMOL] .pse file and new pdb

Suppose one is mouse-oriented and script-averse. He makes a nice figure with a not-fully-refined model and saves the .pse file. Later, refinement is done and he has a new pdb file. He would like to have that same figure that is encoded in the .pse file, but using the final pdb file, without

Re: [PyMOL] .pse file and new pdb

update old_object, new_object delete new_object Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of David

[PyMOL] several copies of the same model

I would like to have several copies of the same model on the screen at once. Each would be offset from the other and surface painted differently with conservation, charge etc. I would then like to rotate them around their own axis at the same time so that I can observe the correspondence or

[PyMOL] How to move aligned objects apart

I have three molecules aligned on each other. I would like to move them apart so that I can make a .png file with all three of them aligned, but simply translated apart. I have tried the translate [x, x, x] command but no success. Advice? thanks, Dave --