[gmx-users] Average and bfactors.pdb

[Justin Lemkul]

On 8/20/17 11:51 AM, farial tavakoli wrote:
>   blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; }  Dear gmx users
> I removed jumps from my .xtc file before by using gmx trjconv and viewed my complex in vmd, it was ok and rhere was no jump. Now i use gmx rmsf and the same .xtc file which was created after using gmx trjconv, but when i view average. Pdb and bfactors.pdb files in pymol, my protein is still brocken. Would you please advice me how to solve this problem?

There is no physical significance to an average set of coordinates.  These may 
appear broken or distorted.

http://www.gromacs.org/Documentation/Terminology/Average_Structure

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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