Re: [PyMOL] Steps to create a movie with objects and cameras moved independently of each other in PyMOL

Found the solution in [this page][1]: *object motions—keeping the camera still, but moving the objects around the scene*. There is a working example: # setup PyMOL for movies reinitialize set matrix_mode, 1 set movie_panel, 1 set scene_buttons, 1 set cache_frames, 1 config

Re: [PyMOL] Preventing Output of pair_fit

Hello Nathan, While we prepare to rollout the "quiet" argument for pair_fit, in the meantime try: cmd.feedback("disable", "executive", "results") Jarrett J. On Sun, Jul 22, 2018 at 6:47 PM, Jarrett Johnson < jarrett.john...@schrodinger.com> wrote: > Hello Nathan, > > We actually just implement

[PyMOL] Amber .nc

Dear Pymol users, Can somebody advise how I can open amber trajectory file in .nc format? Thank you Lenka -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sd

Re: [PyMOL] Amber .nc

Hi Lenka, Let me first state that the command "help load_traj" points to the webpage which in turns says that the .nc format is supported by pymol. I come from the gromacs background. Once you load the topology/state of your system (in my case .gro or .pdb), then use "load_traj", ie *load_traj tr

Re: [PyMOL] Amber .nc

Hi Mat, I have of course read that but I am still unable to load the trajectory. I was looking for an actual successful example not just a guide. Thanks Lenka From: Mateusz Bieniek Sent: 23 July 2018 14:04:22 To: Stejskal, Lenka Cc: pymol-users@lists.source

Re: [PyMOL] Amber .nc

Can you share what error/message you get when you try to load the trajectory with the command? The snippet of code I shared works for me. According to this page it should just work: https://pymolwiki.org/index.php/Load_Traj Do you happen to use a truncated octahedron? Best, Mat On Mon, Jul 23,

Re: [PyMOL] Amber .nc

Hi Lenka and Mat, Unfortunately, Amber ".nc" (NetCDF) files are currently not supported. Can you convert the file to one of the supported formats, like ".crd"? We can probably add NetCDF support to the next release. It's included in the VMD molfile plugins, and only excluded in PyMOL to avoid t

Re: [PyMOL] Amber .nc

I had to change the trajectory into .mdcrd and took the take care of the box I believe. I am not sure you can keep .nc format without the truncated octahedron tbf. Thank you! Lenka From: Mateusz Bieniek Sent: 23 July 2018 14:28:12 To: Stejskal, Lenka Cc: pym

[PyMOL] cartoon range transparency help

Hi I have Pymol version 2 When I try to make a range of a cartoon transparent e.g. I type: set cartoon_transparency, 0.5, /4COF//A/1:20  it comes up with following error: Setting-Warning: 'cartoon_transparency' is a object-state-level setting Does this mean one cannot make

Re: [PyMOL] cartoon range transparency help

Hi Jarrett Thanks for this, however, the trajectories of the cartoon change when only part of it is shown so that the transparent and non-transparent segments to not connect seamlessly. Cheers, Paul Paul Steven Miller (PhD) Postdoctoral Researcher University of Oxford Wellcome Trust C

Re: [PyMOL] cartoon range transparency help

Hi Paul, check out https://pymolwiki.org/index.php/Cartoon#Breaking_Up_a_Visualization_with_Cartoon_Skip You'll want to skip the residues you want to make transparent in the original (opaque) object, and include some more residues on both ends in the copy you want to make transparent. Skip the ad

[PyMOL] Color backbone amide nitrogen

Hi, I want to color backbone nitrogen atoms together with side-chain nitrogen atoms. The side-chain nitrogens get the color, however the backbone nitrogens don’t (see below; I have selected backbone nitrogens). I tried some options such as select bb, name n color by element But, the backbo

Re: [PyMOL] Color backbone amide nitrogen

The problem is that you are not visualising the backbone nitrogens. You only show the side chains as sticks and the backbone is shown as cartoons.These schematic representations of secondary structure are drawn using Calpha atom positions and (typically)

[PyMOL] Add to existing selection

Hi, How can I add a residue to an existing selection? Example: I'm comparing the binding sites of two superposed protein structures, and show the side chains with a certain distance to the ligand. Sometimes the side chain of one protein falls just outside that distance, and thus isn't shown,

Re: [PyMOL] Add to existing selection

Hello Markus, Selection algebra (https://pymolwiki.org/index.php/Selection_Algebra) may be able to help you here. Try doing: "select site, site or res 666" Jarrett J. On Mon, Jul 23, 2018 at 2:02 PM, Markus Heller wrote: > Hi, > > How can I add a residue to an existing selection? > > Example:

Re: [PyMOL] Add to existing selection

Of course! Works like a charm. Thanks Jarrett! From: Jarrett Johnson Sent: Monday, July 23, 2018 11:43 AM To: Markus Heller Cc: Pymol User list Subject: Re: [PyMOL] Add to existing selection Hello Markus, Selection algebra (https://pymolwiki.org/index.php/Selection_Algebra) may be able to

[PyMOL] Unsubscribe pymol user mails

Dear Mr. or Mrs. I don't want to recieve pymol user mails. Please remove my account from pymol-user mailing list. Thanks -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdo