VMD-L Mailing List

From: Lan Hua (lan.hua_at_gmail.com)
Date: Mon Oct 13 2008 - 16:49:07 CDT

Hi,

    I want to locate all the protein atoms with alternate locations for
protein with pdbid 3d1p. The pdb file for this protein downloaded from pdb
bank has hetatm record which I don't want to select. When I used the
following command,

   mol load pdb 3d1p.pdb
   set sel [atomselect top "protein"]
   $sel get {name resid resname altloc}

part of what I got from the last command is

   {N 31 LYS A} {N 31 LYS C} {CA 31 LYS A} {CA 31 LYS C} {C 31 LYS A} {C 31
LYS C} {O 31 LYS A} {O 31 LYS C} {CB 31 LYS A} {CB 31 LYS C} {CG 31 LYS A}
{CG 31 LYS C} {CD 31 LYS A} {CD 31 LYS C} {CE 31 LYS A} {CE 31 LYS C} {NZ 31
LYS A} {NZ 31 LYS C}

However in the pdb file downloaded from pdb bank the coordinates for this
residue with resid 31 look like:

ATOM 95 N ALYS A 31 17.771 -4.079 5.165 0.50 4.72
N
ANISOU 95 N ALYS A 31 950 539 305 32 -118 -10
N
ATOM 96 N CLYS A 31 17.660 -4.089 5.127 0.50 5.40
N
ANISOU 96 N CLYS A 31 1038 575 438 14 -91 -6
N
ATOM 97 CA ALYS A 31 17.941 -5.503 5.166 0.25 5.00
C
ANISOU 97 CA ALYS A 31 936 468 493 67 11 -34
C
ATOM 98 CA BLYS A 31 18.003 -5.680 5.325 0.25 5.14
C
ANISOU 98 CA BLYS A 31 876 425 650 -63 -22 -62
C
ATOM 99 CA CLYS A 31 17.758 -5.524 5.116 0.50 5.89
C
ANISOU 99 CA CLYS A 31 1129 534 573 -4 5 -84
C
ATOM 100 C ALYS A 31 18.911 -5.892 6.320 0.50 4.65
C
ANISOU 100 C ALYS A 31 802 436 528 88 126 -29
C
ATOM 101 C CLYS A 31 18.617 -5.972 6.302 0.50 6.75
C
ANISOU 101 C CLYS A 31 1074 723 764 64 126 45
C
ATOM 102 O ALYS A 31 18.659 -6.843 7.086 0.50 5.54
O
ANISOU 102 O ALYS A 31 1010 467 625 145 176 32
O
ATOM 103 O CLYS A 31 18.289 -6.912 7.046 0.50 7.74
O
ANISOU 103 O CLYS A 31 1256 816 867 56 181 118
O
ATOM 104 CB ALYS A 31 18.436 -5.931 3.780 0.25 5.09
C
ANISOU 104 CB ALYS A 31 1039 397 496 -25 -46 -89
C
ATOM 105 CB BLYS A 31 18.586 -6.306 4.074 0.25 5.83
C
ANISOU 105 CB BLYS A 31 896 618 702 -57 -44 -27
C
ATOM 106 CB CLYS A 31 18.422 -5.994 3.830 0.50 6.99
C
ANISOU 106 CB CLYS A 31 1351 610 694 -92 -8 -131
C
ATOM 107 CG ALYS A 31 18.633 -7.408 3.587 0.25 4.45
C
ANISOU 107 CG ALYS A 31 1121 264 304 53 -116 -23
C
ATOM 108 CG BLYS A 31 17.670 -6.110 2.926 0.25 3.79
C
ANISOU 108 CG BLYS A 31 554 298 589 -99 -146 104
C
ATOM 109 CG CLYS A 31 17.497 -6.457 2.794 0.50 8.51
C
ANISOU 109 CG CLYS A 31 1348 1165 720 29 51 -83
C
ATOM 110 CD ALYS A 31 19.621 -7.678 2.406 0.25 5.89
C
ANISOU 110 CD ALYS A 31 964 523 748 191 35 -122
C
ATOM 111 CD BLYS A 31 18.240 -6.527 1.567 0.25 4.93
C
ANISOU 111 CD BLYS A 31 858 389 624 96 -29 39
C
ATOM 112 CD CLYS A 31 18.178 -7.462 1.851 0.50 8.35
C
ANISOU 112 CD CLYS A 31 1344 1010 817 -309 123 -266
C
ATOM 113 CE ALYS A 31 18.982 -7.379 1.062 0.25 5.98
C
ANISOU 113 CE ALYS A 31 932 798 541 143 -6 18
C
ATOM 114 CE BLYS A 31 19.166 -7.714 1.594 0.25 5.79
C
ANISOU 114 CE BLYS A 31 1141 330 729 212 -74 -129
C
ATOM 115 CE CLYS A 31 19.417 -6.873 1.224 0.50 8.20
C
ANISOU 115 CE CLYS A 31 976 1152 985 -231 18 -409
C
ATOM 116 NZ ALYS A 31 19.966 -7.513 -0.063 0.25 4.92
N
ANISOU 116 NZ ALYS A 31 765 454 650 169 -4 -241
N
ATOM 117 NZ BLYS A 31 19.728 -7.888 0.208 0.25 5.30
N
ANISOU 117 NZ BLYS A 31 991 516 507 121 -34 241
N
ATOM 118 NZ CLYS A 31 19.832 -7.600 -0.041 0.50 7.82
N
ANISOU 118 NZ CLYS A 31 1279 882 809 196 170 -195
N

So, the atomselection "protein" failed to choose the protein atoms with
alternate location B for this residue. Of course, I can use the
atomselection like "protein or altloc B" instead. But I feel confused and it
is not convenient if I need to check which protein atoms with alternate
locations are not chosen. Is there a good day to choose all the protein
atoms with different alternate locations?

Thank you very much

Lan