Molecular

PyMOL, wherethe trajectory landed

Molecular visualization on an Ubuntu desktop of your own.Open the structure where it was written, not where you are.

PyMOL 3.1.82 cores · 4 GBOpens in a browser tab

hub://pymol

$ dxflow workflow create --identity pymol hub://pymol --start --link

01Pick a machinecores, memory and a rate per hour

02Create the workflowpulled from the hub, once

03Run it, then stopstopped when the work is done

The application

Structures,and how they move

Rendering and analysis of 3D structures and trajectories.

Structures and maps

Load a PDB, a density map or a trajectory, and render what you need.

The PyMOL prompt

Drive the whole session from the command line built into the viewer.

Rendering on the CPU

Software OpenGL until a GPU is attached, which big scenes will want.

How you run it

Every defaultis one override away

The session reads its settings from the environment, so you set them on the start line.

VNC_PASSWORDWhat the tab asks for. It ships as dxflow, and everyone reading this knows that.

PANEL and TASKBARThe panel stays, the taskbar goes. PyMOL opens more than one window, and the panel is how you move between them.

AUDIOOff here. Turn it on and the desktop sound is streamed beside the picture.

start it your way

$ dxflow workflow start pymol --override env.app.VNC_PASSWORD=something-long

$ dxflow workflow start pymol --override env.app.PANEL=hide --link

The session

Viewer and controls,side by side

The panel is kept, so PyMOL's windows are easy to arrange.

6082Browserin the tab, at /vnc.html

5901VNCin a native client

/volumeStoragestructures and sessions

Open it from anywhereStart with --link and the session comes back on an HTTPS address.

Set a password firstVNC_PASSWORD defaults to dxflow, and everyone can read this page.

Good to know

It draws on the CPUuntil you give it a card

Software OpenGL carries the viewport by default, which is fine until the structure gets big.

Attach a GPU for the heavy ones

Large assemblies and ray-traced figures move from tolerable to quick. Small structures never need it.

More than one window

The viewer and the controls come up separately, which is why the panel is left on by default.

Sessions belong on the volume

Keep structures, trajectories and saved sessions under /volume and they are there at the next start.

The image

Pulled once,then it stays

PyMOL arrives as one image. This is what comes down the first time, and what the disk should have free for it.

757Mamd64compressed, the way the registry counts it

20GOn diskunpacked, with room to work beside it

ghcr.io/dxflow-ai/pymol:latestPublished from the hub, pulled on the first start and kept for the ones after it.

amd64 onlyOne architecture is published, so pick a machine that matches it.

What it asks for

What it wants,and what it needs

The definition asks for 2 cores and 4 GB. The image comes up on less than that, and a start given --fit trims the ask to whatever the machine actually has.

2 cores · 4 GBAsks forwhat the definition writes down

2 cores · 2 GBRuns onthe least the image comes up on

Not neededGPUit works on the cores alone

The ask is not the floorThe definition writes down what suits the work. The image itself starts on less, which is what the second figure is.

--fit caps it to the hostA start given --fit trims each step to what the machine actually has, for that start alone. The definition is never rewritten.

Machines that fit it

PyMOL asks for 2 cores and 4 GB. Cheapest first.

E2 Medium

$0.0419/ hour2 cores · 4 GBStart this machine

T3 Medium

$0.052/ hour2 cores · 4 GBStart this machine

B2s

$0.052/ hour2 cores · 4 GBStart this machine

Run PyMOL on your own machinePick a machine that meets it, and it opens about a minute after you ask.

Start PyMOL Browse workflows