Thanks!
On 03/25/2017 03:36 PM, Paul Emsley wrote:
On 24/03/2017 03:39, Alex Lee wrote:
Dear All,
Is there a tool or software which can give Ramachandran information of
individual residues
in a plot?
I used Coot to check for Ramachandran plots, but it shows all the residues in a
coordinate
On 24/03/2017 03:39, Alex Lee wrote:
Dear All,
Is there a tool or software which can give Ramachandran information of
individual residues
in a plot?
I used Coot to check for Ramachandran plots, but it shows all the residues in a
coordinate I
put in Coot, not individual one. I also use
On 25/03/2017 07:15, Pavel Afonine wrote:
Except that Procheck is now ages behind the standard, with Molprobity being the
standard.
I'm not sure even if Coot uses the latest libraries.
For the record, it doesn't (yet). If you want to be completely accurate, I recommend
Molprobity.
Paul.
Ls,
It is not possible to determine the secondary structure from the
position in the Ramachandran plot. For a residue to be helical, it must
have hydrogen bonds that correspond with a helix, and so need its
neighbours. If these conditions are met, a residue will by necessity
have backbone
Except that Procheck is now ages behind the standard, with Molprobity being
the standard. I'm not sure even if Coot uses the latest libraries. Those I
quoted in example below come from latest Molprobity (Phenix that is) and
are the latest.
Pavel
On Fri, Mar 24, 2017 at 2:55 PM, Edward A. Berry
On 03/23/2017 11:39 PM, Alex Lee wrote:
Dear All,
Is there a tool or software which can give Ramachandran information of
individual residues in a plot?
I used Coot to check for Ramachandran plots, but it shows all the residues in a coordinate I put in
Coot, not individual one. I also use
May be not exactly what you want, but should be close:
phenix.secondary_structure_restraints 1yjp.pdb
then here you have options
- for output format:
format = *phenix phenix_refine phenix_bonds pymol pdb refmac kinemage
- for search (annotation method):
search_method = *ksdssp mmtbx_dssp
Thanks Pavel, is there a command that can tell secondary structure
assignment based on Rama plot of each residue beside phi and psi? for
example :
A 2 ASN:56.93:-60.58:141.19:Favored:General alpha helix
A 3 ASN:48.44:-119.25:125.15:Favored:General alpha helix
On Fri, Mar 24, 2017 at
Alex
It seems that nobody has answered your question. I'm not sure what you can
do in CCP4, but if I understand your question correctly, you can perform a
comprehensive validation in Phenix complete with Ramachandran plot
including clickable points relating to your residues which allow you to see
Dear All,
Is there a tool or software which can give Ramachandran information of
individual residues in a plot?
I used Coot to check for Ramachandran plots, but it shows all the residues
in a coordinate I put in Coot, not individual one. I also use "residue
info" in coot, it tells Ramachandran
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