VMD-L Mailing List

From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Thu Feb 16 2012 - 14:49:06 CST

Hello all,

This may or may not be a vmd issue however, the problem only appears to happen with vmd1.9.1.

Attached are two small files. The first is a unix formatted file with two residues. I have checked the format of this text file with file, od -a, and cat -e.

Both commands say that each line in file temp1 is terminated with a newline.
If I save the coordinates of this file from the vmd main window and open the new file. vmd has inserted an extra newline between each atom entry (see below). My first thought was the file format was not unix and so I tested that hypothesis with the file, od, cat commands.

Any pointers?
Brian Bennion

temp1.pdb
CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 N GLU X 1 -31.127 -0.715 24.563 1.00 0.00 HUM
ATOM 2 HT1 GLU X 1 -30.703 0.129 24.999 1.00 0.00 HUM
ATOM 3 HT2 GLU X 1 -30.861 -0.705 23.558 1.00 0.00 HUM
ATOM 4 HT3 GLU X 1 -30.654 -1.575 24.907 1.00 0.00 HUM
ATOM 5 CA GLU X 1 -32.554 -0.954 24.872 1.00 0.00 HUM
ATOM 6 HA GLU X 1 -32.823 -1.991 24.736 1.00 0.00 HUM
ATOM 7 CB GLU X 1 -32.712 -0.797 26.494 1.00 0.00 HUM
ATOM 8 HB1 GLU X 1 -32.548 0.267 26.767 1.00 0.00 HUM
ATOM 9 HB2 GLU X 1 -33.769 -1.014 26.761 1.00 0.00 HUM
ATOM 10 CG GLU X 1 -31.731 -1.585 27.351 1.00 0.00 HUM
ATOM 11 HG1 GLU X 1 -30.733 -1.111 27.464 1.00 0.00 HUM
ATOM 12 HG2 GLU X 1 -32.211 -1.699 28.345 1.00 0.00 HUM
ATOM 13 CD GLU X 1 -31.388 -2.971 26.888 1.00 0.00 HUM
ATOM 14 OE1 GLU X 1 -31.976 -3.851 27.516 1.00 0.00 HUM
ATOM 15 OE2 GLU X 1 -30.673 -3.157 25.918 1.00 0.00 HUM
ATOM 16 C GLU X 1 -33.612 0.008 24.212 1.00 0.00 HUM
ATOM 17 O GLU X 1 -34.321 -0.452 23.324 1.00 0.00 HUM
ATOM 18 N GLY X 2 -33.722 1.325 24.747 1.00 0.00 HUM
ATOM 19 HN GLY X 2 -32.992 1.650 25.341 1.00 0.00 HUM
ATOM 20 CA GLY X 2 -34.600 2.189 24.097 1.00 0.00 HUM
ATOM 21 HA1 GLY X 2 -35.333 2.510 24.824 1.00 0.00 HUM
ATOM 22 HA2 GLY X 2 -35.105 1.753 23.248 1.00 0.00 HUM
ATOM 23 C GLY X 2 -33.853 3.414 23.534 1.00 0.00 HUM
ATOM 24 O GLY X 2 -34.481 4.500 23.388 1.00 0.00 HUM

temp2.pdb
CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 N GLU X 1 -31.127 -0.715 24.563 1.00 0.00 HUM
  
ATOM 2 HT1 GLU X 1 -30.703 0.129 24.999 1.00 0.00 HUM
  
ATOM 3 HT2 GLU X 1 -30.861 -0.705 23.558 1.00 0.00 HUM
  
ATOM 4 HT3 GLU X 1 -30.654 -1.575 24.907 1.00 0.00 HUM
  
ATOM 5 CA GLU X 1 -32.554 -0.954 24.872 1.00 0.00 HUM
  
ATOM 6 HA GLU X 1 -32.823 -1.991 24.736 1.00 0.00 HUM
  
ATOM 7 CB GLU X 1 -32.712 -0.797 26.494 1.00 0.00 HUM
  
ATOM 8 HB1 GLU X 1 -32.548 0.267 26.767 1.00 0.00 HUM
  
ATOM 9 HB2 GLU X 1 -33.769 -1.014 26.761 1.00 0.00 HUM
  
ATOM 10 CG GLU X 1 -31.731 -1.585 27.351 1.00 0.00 HUM
  
ATOM 11 HG1 GLU X 1 -30.733 -1.111 27.464 1.00 0.00 HUM
  
ATOM 12 HG2 GLU X 1 -32.211 -1.699 28.345 1.00 0.00 HUM
  
ATOM 13 CD GLU X 1 -31.388 -2.971 26.888 1.00 0.00 HUM
  
ATOM 14 OE1 GLU X 1 -31.976 -3.851 27.516 1.00 0.00 HUM
  
ATOM 15 OE2 GLU X 1 -30.673 -3.157 25.918 1.00 0.00 HUM
  
ATOM 16 C GLU X 1 -33.612 0.008 24.212 1.00 0.00 HUM
  
ATOM 17 O GLU X 1 -34.321 -0.452 23.324 1.00 0.00 HUM
  
ATOM 18 N GLY X 2 -33.722 1.325 24.747 1.00 0.00 HUM
  
ATOM 19 HN GLY X 2 -32.992 1.650 25.341 1.00 0.00 HUM
  
ATOM 20 CA GLY X 2 -34.600 2.189 24.097 1.00 0.00 HUM
  
ATOM 21 HA1 GLY X 2 -35.333 2.510 24.824 1.00 0.00 HUM
  
ATOM 22 HA2 GLY X 2 -35.105 1.753 23.248 1.00 0.00 HUM
  
ATOM 23 C GLY X 2 -33.853 3.414 23.534 1.00 0.00 HUM
  
ATOM 24 O GLY X 2 -34.481 4.500 23.388 1.00 0.00 HUM
  
END