APBS VR Molecular Visualization

Molecular visualization software packages provide the ability for users to explore the 3D representations molecular structures and properties. Examples of these systems include UnityMol, JMol, Polyview, and 3DMol. Typical user interaction is limited to panning, zooming, and rotating the molecule using a mouse and keyboard while viewing on a standard computing monitor. These techniques support a pseudo 3-dimensional view of a molecule to understand its structure but lack the true depth perception people are used to with stereoscopic vision in the real world.

New advancements in virtual reality (VR) technologies has resulted in lower costs and systems that are easier to use to many consumers. Compared to past VR hardware, these new systems have several key advancements including lower latency, higher frame rates, and improved resolution. Additionally, these systems are equipped with better optics and motion tracking and a more robust software ecosystem.

We are extending the visualization capabilities for APBS through the incorporation of a VR device with molecular rendering software. We are currently experimenting with the HTC Vive, which allows a person to walk around a 15' by 15' physical space while wearing a head mounted display. Precise head movements are matched in virtual reality with no noticeable latency. Additionally, the HTC Vive controllers are motion tracked with millimeter precision and provide a valuable method for interacting with virtual objects. We have enabled VR using the HTC Vive in the UnityMol molecular visualization software (created by Baaden, et al.) and incorporated electrostatic surface data (see figure below). New viewing capabilities now include walking around, grabbing (using the motion controllers), and scaling (gestures) of molecules. We are actively working with Dr. Baaden and his group to determine the best use of interaction techniques for users to interact with molecular models through his software.

VR APBS
View of UnityMol form the monitor as it is being used in VR with controllers.

For future work, we would like to further extend UnityMol in the HTC Vive to include natural user interactions for viewing multiple molecules, vary the electrostatic results from APBS, and change molecular attributes. We envision this tool will also enable virtual collaboration for participant in different locations. Each participant will be able to view, gesture and interact with the same data in the same VR space. Finally, we would like to explore the use of VR for research related to docking of different molecules.

PDB2PQR 2.1.1 Released

Dear APBS and PDB2PQR users –

We are pleased to announce the release of PDB2PQR 2.1.1 which is now available from http://www.poissonboltzmann.org/docs/downloads/. There are several improvements and fixes (outlined below) to this release of the software and we encourage all users to upgrade.

Please see PDB2PQR Release History for the complete release notes.

Thank you for your continued support of APBS and PDB2PQR.

Sincerely,

The APBS/PDB2PQR development team

PDB2PQR 2.1.1

Please see PDB2PQR Release History for the complete release history

Notable new features:

The old Monte Carlo method has been replaced with Graph Cut. See http://arxiv.org/abs/1507.07021. (To use the original Monte Carlo method, see version 2.0)

NEW FEATURES

  • Added alternate method to do visualization using 3dmol.
  • Replaced thr Monte Carlo method for generating titration curves with graph cut. See http://arxiv.org/abs/1507.07021 (If you prefer the Monte Carlo method, please use href=”http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/).
  • Added compile options to allow for arbitrary flags to be added. Helps work around some platforms where scons does not detect the needed settings correctly.
  • Added a check before calculating pKa’s for large interaction energies.

BUG FIXES

  • Fixed broken links on APBS submission page.
  • Added some missing files to query status page results.
  • Fixed some pages to use the proper CSS file.
  • Better error message for –assign-only and HIS residues.
  • Fixed PROPKA crash for unrecognized residue.
  • Debumping routines are now more consistent across platforms. This fixes pdb2pka not giving the same results on different platforms.

CHANGES

  • Added fabric script used to build and test releases.
  • The networkx library is now required for pdb2pka.

KNOWN BUGS

  • If more than one extension is run from the command line and one of the extensions modifies the protein data structure it could affect the output of the other extension. The only included extensions that exhibit this problem are resinter and newresinter.
  • Running ligands and PDB2PKA at the same time is not currently supported.
  • PDB2PKA currently leaks memory slowly. Small jobs will use about twice the normally required RAM (ie ~14 titratable residues will use 140MB). Big jobs will use about 5 times the normally required RAM ( 60 titratable residues will use 480MB ). We are working to fix this.

APBS 1.4.2.1 Released

Dear APBS and PDB2PQR users –

We are pleased to announce the release of APBS 1.4.2.1 which is now available from http://www.poissonboltzmann.org/docs/downloads/. There are several improvements and fixes (outlined below) to this release of the software and we encourage all users to upgrade.

Please see APBS Release History for the complete release notes.

Thank you for your continued support of APBS and PDB2PQR.

Sincerely,

The APBS/PDB2PQR development team

APBS 1.4.2.1

NEW FEATURES

  • Poisson-Boltzmann Semi-Anlytical Method (PB-SAM) packaged and built with APBS.
  • New Geometric flow API and improvements in speed.
  • Support for BinaryDX file format.
  • SOR solver added for mg-auto input file option.
  • DXMath improvements.
  • Test suit improvements:
    • APBS build in Travis-CI
    • Geometric Flow tests added.
    • Protein RNA tests enabled.
    • Intermediate resutls testing.
  • Example READMEs onverted to markdown and updated with latest results.

BUG FIXES

  • OpenMPI (mg-para) functionality restored.
  • Fixed parsing PQR files that contained records other than ATOM and HETATM.
  • Geometric Flow boundary indexing bug fixed.
  • Build fixes:
    • Out of source CMake build are again working.
    • Python library may be built.
    • CentOS 5 binary builds for glibc compatibility.
    • Pull requests merged.
  • Removed irrelevant warning messages.

Notes

The following packages are treated as submodules in APBS: * Geometric Flow has been moved to it’s own repository. * FETk has been cloned so that we could effect updates. * PB-SAM Lives here.

Added a chat feature for users. This can also be found from the support tab on .

KNOWN BUGS

  • Travis CI Linux builds are breaking because Geometric Flow relies on C++11 and Travis boxen have an old GCC that does not support C++11. This also and issue for CentOS 5.
  • BEM is temporarily disabled due to build issues.
  • Geometric Flow build is currently broken on Windows using Visual Studio.