This page shows development of the Bioshape Retrieval Contest, one track in SHREC2017.

Evaluation Results

-Feb 17,2017: Preliminary results are now available. Please click here to download them.

Result Submission

  1. Feb 10, 2017: participants submit results (Pacific Time Zone 24:00:00)
  2. Format of the submitted results

(1) you should send the IDs of the 200 best matched models for each query that you processed to the organiser.

The ID of each model is the first 6 characters of each file name, for example, ID for m11111_pdb.ccp4 (or m11111_bead.pdb) is m11111

(2) You can use text file or by replying this email. The format should be this: in each line Query_ID: model_IDxxxxx, model_IDyyyyy, …

For example: q_11: m11111, m11232, …

q_12: m11113, m11114, …

note: using colon after query_ID, and using comma to separate model_IDs, each query+results is in one line.

Data Downloads

To Download the query and model database, using these links:

Each shape model is saved in two formats, the PDB and CCP4. They represent identical models, and the shape is represented using point clouds, i.e., the XYZ coordinates of Carbon atoms.

Query: http://liulab.csrc.ac.cn/download/shrec2017/query_set.tar.bz2

ModelSet (PDB format) : http://liulab.csrc.ac.cn/download/shrec2017/model_pdb.tar.bz2

ModelSet (CCP4 format) : http://liulab.csrc.ac.cn/download/shrec2017/model_ccp4.tar.bz2

Please note that the CCP4 is significantly compressed. Once uncompressed, the file size is about 5GB.

useful notes

There are useful python scripts to read CCP4 files and PDB files, the scripts are based on the CCTBX.

A quick way to install the cctbx is using the following commands:

svn export svn://svn.code.sf.net/p/cctbx/code/trunk/libtbx/auto_build/bootstrap.py
python bootstrap.py --builder=cctbx

Another package branched from CCTBX is under development, the SASTBX, with source codes and manual page available here: SASTBX.

read_ccp4.py

from iotbx import ccp4_map
import sys
 
if __name__ == "__main__":
  file_name = sys.argv[1]
  this_map = ccp4_map.map_reader(file_name)
  raw_map = this_map.data
  print "Number of Grid points: ", raw_map.size()
  print "Unit cell dimension: ", this_map.unit_cell_grid

read_pdb.py

from iotbx import pdb
import sys
 
if __name__ == "__main__":
  file_name = sys.argv[1]
  pdbi = pdb.hierarchy.input(file_name=file_name)
  atoms = pdbi.hierarchy.models()[0].atoms()
  xyz = atoms.extract_xyz()
  print "Total number of points: ", xyz.size()
  print "Position of the first Atom", xyz[0]

Test CCP4 READER program

cctbx.python read_ccp4.py query_set/q_11_pdb.ccp4

The output should be something like:

Number of Grid points:  226981
Unit cell dimension:  (61, 61, 61)

Test PDB READER program

cctbx.python read_pdb.py query_set/q_11_bead.pdb

With output looks like this:

Total number of points:  6386
Position of the first point (13.0, 15.0, 23.0)

Time line

  1. Jan 18, 2017: circulating the SHREC call for this track (Done)
  2. Jan 18-25, 2017: Registration (Finished, with 7 teams registered before the deadline, will keep open during the contest, until Feb 10, 2017)
  3. Jan 25, ,2017: release the query and the model database (released)
  4. Feb 10, 2017: participants submit results
  5. Feb 16, 2017: circulating the evaluation results
  6. Feb 17, 2017: call for a method description from participants
  7. Feb 24, 2017: circulating track paper draft
  8. Feb 28, 2017: submit track paper

Richard Feynman

“everything that is living can be understood in terms of the jiggling and wiggling of atoms”.

and now, we want to watch atoms jiggling and wiggling.

X-rays, electrons, fluorescence light, the advances of photon sciences, together with computational modeling, are making this happen.