[MMTK] atom position error

Michael Sorich mike_sorich@hotmail.com
Fri, 19 Apr 2002 16:32:52 +0930


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Hi,
=20
I have just started to use the MMTK and I am not sure where I have gone
wrong. I have a small molecule in a pdb file and I am trying to extract
the co-ordinates of each atom. An example of the code I have used is
below:
=20
from MMTK import *
from MMTK.PDB import PDBConfiguration
=20
pdb_conf1 =3D PDBConfiguration("=85\\bilr.pdb")
moleculeCollection =3D pdb_conf1.createMolecules()
bilirubin =3D moleculeCollection.objectList()[0]
=20
print bilirubin.atoms[0].position()
print bilirubin.atoms[1].position()
=20
=20
This outputs:
[-1.1456999999999999, 0.074399999999999994, 0.1062]
[-0.50519999999999987, -0.27289999999999998, 0.58729999999999993]
=20
However the co-ordinates in my pdb file are ten times greater, i.e.
REMARK   4 Bili COMPLIES WITH FORMAT V. 2.0=20
HETATM    1  N1  UNK     0     -11.457   0.744   1.062  1.00  0.00
N =20
HETATM    2  O2  UNK     0      -5.052  -2.729   5.873  1.00  0.00
O
=85
=20
Any help would be appreciated
=20
Michael Sorich
PhD Student
School of Pharmaceutical, Molecular and Biomedical Sciences
University of South Australia
Email: michael.sorich@postgrads.unisa.edu.au
           mike_sorich@hotmail.com
=20

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<div class=3DSection1>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Hi,<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>I have just started to use the MMTK and I am not sure =
where
I have gone wrong. I have a small molecule in a <span =
class=3DSpellE>pdb</span>
file and I am trying to extract the co-ordinates of each atom. An =
example of
the code I have used is below:<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><span class=3DGramE><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>from</span></font></span><fo=
nt
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'> MMTK import
*<o:p></o:p></span></font></p>

<p class=3DMsoNormal><span class=3DGramE><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>from</span></font></span><fo=
nt
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'> MMTK.PDB
import <span =
class=3DSpellE>PDBConfiguration</span><o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>pdb_conf1 =3D <span class=3DSpellE><span =
class=3DGramE>PDBConfiguration</span></span><span
class=3DGramE>(</span>&quot;=85\\bilr.pdb&quot;)<o:p></o:p></span></font>=
</p>

<p class=3DMsoNormal><span class=3DSpellE><span class=3DGramE><font =
size=3D2
face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'>moleculeCollection</span></f=
ont></span></span><font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'> =3D
pdb_conf1.createMolecules()<o:p></o:p></span></font></p>

<p class=3DMsoNormal><span class=3DGramE><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>bilirubin</span></font></spa=
n><font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'> =3D <span
class=3DSpellE>moleculeCollection.objectList</span>()[0]<o:p></o:p></span=
></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><span class=3DGramE><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>print</span></font></span><f=
ont
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'> <span
class=3DSpellE>bilirubin.atoms</span>[0].position()<o:p></o:p></span></fo=
nt></p>

<p class=3DMsoNormal><span class=3DGramE><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>print</span></font></span><f=
ont
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'> <span
class=3DSpellE>bilirubin.atoms</span>[1].position()<o:p></o:p></span></fo=
nt></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><span class=3DGramE><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>This =
outputs</span></font></span><font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'>:<o:p></o:p></span></font></=
p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>[-1.1456999999999999, 0.074399999999999994, =
0.1062]<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>[-0.50519999999999987, -0.27289999999999998,
0.58729999999999993]<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>However the co-ordinates in my <span =
class=3DSpellE>pdb</span>
file are ten times greater, i.e.<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'>REMARK<span
style=3D'mso-spacerun:yes'>&nbsp;&nbsp; </span>4 <span =
class=3DSpellE>Bili</span>
COMPLIES WITH FORMAT V. 2.0 <o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'>HETATM<span
style=3D'mso-spacerun:yes'>&nbsp;&nbsp;&nbsp; </span><span =
class=3DGramE>1<span
style=3D'mso-spacerun:yes'>&nbsp; </span>N1</span><span
style=3D'mso-spacerun:yes'>&nbsp; </span>UNK<span
style=3D'mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp; </span>0<span
style=3D'mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp; </span>-11.457<span
style=3D'mso-spacerun:yes'>&nbsp;&nbsp; </span>0.744<span
style=3D'mso-spacerun:yes'>&nbsp;&nbsp; </span>1.062<span
style=3D'mso-spacerun:yes'>&nbsp; </span>1.00<span
style=3D'mso-spacerun:yes'>&nbsp; </span>0.00<span
style=3D'mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;
</span>N<span style=3D'mso-spacerun:yes'>&nbsp; =
</span><o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;
font-family:"Courier New"'>HETATM<span
style=3D'mso-spacerun:yes'>&nbsp;&nbsp;&nbsp; </span><span =
class=3DGramE>2<span
style=3D'mso-spacerun:yes'>&nbsp; </span>O2</span><span
style=3D'mso-spacerun:yes'>&nbsp; </span>UNK<span
style=3D'mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp; </span>0<span
style=3D'mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
</span>-5.052<span
style=3D'mso-spacerun:yes'>&nbsp; </span>-2.729<span
style=3D'mso-spacerun:yes'>&nbsp;&nbsp; </span>5.873<span
style=3D'mso-spacerun:yes'>&nbsp; </span>1.00<span
style=3D'mso-spacerun:yes'>&nbsp; </span>0.00<span
style=3D'mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;
</span>O<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;
font-family:"Courier New"'>=85</span></font><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p=
>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Any help would be =
appreciated<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>Michael =
Sorich<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>PhD =
Student<o:p></o:p></span></font></p>

<p class=3DMsoNormal><st1:place><st1:PlaceType><font size=3D2 =
face=3DArial><span
  =
style=3D'font-size:10.0pt;font-family:Arial;mso-no-proof:yes'>School</spa=
n></font></st1:PlaceType><font
 size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial;mso-no-proof:
 yes'> of </span></font><st1:PlaceName><font size=3D2 face=3DArial><span
  =
style=3D'font-size:10.0pt;font-family:Arial;mso-no-proof:yes'>Pharmaceuti=
cal</span></font></st1:PlaceName></st1:place><font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial;mso-no-proof:
yes'>, Molecular and Biomedical Sciences<o:p></o:p></span></font></p>

<p class=3DMsoNormal><st1:place><st1:PlaceType><font size=3D2 =
face=3DArial><span
  =
style=3D'font-size:10.0pt;font-family:Arial;mso-no-proof:yes'>University<=
/span></font></st1:PlaceType><font
 size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial;mso-no-proof:
 yes'> of </span></font><st1:PlaceName><font size=3D2 face=3DArial><span
  style=3D'font-size:10.0pt;font-family:Arial;mso-no-proof:yes'>South =
Australia</span></font></st1:PlaceName></st1:place><font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial;mso-no-proof:
yes'><o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>Email:
michael.sorich@postgrads.unisa.edu.au<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><span
style=3D'mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;
</span>mike_sorich@hotmail.com<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

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