[PyMOL] Problems with space group recognition

2008-01-12 Thread Mark Wehner
#x27;C 1 2 1'. Symmetry-Error: Unable to get matrices from sglite. CmdLoad: "pdb/1f5n.pdb" loaded as "1f5n".' I'm using Gentoo Linux and compiled against Python 2.5 using gcc-4.1.2 on a 64-bit architecture (not using too much optimization [-Os]). Any help on this would be greatly appreciated. Thanks in advance. Mark Wehner

Re: [PyMOL] Problems with space group recognition

2008-01-13 Thread Mark Wehner
t sounds like the sglite module may not have compiled correctly. > > Cheers, > Warren > > -- > DeLano Scientific LLC > Subscriber Support Services > mailto:del...@delsci.info > > > -Original Message- > > From: pymol-users-boun...@lists.sourceforge.net

[PyMOL] electrostatics

2008-01-15 Thread Mark Wehner
Hi, 1. Use 'util.protein_vacuum_esp("object")' to generate the electrostatic surface. 2. Use 'show surface, object' to show the surface or if you only need the surface representation use 'as surface, object' Regards, Mark

[PyMOL] Vacuum electrostatics

2009-05-11 Thread Mark Wehner
Hi everyone, in the newer version of pymol I realized it is not possible to generate vacuum electrostatics, there's an error while assigning the formal charges. The error message is: Alter-Error: Aborting on error. Assignment may be incomplete. File "", line 1 formal_charge=0;flags=flags&

Re: [PyMOL] Unequal sizes of spheres - how?

2009-08-27 Thread Mark Wehner
Hi Andy, hi everyone, if you only want a few water molecules in a different size you can always change the size by altering their van-der-Waals radii. For example, if you want to change water number 3: alter r. hoh & i. 3, vdw=vdw+3 The CA atoms could be changed similarly, but if you want to c