[PyMOL] Transparency of VASCo surfaces

Hi all, I often use  VASCo surfaces and I am experiencing a strange behaviour on transparency settings as VASCo surfaces do not "respond" to: set transparency, value, object  Not from the command line, not from the plugin itself. Pymol's surfaces get transparent but not the object corresponding

Re: [PyMOL] Problems with H_add when theres alternate conformations present

Thanks, valence guess was the key :-) This makes sense, valence/bond assignment is run once the PDB is loaded, but unfortunately fails with the alternate conformations. Removing the alternate conformation doesnt update the bond information, making the save/reload of the structure or valence gue

Re: [PyMOL] Problems with H_add when theres alternate conformations present

Hi Esben, this works for me: fetch 1zw9, async=0 remove not alt +A valence guess, 1zw9 h_add 1zw9 Cheers, Thomas Esben Jannik Bjerrum wrote, On 04/22/13 13:15: > Hi Jason and Troels > Thanks for your suggestions, but removing the alternate conformation > doesnt solve the problem in itself

Re: [PyMOL] Problems with H_add when theres alternate conformations present

Hi Jason and Troels     Thanks for your suggestions, but removing the alternate conformation doesnt solve the problem in itself.  I have already played around with removing the alternate conformation using the alt selection method, and the only way successfull is to delete the alternate conforma