Re: [PyMOL] representation of residue sidechain within a beta strand?

ain_helper, on > > Hope that helps, > Tomas > > On Mon, Jan 18, 2021 at 7:52 AM Emilia C. Arturo (Emily) > wrote: > > > > Hi All, > > > > I'm wondering if anyone here knows how to represent an amino acid > residue side chain that resides within a

[PyMOL] representation of residue sidechain within a beta strand?

Hi All, I'm wondering if anyone here knows how to represent an amino acid residue side chain that resides within a beta strand in stick representation such that the residue is linked in space with the backbone. This works fine when representing as sticks a residue that is within a loop or helix, b

Re: [PyMOL] problem with symexp

orrey Pines Road, La Jolla, CA 92037 > *T *858.646.3100 ext. 4216 <http://sbpdiscovery.org/> > blechtenb...@sbpdiscovery.org > > *Science Benefiting Patients™* > > On Feb 7, 2017, at 12:55 PM, Emilia C. Arturo (Emily) > wrote: > > Hmm. I've stumbled on a c

Re: [PyMOL] problem with symexp

EN-Phe131') is a selection I'd made of 'resi 131' from PDB id 5DEN. Clearly the two calls to symexp are not identical, but I don't (yet) understand why. Emily. On Tue, Feb 7, 2017 at 2:29 PM, Emilia C. Arturo (Emily) < ecgart...@gmail.com> wrote: > Hello. &g

[PyMOL] problem with symexp

Hello. I am trying to use symexp to inspect symmetry mates of several structures. I'm mystified about why some input structures lead to quick generation of symmetry mates, while others seem to lead to apparently never-ending symexp execution. All pdb files I've used as input contain a CRYST1 recor

Re: [PyMOL] Details of the morph interpolation?

> > You can also "fix" atoms, e.g. all non-polymer atoms, like free ions, > which tend to bounce around as a result of the refinement: > > PyMOL> morph mout, sele1, sele2, refinement=0 > PyMOL> from epymol.rigimol import refine > PyMOL> flag fix, (not polyme

[PyMOL] migrating Fe ions and the use of 'morph'

Hello all. I'm struggling to comprehend why the morph function, as called using MacPyMOL version 1.7.6.2, is making iron ions either migrate out of the active site during the interpolation, or completely absent from the interpolation. I call the morph function like so: morph morphresult, pdb1, p

[PyMOL] Details of the morph interpolation?

Hello. I would like to know more about the type of interpolation that is done when morph is called, and what calculations are done at each refinement cycle. Is there a literature reference or previous forum discussion to which you can point me? >From my sifting through the internet, I settled on

[PyMOL] Details of the morph interpolation?

Hello. I would like to know more about the type of interpolation that is done when morph is called, and what calculations are done at each refinement cycle. Is there a reference or previous forum discussion to which you can point me? I am using MacPyMOL version 1.7.6.2. Regards, Emily. -- "St

Re: [PyMOL] spectrum and the default minimum and maximum values

> > Tsjerk > > On Tue, Jul 7, 2015 at 4:11 AM, Emilia C. Arturo (Emily) > wrote: >> >> Hello All. >> >> Can anyone tell me what values are assigned by default to the minimum >> and maximum arguments of the spectrum command? To be clear, I know how

Re: [PyMOL] spectrum and the default minimum and maximum values

Hello All. Can anyone tell me what values are assigned by default to the minimum and maximum arguments of the spectrum command? To be clear, I know how to change the value of these arguments, but what does PyMOL assign to these values if one calls the spectrum tool using the pull-down menus to col

Re: [PyMOL] SCWRL version with educational-use PyMOL?

ion? > > -David > > > > On Jun 1, 2015, at 1:32 PM, Emilia C. Arturo (Emily) > wrote: > > > > Hello. > > > > Does anyone know which version of SCWRL (backbone-dependent rotamer > library) is used in the educational-us

[PyMOL] SCWRL version with educational-use PyMOL?

Hello. Does anyone know which version of SCWRL (backbone-dependent rotamer library) is used in the educational-use-only version of PyMOL? Regards, Emily. -- ___ PyMOL-users mail