[PyMOL] best way to rotate molecular bonds without dihedral context?

Hello, PyMOL users! I am trying to figure out within the Python interface how to rotate the parts of a molecule on one side of a bond about that bond's axis, given only the two atoms defining the bond and a angle to rotate by (that is, without requiring me to specify four atoms and a final dihedra

Re: [PyMOL] best way to rotate molecular bonds without dihedral context?

Hi John, Does the 'torsion' command work? Cheers, Doug Quoting johnbax...@cs.unm.edu on Thu, 20 Nov 2014 01:06:04 -0700: > Hello, PyMOL users! > > I am trying to figure out within the Python interface how to rotate the > parts of a molecule on one side of a bond about that bond's axis, given

[PyMOL] set size nb_spheres

Dear all, I would like to change the size of nonbonded spheres. They are nonbonded c-alpha atoms not heteroatoms therefore I don't know how to specifically select them in order to change them. Thanks a lot in advance, Erica -- Erica Valentini EMBL-Hamburg Notkestrasse 85, +49 040 899 02 182

Re: [PyMOL] set size nb_spheres

Hi Erica, I think something like: alter name ca, vdw=10 should help. Change "10" for the value you want. Best Regards, Osvaldo. On Wed, Nov 19, 2014 at 11:16 AM, Erica Valentini wrote: > Dear all, > > I would like to change the size of nonbonded spheres. > They are nonbonded c-alpha atoms n

Re: [PyMOL] how to add an oxygen atom in carbonyl group?

Hi Tumpa, What about using the builder . Is this what you need? Osvaldo. On Thu, Nov 20, 2014 at 4:02 AM, wrote: Hi, > I am a new user of pymol. My question is how to add an oxygen atom in > carbonyl group? > > Thanks, > Tumpa Sadhukhan. > Ph.D Sch

Re: [PyMOL] set size nb_spheres

Hi, Just to chime in, you might need to call 'sort' and/or 'rebuild' after using the alter command to see the changes. Matt Baumgartner On 11/20/2014 08:20 AM, Osvaldo Martin wrote: Hi Erica, I think something like: alter name ca, vdw=10 should help. Change "10" for the value you want. Be

[PyMOL] map symmetry expansion on 1.7.2.1

Hello, PHENIX has calculated a *_refine_001_mFo-DFc.ccp4 map for me, which I “meshed” with isomesh mesh, map, 3. I understand map_auto_expand_sym is enabled by default. Yet when I translate using the middle mouse button, I can easily go beyond the extent of the mesh. How can I make the mesh fellow

Re: [PyMOL] best way to rotate molecular bonds without dihedral context?

It does! Thank you very much; I don't know how I missed that command. > Hi John, > > Does the 'torsion' command work? > > Cheers, > Doug > > > Quoting johnbax...@cs.unm.edu on Thu, 20 Nov 2014 01:06:04 -0700: > >> Hello, PyMOL users! >> >> I am trying to figure out within the Python interface how

Re: [PyMOL] best way to rotate molecular bonds without dihedral context?

That's alright, I only discovered the "Volume" feature yesterday and that's been around since v1.4 ... Quoting johnbax...@cs.unm.edu on Thu, 20 Nov 2014 11:06:39 -0700: > It does! Thank you very much; I don't know how I missed that command. > >> Hi John, >> >> Does the 'torsion' command work?