Hi Jiri,
I agree with Paul that you need to make sure these are actually wrong before "fixing" them. Definitely look at them in the context of the map for a start, and study their local environment remembering that cis-peptide bonds need to be quite strongly stabilised to become favourable. As a rough rule of thumb you'd expect both the hydrogen and oxygen in the peptide bond to be involved in good H-bonds, and/or lots of steric crowding acting to prevent the trans conformation. If neither criterion is met, I'd say it's most likely wrong.
VMD does have a plugin (accessible from the Modelling menu) that can check for and semi-automatically correct cis bonds. For each bond it will ask to to select either the hydrogen or the oxygen to move to the other side of the backbone, then run a brief NAMD energy minimisation of the local area to regularise the geometry.
If the cis bonds do turn out to be incorrect, though, I'd suggest you may have other things to worry about. What do the other stats (Ramachandran outliers, clashscore, sidechain outliers) look like? What sort of resolution are we talking about? If you have incorrect cis bonds, chances are there are other less-easily spotted problems that may mess with any simulation.
Best regards,
Tristan
Tristan Croll
Lecturer
Faculty of Health
School of Biomedical Sciences
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443
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> On 14 Jun 2016, at 3:29 AM, chemocev marker <[log in to unmask]> wrote:
>
> HI All
> 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.
>
> best
> Jiri
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