Re: [PyMOL] counting number of standard amino acids in PDB

[Jared S. <jar...@co...>]

Hi James - 

Do any of the options from this previous BB discussion help?

https://sourceforge.net/p/pymol/mailman/message/28466955/

Cheers,
Jared


On June 24, 2019 at 8:13:47 AM, James Starlight (jms...@gm...) wrote:

Dear Pymol Users,  

that is not very related to pymol question but however probably it can  
be solved via pymol as well ;-)  

I am looking for some script (e.g. via running in pymol no-gui), which  
will count the number of standard amino acid residues in the given  
PDB. E.g. for particular pdb consisted of 9 residues complexed with  
part of the ligand I need to print the value of 9 (the end value of  
6th column before TER)  

ATOM 1 N MET A 1 24.950 5.224 -5.601 1.00 30.01 N  
ATOM 2 CA MET A 1 24.822 3.740 -5.655 1.00 30.25 C  
ATOM 3 C MET A 1 23.719 3.091 -4.771 1.00 28.98 C  
ATOM 4 O MET A 1 23.417 1.937 -4.989 1.00 28.27 O  
ATOM 5 CB MET A 1 26.187 3.043 -5.448 1.00 31.03 C  
ATOM 6 CG MET A 1 26.869 3.182 -4.084 1.00 32.21 C  
ATOM 7 SD MET A 1 28.713 3.095 -4.227 1.00 34.63 S  
ATOM 8 CE MET A 1 29.205 3.597 -2.564 1.00 33.32 C  
ATOM 9 N LYS A 2 23.111 3.804 -3.818 1.00 27.78 N  
ATOM 10 CA LYS A 2 21.869 3.310 -3.188 1.00 27.21 C  
ATOM 11 C LYS A 2 20.671 4.237 -3.440 1.00 26.27 C  
ATOM 12 O LYS A 2 20.787 5.445 -3.300 1.00 25.96 O  
ATOM 13 CB LYS A 2 22.027 3.091 -1.684 1.00 27.32 C  
ATOM 14 CG LYS A 2 20.820 2.362 -1.065 1.00 27.75 C  
ATOM 15 CD LYS A 2 20.953 2.147 0.439 1.00 28.18 C  
ATOM 16 CE LYS A 2 19.928 1.130 0.938 1.00 29.30 C  
ATOM 17 NZ LYS A 2 20.083 0.809 2.386 1.00 30.36 N1+  
ATOM 18 N PHE A 3 19.528 3.658 -3.808 1.00 24.92 N  
ATOM 19 CA PHE A 3 18.306 4.421 -4.054 1.00 24.39 C  
ATOM 20 C PHE A 3 17.161 3.823 -3.246 1.00 24.12 C  
ATOM 21 O PHE A 3 16.991 2.597 -3.202 1.00 23.77 O  
ATOM 22 CB PHE A 3 17.940 4.222 -5.535 1.00 23.83 C  
ATOM 23 CG PHE A 3 19.003 4.968 -6.434 1.00 23.81 C  
ATOM 24 CD1 PHE A 3 19.132 6.337 -6.585 1.00 23.27 C  
ATOM 25 CD2 PHE A 3 19.876 4.135 -7.129 1.00 23.46 C  
ATOM 26 CE1 PHE A 3 20.110 6.868 -7.412 1.00 23.22 C  
ATOM 27 CE2 PHE A 3 20.862 4.660 -7.952 1.00 23.19 C  
ATOM 28 CZ PHE A 3 20.975 6.027 -8.102 1.00 23.07 C  
ATOM 29 N THR A 4 16.374 4.691 -2.624 1.00 23.47 N  
ATOM 30 CA THR A 4 15.326 4.278 -1.704 1.00 23.33 C  
ATOM 31 C THR A 4 13.946 4.720 -2.188 1.00 22.67 C  
ATOM 32 O THR A 4 13.779 5.810 -2.726 1.00 22.24 O  
