pymol-open-source

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Transparency rendering issue with stick_ball representation

4

Hi, This [pse](https://www.dropbox.com/s/5do6ylbcragiphi/issue_stick_ball_orthoscopic_transparency.pse?dl=0) should explain the issue, just try to render it (older versions of pymol have the same issue). Basically, as you can see from the rendered image, transparent...

giagitom

Most of pymol's commands can be executed with something like `cmd.(parameters)`. How is it possible to call a script / function like `select_distances` from a pymol plugin?

aanastasiou

Inconsistent behaviour of pymol API's `delete` and `get_vis` with the name `sele`

1

I understand that PyMOL strips characters like `(` in the object name when loading in a new molecule object. However, since it is allowed to name objects "sele", this causes...

bzoracler

New command syntax

4

I would love to define commands like this to get automatic object completion and automated usage help. ```python3 @pm.extend2 def nearby_aminoacids_similarity( sel1: Selection, sel2: Selection, polymer1: Selection="polymer", polymer2: Selection="polymer", radius:...

pslacerda

alter_state changes all states in object ?

2

I'm now using the free version of **PyMOL v. 2.4.0a0.** According to Wiki, the `alter_state` command should alter specified states in a given object: `alter_state state, (selection), expression`. It seems...

vlado-s

Issue building surface

4

I am having issues trying to open this [pse](https://www.dropbox.com/s/6payiclp7tyl94d/error.pse?dl=0) . Seems that pymol crashes at some point during the surfaces building.

giagitom

some options are not saved between scenes

3

It looks like some option settings are not saved along with scenes, e.g. `grid_mode`, `all_states`, `cartoon_cylindrical_helices`. Is there a plan to include these along with scenes in the future? Is...

smsaladi

Looks like there's a 2010 rotamer library from Dunbrack and co: http://dunbrack.fccc.edu/bbdep2010/ It's CC BY licensed and also integrated in Chimera. Might be nice to pull into Pymol (doesn't affect...

smsaladi

PyMOL Glow/Highlight Feature?

1

Hello! It's my first post here and I apologize if this isn't meant to be in issues; it's my first time on GitHub. I've been using PyMOL for a while...

ivan-the-bio-lover-42

Pymol can not import python scripts when called in perl

1

Hi, I tried to call pymol in perl for calculations with the following command: ```bash perl -e 'system("/Applications/PyMOL.app/Contents/bin/pymol -c pymol.pml >test.txt")' ``` the pymol.pml script is below: ``` load 2nx5_DE_changepos.pdb...

shengzizhang