[Chimera-users] Wrong formtting into pdb file after "Chimera"

[Elaine Meng]

Hello,
I'm not sure what you are trying to do.  There is no need to combine anything because any single PDB entry is already a single model.  When you open 3GBM there is only one model, although it does have multiple chains (A,B,C,D, H,I,L,M ... I can tell by looking in the menu: Select... Chain).  

If all you want is to remove the other chains, just delete them.  For example, commands:

open 3gbm
select :.h:.l
delete ~sel

(open structure, select chains H and L, delete all the unselected stuff).  Then you can just save a PDB.  I tried that and the 52A residue numbering was kept.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 29, 2012, at 12:15 PM, Hsih-Te Yang wrote:

> Hello:
> 
> By using "Chimera" under its environment, I retrieved the 3GBM from
> internet of PDB. Then "H" and "L" chains were selected and then
> combined into one model.
> 
> The formats before and after using Chimera are different:
> 
> Before and download from PDB: original 3GBM.pdb:
> --------------------------------------------------------------------------
> ATOM   8198  N   ILE H  52      21.400 -46.642 -15.670  1.00 34.21           N
> ATOM   8199  CA  ILE H  52      21.907 -48.031 -15.705  1.00 34.50           C
> ATOM   8200  C   ILE H  52      22.650 -48.325 -17.003  1.00 34.35           C
> ATOM   8201  O   ILE H  52      22.192 -47.956 -18.089  1.00 34.71           O
> ATOM   8202  CB  ILE H  52      20.781 -49.070 -15.662  1.00 34.67           C
> ATOM   8203  CG1 ILE H  52      19.817 -48.868 -14.495  1.00 35.26           C
> ATOM   8204  CG2 ILE H  52      21.375 -50.440 -15.579  1.00 36.91           C
> ATOM   8205  CD1 ILE H  52      20.481 -48.373 -13.235  1.00 36.77           C
> ATOM   8206  N   PRO H  52A     23.772 -49.033 -16.926  1.00 34.41           N
> ATOM   8207  CA  PRO H  52A     24.505 -49.283 -18.185  1.00 34.55           C
> ATOM   8208  C   PRO H  52A     23.750 -50.255 -19.109  1.00 34.33           C
> ATOM   8209  O   PRO H  52A     22.874 -51.013 -18.645  1.00 34.29           O
> ATOM   8210  CB  PRO H  52A     25.817 -49.905 -17.709  1.00 34.19           C
> ATOM   8211  CG  PRO H  52A     25.402 -50.687 -16.528  1.00 35.46           C
> ATOM   8212  CD  PRO H  52A     24.336 -49.808 -15.815  1.00 34.63           C
> --------------------------------------------------------------------------
> 
> After using Chimera and saved as ".pdb" file:
> --------------------------------------------------------------------------
> ATOM    371  N   ILE H  52     -61.722 -45.711 -51.406  1.00 34.21           N
> ATOM    372  CA  ILE H  52     -62.988 -46.402 -51.737  1.00 34.50           C
> ATOM    373  C   ILE H  52     -63.058 -46.767 -53.215  1.00 34.35           C
> ATOM    374  O   ILE H  52     -62.716 -45.957 -54.082  1.00 34.71           O
> ATOM    375  CB  ILE H  52     -64.219 -45.520 -51.499  1.00 34.67           C
> ATOM    376  CG1 ILE H  52     -64.272 -44.923 -50.094  1.00 35.26           C
> ATOM    377  CG2 ILE H  52     -65.457 -46.324 -51.739  1.00 36.91           C
> ATOM    378  CD1 ILE H  52     -63.739 -45.839 -49.022  1.00 36.77           C
> ATOM    379  N   PRO H  52     -63.548 -47.961 -53.533  1.00 34.41           N
> ATOM    380  CA  PRO H  52     -63.580 -48.321 -54.966  1.00 34.55           C
> ATOM    381  C   PRO H  52     -64.618 -47.494 -55.747  1.00 34.33           C
> ATOM    382  O   PRO H  52     -65.552 -46.927 -55.145  1.00 34.29           O
> ATOM    383  CB  PRO H  52     -63.975 -49.797 -54.948  1.00 34.19           C
> ATOM    384  CG  PRO H  52     -64.891 -49.879 -53.793  1.00 35.46           C
> ATOM    385  CD  PRO H  52     -64.271 -48.943 -52.718  1.00 34.63           C
> --------------------------------------------------------------------------
> 
> The "52A" -> "52", there is no discrimination between "ILE" and "PRO"
> on the position 52 of H chain.
> 
> Please let me know, what wrong with my data processing?
> Thank you a lot.
> 
> Hsih-Te