Support for PyMOL on the iPad

This page provides some basic help. If you have a current Incentive PyMOL license and cannot find the help you need on this page, please email for tech support and we'll be glad to assist you.

Free Community-based Support

Users can access the active pymol-users group email list for free community-based support. Here, users can discuss all things PyMOL and help each other.


Finding Structures

  • You can search the PDB by structure ID, name, or author name. The following are valid searches for the PDB
    • 1oky
    • kinase
    • brunger
  • You can search PubChem by chemical name. If a molecule is known by another name, PyMOL will find it for you. The following are all acceptable PubChem searches
    • plavix
    • clopidogrel
    • caffeine

Update (Nov 2nd 2012): On Sept 28th, the PDB made unexpected changes that break PyMOL's ability to search for structures on the PDB. We are working with them to correct the issue. In the meantime, please use Safari to browse to a structure on the PDB and then download the PDB file. Upon downloading you will be prompted to open the file in PyMOL.

Memory Usage

PyMOL on the iPad has been optimized to use as little memory as possible, however you can easily exhaust the memory available on the iPad. When you attempt an operation that requires more memory than is available, PyMOL will show you a warning and halt the operation.

When visualizing medium- to large-sized structures we advise closing other iPad apps to free up memory. If you're going to work with very large structures then completely restarting the iPad may be necessary.



Using Dropbox

We built native Dropbox support into PyMOL on the iPad. You can download files from Dropbox to view on the iPad or upload screenshots and ray traced images. Setting up the connection between PyMOL and Dropbox is easy. Let PyMOL do all the work for you, here's how:

  1. In the Remote menu click PyMOL Dropbox. PyMOL will temporarily switch to Dropbox.
  2. Login to your Dropbox account and grant PyMOL permission to use Dropbox by clicking "Allow". PyMOL will be restarted and you will be in your Dropbox folder. In your Dropbox, you will now see an Apps directory.  If you open the Apps directory, you will see the PyMOL directory.  You do not have to create these directories -- they are automatically made for you when you grant PyMOL permission to use Dropbox.
  3. Your PyMOL Dropbox folder is ready for use. Now you need to put files in it for use on the iPad.
  4. Send files from your computer to the Apps/PyMOL directory on Dropbox. Once there are files in the Apps/PyMOL directory they will be listed on the iPad whenver you're searching the "PyMOL Dropbox" portion of the Remote menu.



  • iPad with iOS 5.0 or later



We gratefully acknowledge these open-source projects that were incorporated into PyMOL on the iPad