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VuisterLab / cing

Automated Validation of NMR Structures
http://nmr.le.ac.uk
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What produces values for PL3CHK for amino acids #63

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
even though the check is meant for nucleic acids only:
From check.db:
ID        : model_000.pdb
CheckID   : PL3CHK
 Program  : WHAT IF
 Version  : 6.0 (20080412-0930)
 Text     : Side chain planarity check
 DocURL   : http://swift.cmbi.ru.nl/whatif/
 Date     : 2008-05-27
  Level   : RESIDUE   
   LText  : For all DNA/RNA residues, the RMS deviation of all planar atoms to
   LText  : a fitted plane was determined. This number is given here.

Original issue reported on code.google.com by jurge...@gmail.com on 27 May 2008 at 2:18

GoogleCodeExporter commented 9 years ago 
See: http://nmr.cmbi.ru.nl/~jd/cing/out/1i1s.cing

Original comment by jurge...@gmail.com on 29 May 2008 at 12:08

GoogleCodeExporter commented 9 years ago

Original comment by jurge...@gmail.com on 5 Jun 2008 at 2:48

GoogleCodeExporter commented 9 years ago 
Waited long enough. Let's keep this list fresh.

Original comment by jurge...@gmail.com on 17 Oct 2008 at 1:26

GoogleCodeExporter commented 9 years ago 
Also occurs for entry 1brv

ID        : model_000.pdb
CheckID   : PL3CHK
 Program  : WHAT IF
 Version  : 8.0 (20100115-2150)
 Text     : Side chain planarity check
 DocURL   : http://swift.cmbi.ru.nl/whatcheck/
 Date     : 2010-01-19
  Level   : RESIDUE   
   LText  : For all DNA/RNA residues, the RMS deviation of all planar atoms to
   LText  : a fitted plane was determined. This number is given here.
   LText  :  
   Type   : FLOAT     
   Poor   : >    4.00
   Bad    : >    6.00
   Name   :    0 ; A    ;  171 ; VAL  ; _
    Value :  0.000
   Name   :    0 ; A    ;  172 ; PRO  ; _
    Value :  0.000
   Name   :    0 ; A    ;  173 ; CYS  ; _
    Value :  0.000
   Name   :    0 ; A    ;  174 ; SER  ; _
    Value :  0.000
   Name   :    0 ; A    ;  175 ; THR  ; _
    Value :  0.000
   Name   :    0 ; A    ;  176 ; CYS  ; _
    Value :  0.000
   Name   :    0 ; A    ;  177 ; GLU  ; _
    Value :  0.002
   Name   :    0 ; A    ;  178 ; GLY  ; _
    Value :  0.000
   Name   :    0 ; A    ;  179 ; ASN  ; _
    Value :  0.005
   Name   :    0 ; A    ;  180 ; LEU  ; _
    Value :  0.000
   Name   :    0 ; A    ;  181 ; ALA  ; _
    Value :  0.000
   Name   :    0 ; A    ;  182 ; CYS  ; _
    Value :  0.000
   Name   :    0 ; A    ;  183 ; LEU  ; _
    Value :  0.000
   Name   :    0 ; A    ;  184 ; SER  ; _
    Value :  0.000
   Name   :    0 ; A    ;  185 ; LEU  ; _
    Value :  0.000
   Name   :    0 ; A    ;  186 ; CYS  ; _
    Value :  0.000
   Name   :    0 ; A    ;  187 ; HIS  ; _
    Value :  0.050
   Name   :    0 ; A    ;  188 ; ILE  ; _
    Value :  0.000
   Name   :    0 ; A    ;  189 ; GLU  ; _
    Value :  0.002

What is this check?

Original comment by jurge...@gmail.com on 19 Jan 2010 at 1:04

GoogleCodeExporter commented 9 years ago 
Asking Gert again.

Original comment by jurge...@gmail.com on 8 Feb 2010 at 12:49

GoogleCodeExporter commented 9 years ago 
Reminded again.

Original comment by jurge...@gmail.com on 11 Feb 2010 at 2:12

GoogleCodeExporter commented 9 years ago 
The check got corrupted with proton specific checks in the past and they have 
persisted. It should be in the 
manual by now.

Original comment by jurge...@gmail.com on 17 Mar 2010 at 8:40