On 13/06/16 18:29, chemocev marker wrote:
> HI All
Hello.
> I have some residues in my x-ray structure with the high B-value and
> they make cis peptide. Is there is option either in Pymol or in VMD
> viewer to correct them automatically if I want to use the X-ray
> structure for input in simulations experiment.
Do I take it from this that you think these cis-peptides are wrong? What
makes you think so? I doubt that any program will automatically convert
cis-peptides to trans-peptides. Might you consider a non-automatic
solution that is not PyMOL or VMD?
Paul.
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