[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[ccp4bb]: topological/atomic comparision

***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***


Dear all,
I would like to comapare the topology of two homologous chains 
using top3d (to get residue by residue rms deviation). But TOPP 
assigns secocndary structures to theses chains and compares only 
those secondary structure to give average angle/distance deviations,
giving an output like this 

---------------

  222 Ca atoms read 0 helixes 17 strands in file a2C.pdb
            1 chains in Mol2
 Chain C Nr 1 17
 ----------------------------------------------------------------------
  17 of ( 17, 17) secondary structure could be aligned
 ---------------------------------------------------+-----+-----+------
  Nr.E Mol1 start end match Nr.E Mol2 start end !angle! dst ! r.m.s
 ---------------------------------------------------+-----+-----+------
   1-b:  11 A 16-A 20 ==== 1-b:  11 C 18-C 22 !  3.2!  0.5!  1.3
   2-b:  22 A 34-A 47 ==== 2-b:  22 C 36-C 49 !  4.5!  0.2!  1.5
   3-b:  33 A 50-A 53 ==== 3-b:  33 C 52-C 55 !  2.0!  0.2!  0.4
   4-b:  44 A 62-A 63 ==== 4-b:  44 C 64-C 65 !  5.1!  0.4!  0.5
   5-b:  55 A 72-A 74 ==== 5-b:  55 C 75-C 77 !  7.5!  0.4!  3.4
   6-b:  66 A 80-A 82 ==== 6-b:  66 C 81-C 83 !  8.1!  0.5!  3.5
   7-b:  77 A 88-A 92 ==== 7-b:  77 C 90-C 94 !  4.9!  0.2!  0.7
   8-b:  88 A 105-A 106 ==== 8-b:  88 C 105-C 106 !  4.9!  0.6!  0.8
   9-b:  99 A 116-A 121 ==== 9-b:  99 C 116-C 121 !  4.1!  0.2!  1.2
  10-b: 100 A 126-A 130 ==== 10-b: 100 C 126-C 130 !  6.1!  0.0!  0.9
  11-b: 111 A 144-A 156 ==== 11-b: 111 C 143-C 156 !  6.0!  0.6!  1.9
  12-b: 122 A 162-A 164 ==== 12-b: 122 C 162-C 164 !  4.6!  0.6!  0.7
  13-b: 133 A 173-A 174 ==== 13-b: 133 C 173-C 174 !  2.8!  0.3!  0.7
  14-b: 144 A 182-A 186 ==== 14-b: 144 C 182-C 185 ! 10.1!  0.3!  2.7
  15-b: 155 A 190-A 192 ==== 15-b: 155 C 191-C 193 ! 10.6!  0.2!  0.9
  16-b: 166 A 198-A 201 ==== 16-b: 166 C 199-C 202 !  1.3!  0.3!  0.4
  17-b: 177 A 230-A 235 ==== 17-b: 177 C 231-C 237 !  5.3!  0.1!  1.9
 ---------------------------------------------------+-----+-----+------
 Mean Angle:  5.4 Mean Distance:  0.3 RMS:  1.8
 Max Anlge:  10.6 Max Distance:  0.6
 SS match # 17 topological diversity 3.6 in match 1 of a2C

---------------------

I would appreciate if any one can suggest any key word to be included
(or any other program) to get residue by residue rms deviation while 
comapring two pdb files.

Thanks in advance
muthu