Re: [PyMOL] weird distance measurements when pdb file contains symmetric atoms

Hi Pascal, the problem is that PyMOL looks up atoms by ID, which are not unique in your structure. Possible workarounds: 1) disable dynamic measures: PyMOL unset dynamic_measures 2) assign unique atom IDs: PyMOL stored.ID = 0 PyMOL alter all, ID=stored.ID=stored.ID+1 Cheers, Thomas Pascal

Re: [PyMOL] Help auto interpolate

Hi Anke, we are currently trying to do movies and are running into some problems concerning the “auto interpolate” function of pymol. We realized that camera and molecule positions are always interpolated back to the position of frame 1 at the end of the movie. Autointerpolate is not the

[PyMOL] Preparation of the pdb for MD simulation

Dear PyMol users! I have pdb structure wich I'd like to prepare for my MD simulation. In that case this structure consist of some non-standart residue ( chromophore) wich is covalently bonded to the protein's backbone. The main problem is that this structure has some missing residues on both of

Re: [PyMOL] Ca sphere size from b-factor value

Hi Jason, Thanks -- is there any way to add some limits to the scaling, say to alter the vdw radius from a value of 1 to 5 based on a b-factor range of values? Doug On Jul 31, 2012, at 4:44 PM, Jason Vertrees wrote: Hi Douglas, You can do something as simple as this: # fetch a