ATOM 33 CB THR A 4 15.584 4.875 -0.295 1.00 23.52 C  
ATOM 34 CG2 THR A 4 14.441 4.560 0.650 1.00 23.80 C  
ATOM 35 OG1 THR A 4 16.798 4.328 0.245 1.00 23.98 O  
ATOM 36 N VAL A 5 12.955 3.866 -1.980 1.00 22.25 N  
ATOM 37 CA VAL A 5 11.577 4.216 -2.276 1.00 22.46 C  
ATOM 38 C VAL A 5 10.685 4.011 -1.038 1.00 22.44 C  
ATOM 39 O VAL A 5 10.951 3.145 -0.201 1.00 21.37 O  
ATOM 40 CB VAL A 5 11.033 3.456 -3.533 1.00 21.81 C  
ATOM 41 CG1 VAL A 5 11.786 3.902 -4.782 1.00 20.47 C  
ATOM 42 CG2 VAL A 5 11.127 1.940 -3.368 1.00 21.55 C  
ATOM 43 N GLY A 6 9.660 4.845 -0.908 1.00 23.27 N  
ATOM 44 CA GLY A 6 8.676 4.684 0.154 1.00 24.59 C  
ATOM 45 C GLY A 6 8.727 5.731 1.249 1.00 25.69 C  
ATOM 46 O GLY A 6 7.834 5.767 2.101 1.00 26.30 O  
ATOM 47 N ASN A 7 9.764 6.568 1.261 1.00 26.66 N  
ATOM 48 CA ASN A 7 9.775 7.728 2.155 1.00 27.39 C  
ATOM 49 C ASN A 7 10.165 9.028 1.436 1.00 27.80 C  
ATOM 50 O ASN A 7 11.263 9.569 1.622 1.00 28.37 O  
ATOM 51 CB ASN A 7 10.619 7.470 3.421 1.00 28.21 C  
ATOM 52 CG ASN A 7 12.089 7.278 3.127 1.00 29.85 C  
ATOM 53 ND2 ASN A 7 12.938 7.964 3.897 1.00 32.41 N  
ATOM 54 OD1 ASN A 7 12.466 6.525 2.229 1.00 32.61 O  
ATOM 55 N GLY A 8 9.232 9.521 0.622 1.00 27.41 N  
ATOM 56 CA GLY A 8 9.422 10.752 -0.139 1.00 27.40 C  
ATOM 57 C GLY A 8 9.309 10.498 -1.629 1.00 27.35 C  
ATOM 58 O GLY A 8 8.449 11.071 -2.303 1.00 27.93 O  
ATOM 59 N GLN A 9 10.178 9.630 -2.136 1.00 26.80 N  
ATOM 60 CA GLN A 9 10.215 9.294 -3.552 1.00 26.37 C  
ATOM 61 C GLN A 9 9.834 7.833 -3.736 1.00 25.75 C  
ATOM 62 O GLN A 9 10.308 6.970 -2.997 1.00 25.25 O  
ATOM 63 CB GLN A 9 11.622 9.522 -4.115 1.00 26.74 C  
ATOM 64 CG GLN A 9 12.197 10.924 -3.899 1.00 27.40 C  
ATOM 65 CD GLN A 9 11.327 12.028 -4.475 1.00 29.17 C  
ATOM 66 NE2 GLN A 9 10.896 11.863 -5.726 1.00 29.46 N  
ATOM 67 OE1 GLN A 9 11.048 13.025 -3.800 1.00 31.02 O  
TER  
ATOM 1719 C1 0XB B 220 6.613 3.931 -16.928 1.00 11.35 C  
ATOM 1720 C2 0XB B 220 7.042 5.128 -16.070 1.00 14.60 C  
ATOM 1721 O2 0XB B 220 6.347 5.144 -14.862 1.00 15.67 O  
ATOM 1722 C3 0XB B 220 6.767 6.445 -16.786 1.00 17.91 C  
ATOM 1723 O3 0XB B 220 7.304 7.499 -15.962 1.00 20.75 O  
ATOM 1724 C4 0XB B 220 7.275 6.470 -18.142 1.00 17.97 C  
ATOM 1725 O4 0XB B 220 6.793 7.605 -18.882 1.00 21.45 O  
ATOM 1726 C5 0XB B 220 6.856 5.264 -18.860 1.00 15.05 C  
ATOM 1727 O5 0XB B 220 7.286 4.049 -18.182 1.00 12.43 O  

Thanks in advance!  


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