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Note that we are not the developers of HOLLOW — we just forked it a long time ago to make some local modifications. We do not support HOLLOW in any form and we haven't used it ourselves in a long time.

You are welcome to file issues (as a documentation of problems for other users) and to either fork the project or submit fixes via pull requests but please understand that we just leave the code up in case someone wants to take over maintenance.

Installation

Only Python 2.7 is supported. You can create a virtual Python 2.7 environment, e.g., using conda:

conda create -n hollow27 python=2.7 setuptools numpy

Then install the package from source

conda activate hollow27
git clone https://github.com/Becksteinlab/hollow.git
cd hollow
python setup.py install

You should now be able to run the hollow command (hollow-asa and hollow-volume may or may not work).

Documentation

See the hollow/examples directory in the source code.

For example

conda activate hollow27

cd hollow/examples/channel

# run example
hollow -c constraint -o hollow.pdb 2o4v-a.pdb

should produce

Loading 2o4v-a.pdb
Skipping water molecules
Loading constraints from constraint
cylinder constraints: center = Vector3d(63.830889, 20.704390, 23.233890), axis = Vector3d(4.637000, -0.860000, -31.647000), radius = 16
Setting up grid: 92 x 92 x 92, spacing 0.500, width 46.3
   >>>>> 00.21s
Excluding protein bulk from grid with 1.4 angstrom probe
   >>>>> 03.54s
Excluding grid points outside constraint
   >>>>> 02.56s
Excluding surrounded points
is_hollow (hollow -i commandline option) has been set to: True
   >>>>> 00.85s
Saving hollow spheres to hollow.pdb

I can visualize in VMD

vmd 2o4v-a.pdb -m hollow.pdb

The hollow surface is rendered with the QuickSurf representation: