VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 16 2012 - 15:51:08 CST

Brian,
  Can you tell me precisely how both of these files were generated?
(what commands you used etc)
When I load an arbitrary file of my own and write it back out as a
PDB, I do not have this problem.

Cheers,
  John

On Thu, Feb 16, 2012 at 12:49:06PM -0800, Bennion, Brian wrote:
> 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 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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