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 torsion angles phi,psi that place it in the Ramachandran
plot in the area known as helix.
However, if you look at a Ramachandran plot, you see that most residues
are in the so called alpha helix, beta strand, or left-handed alpha
helix regions. Actually, the percentage of residues that falls in these
areas is the basis of the second oldest protein structure validation
method. But on average almost half of all residues are in a loop. So
where is the loop area in the Ramachandran plot? Well, there is no such
area as residues in a loop tend to have in irregular succession of helix
and strand torsion angles. So, if the torsion angles seem to suggest
HHSHHHSSH then actually, we have a loop.
Due to the cooperativity of the hydrogenbonding patterns in regular
secondary structure elements the torsion angles for a
Ramachandran-helical residue are not the same when the residue is in a
helix or in a loop, but those are details for the validation people, and
will not displace the cross in the Ramachandran plot too much.
If you are interested in the secondary structure assignments, use DSSP.
We made it open source and gave it to CCP4 already a while ago, so
everybody can use it. DSSP has so its issues, but as everybody uses it,
these issues are known, and softwares for which they are critical deal
with those issues properly, normally.
Gert
On 03/24/2017 09:24 PM, Pavel Afonine wrote:
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 from_ca cablam
I suggest you please with them and see which one suits you most.
Pavel
On Fri, Mar 24, 2017 at 1:18 PM, Xiao Lei <xiaolei...@gmail.com
<mailto:xiaolei...@gmail.com>> wrote:
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 1:09 PM, Pavel Afonine <pafon...@gmail.com
<mailto:pafon...@gmail.com>> wrote:
Trivial using command line. Example:
- get a file from PDB:
phenix.fetch_pdb 1yjp
- get all phi/psi for all residues:
phenix.ramalyze 1yjp.pdb
residue:score%:phi:psi:evaluation:type
A 2 ASN:56.93:-60.58:141.19:Favored:General
A 3 ASN:48.44:-119.25:125.15:Favored:General
A 4 GLN:16.23:-126.16:112.81:Favored:General
A 5 GLN:55.13:-114.98:126.76:Favored:General
A 6 ASN:6.17:-116.42:97.69:Favored:General
SUMMARY: 5 Favored, 0 Allowed, 0 Outlier out of 5 residues
(altloc A where applicable)
SUMMARY: 0.00% outliers (Goal: < 0.2%)
SUMMARY: 100.00% favored (Goal: > 98%)
Pavel
On Fri, Mar 24, 2017 at 10:37 AM, Nigel Moriarty
<nwmoria...@lbl.gov <mailto:nwmoria...@lbl.gov>> wrote:
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 the residues in Coot.
Happen to help further on the PHENIXBB or off-line.
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated
Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 <tel:%28510%29%20486-5709> Email :
nwmoria...@lbl.gov
Fax : 510-486-5909 <tel:%28510%29%20486-5909> Web
: CCI.LBL.gov <http://CCI.LBL.gov>
On Thu, Mar 23, 2017 at 8:39 PM, Alex Lee
<alexlee198...@gmail.com <mailto:alexlee198...@gmail.com>>
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 "residue info" in coot,
it tells Ramachandran "phi psi" angles of individual
residue, but it does not show it in a plot, only numbers.
Thanks ahead for any input.
