[Chimera-users] TERs in PDB ?

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 21 16:27:08 PST 2017


Hi Marek,
Not to my knowledge.  In my tests, this is written out from Chimera with HETATM lines instead of ATOM, which already means that the residues should not be connected to each other automatically.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Nov 21, 2017, at 4:03 PM, Marek Maly <marek.maly at ujep.cz> wrote:
> 
> Hello,
> 
> is it possible to save the given molecular model (which is open in Chimera) in PDB format but with
> the TER string between consequent residues ?
> 
> example:
> ---------------------------
> ATOM      1  Si1 CEN A   1      56.395  15.633  50.147  1.00  0.00          Si
> TER
> ATOM      2  C1  RE1 A   2      54.892  16.772  50.453  1.00  0.00           C
> ATOM      3  H1  RE1 A   2      54.289  16.821  49.538  1.00  0.00           H
> ATOM      4  H2  RE1 A   2      54.219  16.552  51.290  1.00  0.00           H
> ATOM      5  C2  RE1 A   2      55.394  18.185  50.780  1.00  0.00           C
> ATOM      6  H3  RE1 A   2      55.896  18.665  49.932  1.00  0.00           H
> ATOM      7  H4  RE1 A   2      56.038  18.053  51.659  1.00  0.00           H
> ATOM      8  C3  RE1 A   2      54.181  19.075  51.202  1.00  0.00           C
> ATOM      9  H6  RE1 A   2      53.674  18.496  51.984  1.00  0.00           H
> ATOM     10  H5  RE1 A   2      53.589  19.325  50.313  1.00  0.00           H
> ATOM     11  Si3 RE1 A   2      54.714  20.646  51.949  1.00  0.00          Si
> ATOM     12  C4  RE1 A   2      53.140  21.420  52.746  1.00  0.00           C
> ATOM     13  H8  RE1 A   2      53.430  22.271  53.376  1.00  0.00           H
> ATOM     14  H7  RE1 A   2      52.690  20.675  53.413  1.00  0.00           H
> ATOM     15  H9  RE1 A   2      52.466  21.649  51.911  1.00  0.00           H
> ATOM     16  C5  RE1 A   2      55.491  21.841  50.620  1.00  0.00           C
> ATOM     17  H12 RE1 A   2      56.423  21.426  50.217  1.00  0.00           H
> ATOM     18  H10 RE1 A   2      55.768  22.733  51.196  1.00  0.00           H
> ATOM     19  H11 RE1 A   2      54.875  22.300  49.836  1.00  0.00           H
> TER
> ATOM     20  C1  RE1 A   3      57.436  16.272  48.673  1.00  0.00           C
> ATOM     21  H1  RE1 A   3      58.039  17.117  49.028  1.00  0.00           H
> ATOM     22  H2  RE1 A   3      58.209  15.633  48.228  1.00  0.00           H
> ATOM     23  C2  RE1 A   3      56.488  16.820  47.464  1.00  0.00           C
> ATOM     24  H3  RE1 A   3      55.675  17.467  47.819  1.00  0.00           H
> ATOM     25  H4  RE1 A   3      55.960  16.034  46.910  1.00  0.00           H
> ATOM     26  C3  RE1 A   3      57.354  17.603  46.475  1.00  0.00           C
> ATOM     27  H6  RE1 A   3      58.241  17.015  46.210  1.00  0.00           H
> ATOM     28  H5  RE1 A   3      57.812  18.464  46.978  1.00  0.00           H
> ATOM     29  Si3 RE1 A   3      56.645  18.300  44.851  1.00  0.00          Si
> ATOM     30  C4  RE1 A   3      55.474  17.030  44.146  1.00  0.00           C
> ATOM     31  H8  RE1 A   3      54.666  17.578  43.646  1.00  0.00           H
> ATOM     32  H7  RE1 A   3      54.864  16.542  44.918  1.00  0.00           H
> ATOM     33  H9  RE1 A   3      55.893  16.349  43.396  1.00  0.00           H
> ATOM     34  C5  RE1 A   3      58.034  18.987  43.812  1.00  0.00           C
> ATOM     35  H12 RE1 A   3      59.000  18.584  44.141  1.00  0.00           H
> ATOM     36  H10 RE1 A   3      58.180  20.062  43.974  1.00  0.00           H
> ATOM     37  H11 RE1 A   3      58.009  18.601  42.786  1.00  0.00           H
> TER
> ATOM     38  C1  RE1 A   4      57.426  15.522  51.783  1.00  0.00           C
> ATOM     39  H1  RE1 A   4      58.370  14.991  51.606  1.00  0.00           H
> ATOM     40  H2  RE1 A   4      57.769  16.539  52.007  1.00  0.00           H
> ATOM     41  C2  RE1 A   4      56.787  14.966  52.995  1.00  0.00           C
> ATOM     42  H3  RE1 A   4      57.587  14.881  53.741  1.00  0.00           H
> ATOM     43  H4  RE1 A   4      56.321  13.982  52.869  1.00  0.00           H
> ATOM     44  C3  RE1 A   4      55.776  15.938  53.682  1.00  0.00           C
> ATOM     45  H6  RE1 A   4      54.722  15.759  53.439  1.00  0.00           H
> ATOM     46  H5  RE1 A   4      55.920  17.004  53.467  1.00  0.00           H
> ATOM     47  Si3 RE1 A   4      55.756  16.172  55.603  1.00  0.00          Si
> ATOM     48  C4  RE1 A   4      57.359  16.942  56.191  1.00  0.00           C
> ATOM     49  H8  RE1 A   4      57.601  17.853  55.629  1.00  0.00           H
> ATOM     50  H7  RE1 A   4      58.242  16.306  56.061  1.00  0.00           H
> ATOM     51  H9  RE1 A   4      57.248  17.148  57.263  1.00  0.00           H
> ATOM     52  C5  RE1 A   4      55.827  14.369  56.251  1.00  0.00           C
> ATOM     53  H12 RE1 A   4      56.581  13.702  55.818  1.00  0.00           H
> ATOM     54  H10 RE1 A   4      54.854  13.866  56.186  1.00  0.00           H
> ATOM     55  H11 RE1 A   4      56.205  14.393  57.280  1.00  0.00           H
> TER
> .
> .
> .
> ---------------------------
> 
> If yes, how to do it ?
> 
>    Thank you in advance for your advice.
> 
> Best wishes,
> 
>    Marek




More information about the Chimera-users mailing list