[PyMOL] nuccyl 1.5.2 released

Dear PyMOL users, A new version of nuccyl has been released: http://www.mssm.edu/students/jovinl02/research/nuccyl.html Version 1.5.2 fixes a bug that prevented nuccyl to process correctly nucleic acids containing palindromic sequences or nucleotides with identical type and name that

[PyMOL] residue replacements / modified amino acids

Hi everyone, Two part'er here: 1. Is there a simple way in pymol to replace an amino acid in a given structure? If so, how can you then check (other than visibly) if there are any glaring steric/electrostatic clashes? 2. Is there a way of incorporating non-native or modified amino acids into the

RE: [PyMOL] residue replacements / modified amino acids

1. Is there a simple way in pymol to replace an amino acid in a given structure? If so, how can you then check (other than visibly) if there are any glaring steric/electrostatic clashes? Yes, using the mutagenesis wizard. But no, there's no refinement/validation possible so it isn't as

Re: [PyMOL] secondary structures, spheres and plugins

Hi Einat, * Einat Sitbon einat_sit...@hotmail.com [2005-03-03 14:27] wrote: 1) Secondary structure can be viewed as cartoons, or as colors. The problem is the boundaries are not the same. If I color a strand by secondary structure, it seems that the following loop is a strand as well. I?m