[PyMOL] Significant digits get lost when calculating in script (pymol rounding)

Hi, I'm experiencing trouble when calculating with floats inside my pymol script: #-Zoom active site v1 = 0.82406 v2 = -0.321197331 v3 = -0.294621944 v4 = 0.222588494 v5 = 0.919873238 v6 = -0.322858661 v7 = 0.374718130 v8 = 0.224984407 v9 = 0.899412513 v10 = -0.003328383 v11 = 0.

[PyMOL] Surface Edge

Hi, please have a look at this image: http://pwe.no-ip.org/other/1.png I'm having trouble with the edge of a surface selection. It seems that there is always some more surface shown than the selected part. What I did is, that I selected the red part to show the surface in obj1 and to hide the s

[PyMOL] Change clipping plane only for one object

Hi guys, let's say we have a scene with two objects. Can I have different clipping planes for these two objects? For now I tried clip far, 10, object1 but this effects both objects. Any ideas? Paul

[PyMOL] Retrieve color settings

Hi, is there a way to get the color settings for objects inside pymol? Something like the grepset.py script. Paul

[PyMOL] RMS of two small molecules

Hi, lets say I have a set of docked conformations and want to compare them with the conformation observed in a crystal structure (aka redocking). How can I get pymol to calculate RMS values for pairs of small molecules that probably don't have the same numbering? For now I tried to use the rms_c

[PyMOL] Re: Ray-tracing inner surface backside

So, I tried rendering using transparency_mode = 1 or 0 and got this result: http://pwe.no-ip.org/other/Pymol2.png Is there a way to get rid of the transparency that darkens some parts of the surface where something lies behind? I also tried povray to render the surface and it gives me a tex

[PyMOL] Ray-tracing inner surface backside

Hi folks, what I did for now is that I selected a subset of residues that sit around a cavity. Then I showed the surface of the original protein inside the selection to get only the inside surface of the cavity. Now it looks sort of like a hose with inside and outside just as I wanted. Now I'd

[PyMOL] Surface of cavity

Hi, a little question regarding cavity surfaces :-) I have a set of active atoms (GOLD output) that surround a cavity. Now I want to dipslay the surface only for the cavity wall, not on the outside. Any ideas? Paul signature.asc Description: This is a digitally signed message part

[PyMOL] HETATM in pdb

Hi, I was wondering if I can get PyMol to add consecutive numbers to the HETATM labels of my ligand. So I'd like to get this: > HETATM1 N1 PWE 1 0.459 60.194 72.834 1.00 0.00 N > HETATM2 N2 PWE 1 1.778 68.314 67.268 1.00 0.00 N > HETA