ProteinShader: illustrative rendering of macromolecules

BMC Structural Biology

Table 3 Proteins used in performance testing.

PDB ID	Residues	Atoms	Protein
1AQB	175	1574	retinol-binding protein
1BL8	388	2824	potassium channel
6ADH	748	5669	alcohol dehydrogenase
13PK	1660	12508	phosphoglycerate kinase
1E79	3315	25248	F1 ATPase inhibited by DCCD
1AON	8015	59674	GroEL-GroES-(ADP)7 chaperonin complex

The performance tests graphed in Figures 10 to 12 were made on a Macintosh 2.16 GHz Intel Core 2 Duo with 2 GB of RAM and an ATI Radeon X1600 graphics card with 256 MB VRAM. To prevent an out of memory error for the largest protein tested, the chaperonin complex, the maximum size of the Java heap was increased to 512 MB by adding "-Xmx512m" as an argument to the java command in the run.sh script provided with the ProteinShader distribution.

ISSN: 1472-6807