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nglviewer / ngl

WebGL protein viewer
http://nglviewer.org/ngl/
MIT License
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More flexible polymer backbone detection and rendering #192

Open hainm opened 8 years ago

hainm commented 8 years ago

screenshot 10

pdb id: 3BBM and I am using current ngl-dev code.

arose commented 8 years ago

Seems ok to me, the two parts are connected with S2L

hainm commented 8 years ago

I just feel like there is disruption. This is from VMD

screenshot-4

arose commented 8 years ago

I see, that would be nice but needs changes in how I detect/handle polymer backbones.

arose commented 8 years ago

A protein example: http://www.rcsb.org/pdb/explore.do?structureId=5emg

arose commented 8 years ago

An example with modified nucleotides http://www.rcsb.org/pdb/explore.do?structureId=1xv6

arose commented 7 years ago

Mixed RNA/DNA structure: http://www.rcsb.org/pdb/ngl/ngl.do?pdbid=5HBX&bionumber=1

ppillot commented 7 years ago

Maybe a related issue: with GFP where residues 65,66,67 are modified and ribbon gets interrupted http://www.rcsb.org/pdb/ngl/ngl.do?pdbid=1GFL&bionumber=1 capture d ecran 2017-04-17 a 09 10 29

excerpts from the pdb file

REMARK 999 SEQUENCE                                                             
REMARK 999                                                                      
REMARK 999 THE FLUOROPHORE IS FORMED BY SER 65, TYR 66 AND GLY 67.              
REMARK 999 THE CARBONYL CARBON OF TYR 66 IS BONDED TO THE NITROGEN              
REMARK 999 OF GLY 67.  THE CARBONYL OXYGEN IS DELETED.                          
REMARK 999 THE SIDE CHAIN OF TYR 66 IS DEHYDROGENATED.                          
...
LINK         C   SER A  65                 N   GLY A  67     1555   1555  1.35  
LINK         C   SER B  65                 N   GLY B  67     1555   1555  1.35  
...
ATOM    478  N   SER A  65      11.385  68.446 -10.896  1.00 15.50           N  
ATOM    479  CA  SER A  65      10.237  67.920 -10.172  1.00 14.40           C  
ATOM    480  C   SER A  65       9.431  69.147  -9.749  1.00 15.10           C  
ATOM    481  CB  SER A  65      10.723  67.085  -8.984  1.00 15.00           C  
ATOM    482  OG  SER A  65       9.652  66.344  -8.424  1.00 15.30           O  
ATOM    483  N   TYR A  66       9.543  69.559  -8.452  1.00 14.90           N  
ATOM    484  CA  TYR A  66       8.729  70.767  -8.479  1.00 14.30           C  
ATOM    485  C   TYR A  66       8.131  70.900  -9.852  1.00 14.90           C  
ATOM    486  O   TYR A  66       7.326  71.733 -10.289  1.00 14.80           O  
ATOM    487  CB  TYR A  66       8.491  71.711  -7.501  1.00 14.00           C  
ATOM    488  CG  TYR A  66       8.987  71.776  -6.180  1.00 13.70           C  
ATOM    489  CD1 TYR A  66       9.853  70.805  -5.669  1.00 13.80           C  
ATOM    490  CD2 TYR A  66       8.622  72.829  -5.348  1.00 14.00           C  
ATOM    491  CE1 TYR A  66      10.348  70.900  -4.352  1.00 14.00           C  
ATOM    492  CE2 TYR A  66       9.098  72.935  -4.033  1.00 14.70           C  
ATOM    493  CZ  TYR A  66       9.954  71.973  -3.543  1.00 14.50           C  
ATOM    494  OH  TYR A  66      10.379  72.087  -2.245  1.00 14.50           O  
ATOM    495  N   GLY A  67       8.653  69.907 -10.550  1.00 15.30           N  
ATOM    496  CA  GLY A  67       8.418  69.770 -11.975  1.00 15.70           C  
ATOM    497  C   GLY A  67       7.239  68.914 -12.412  1.00 15.80           C  
ATOM    498  O   GLY A  67       6.736  69.089 -13.541  1.00 16.20           O
arose commented 7 years ago

thanks, interesting and important example