This uses the included input script and PDB file for hemoglobin to run through using the Fortran code to generate output. The output .pnm
file is then converted to a PNG
.
Everything is installed and ready to run if you are accessing this using a link that involves MyBinder.org.
Learn more about David Goodsell's work and software here and here.
You can exectute Run all
to run the code all in one step or step through each cell entering shift-enter
to trigger running each.
Copy the input files from the previously cloned repository to the current working directory. (See postBuild
for previous set-up steps and compiling.)
cp ~/.local/bin/Illustrate/* .
Show the compiled fortran code for illustrate
is now in the working directory along with input files, 2hhb.inp
(script file) and 2hhb.pdb
(standard structure file in PDB format).
!ls
2hhb_image.png demo_colors.ipynb illustrate_std_demo.ipynb 2hhb.inp demo_fetch.ipynb image.png 2hhb.pdb demo_orient.ipynb LICENSE 2hhb.pnm demo_palette.ipynb README.md converted_image.png illustrate demo_apply_combo.ipynb illustrate.f
!./illustrate < 2hhb.inp
atom descriptors: 15 type, color, radius 1 0.500000000 0.500000000 0.500000000 0.00000000 type, color, radius 2 0.500000000 0.500000000 0.500000000 0.00000000 type, color, radius 3 0.500000000 0.500000000 0.500000000 0.00000000 type, color, radius 4 1.00000000 0.600000024 0.600000024 1.60000002 type, color, radius 5 1.00000000 0.500000000 0.500000000 1.79999995 type, color, radius 6 1.00000000 0.500000000 0.500000000 1.50000000 type, color, radius 7 1.00000000 0.600000024 0.600000024 1.60000002 type, color, radius 8 1.00000000 0.500000000 0.500000000 1.79999995 type, color, radius 9 1.00000000 0.500000000 0.500000000 1.50000000 type, color, radius 10 1.00000000 0.800000012 0.600000024 1.60000002 type, color, radius 11 1.00000000 0.699999988 0.500000000 1.79999995 type, color, radius 12 1.00000000 0.699999988 0.500000000 1.50000000 type, color, radius 13 1.00000000 0.800000012 0.00000000 1.79999995 type, color, radius 14 1.00000000 0.300000012 0.300000012 1.60000002 type, color, radius 15 1.00000000 0.100000001 0.100000001 1.50000000 Number of BIOMT 0 Chains in Biological Assembly 1 A 2 B 3 C 4 D Number of BIOMT 1 BIOMAT 1 1.00000000 0.00000000 0.00000000 0.00000000 BIOMAT 1 0.00000000 1.00000000 0.00000000 0.00000000 BIOMAT 1 0.00000000 0.00000000 1.00000000 0.00000000 atoms read: 4556 from: 2hhb.pdb number of subunits: 8 translation vector : 0.00000000 0.00000000 0.00000000 scale factor : 12.0000000 z rotation : 90.0000000 background inten. : 1.00 1.00 1.00 fog intensity : 1.00 1.00 1.00 upper fog percent : 100.00 lower fog percent : 100.00 draw conical shadow input value for image size -30 -30 illustration parameters l parameters: 3.00000000 10.0000000 g parameters: 3.00000000 8.00000000 *begin calculation* min coordinates : -26.4710026 -34.0060005 -29.9990005 max coordinates : 27.4800034 34.3030014 29.9880009 automating centering centering vector : -0.504499435 -0.148502350 -52.5879974 applying autosizing x and y frame width: 30 30 xsize and ysize: 750 922 output pnm filename: 2hhb.pnm 0 spheres added of type: 1 0 spheres added of type: 2 0 spheres added of type: 3 685 spheres added of type: 4 3 spheres added of type: 5 381 spheres added of type: 6 685 spheres added of type: 7 3 spheres added of type: 8 381 spheres added of type: 9 1448 spheres added of type: 10 6 spheres added of type: 11 792 spheres added of type: 12 4 spheres added of type: 13 136 spheres added of type: 14 32 spheres added of type: 15 shading maps written into depth buffer zpix_min,zpix_max -818.827271 -253.199951 Pixel processing beginning 99999999999999999999999999999999999999999999999 99999999999999109884999990095999999999999999999 99999999999999995899999999989887799999999999999 99999999999968994878899999768789976999999999999 99999999992798889999693957746519995999999999999 99999999967697998982898045194898995999999999999 99999999907698999989989986889899688890999999999 99999990778888980888989957688988888888999999999 99999977776708981729999979967888777788828999999 99999288869898870988588809978807089656788999999 99990998799977868929888789878869997859967809999 99976499709898998979899889577059999789978879999 99979888889988990887839899007748699889978709999 99999989987899867881880888885769997899668999999 99999099987999989998988986900549998905678999999 99997588762888886998089869998969989989378999999 99997687086899889896269887899988988998567879999 99999909989999998899889988888999498890895999999 99999904638900996999787908989958798899816999999 99995885499998999998994639881989598888561699999 99999886099989999099998800448728885886789978099 99999884899899999696969995898178889908898538999 99999877999978154776599998909998888308908999999 99998987763296668870007999989906759890968979999 99968846367760650998088897888878999899898709999 99999667688887756998099995890989987491078879999 99999878778088987488899989998970078867578989999 99999789798509998298485788479957888888889999999 99999999888888882665446889988772888086832999999 99999999979998958862059988977268899967899999999 99999999989998989986769948908897884578999999999 99999999908999989906778808978898978657999999999 99999999999999556876899999787909959799999999999 99999999999056588788999999188568986799999999999 99999999999999887998999999997977999999999999999 99999999999999999999999999999999999999999999999 99999999999999999999999999999999999999999999999
That produces the file 2hhb.pnm
, which is in the portable anymap format
, see here.
!ls 2hhb.pnm
2hhb.pnm
portable anymap format
to standard PNG format¶Conversion uses the Netpbm project's pnmtopng
.
!pnmtopng 2hhb.pnm > 2hhb_image.png
Display the output here.
from IPython.display import Image
Image("2hhb_image.png")