Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

[Edward A. Berry]

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 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.


Put this in your ~/.coot-preferences directory and when you want to Rama-check 
a residue,
bring it to the centre of the screen, click on Rama -> Rama Plot for this 
Residue.

Paul.

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

[Paul Emsley]

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 "residue info" in coot, it tells 
Ramachandran
"phi psi" angles of individual residue, but it does not show it in a plot, only 
numbers.


Put this in your ~/.coot-preferences directory and when you want to Rama-check a residue, 
bring it to the centre of the screen, click on Rama -> Rama Plot for this Residue.


Paul.


(if (defined? 'coot-main-menubar)
(let ((menu (coot-menubar-menu "Rama")))

  (add-simple-coot-menu-menuitem
   menu "Rama Plot for This Residue"
   (lambda ()
 (using-active-atom
  (let* ((sel-str (string-append "//" aa-chain-id "/"
 (number->string (- aa-res-no 1))
 "-"
 (number->string (+ aa-res-no 1
 (imol (new-molecule-by-atom-selection aa-imol sel-str)))
(do-ramachandran-plot imol)
(set-mol-displayed imol 0)
(set-mol-activeimol 0)))

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

[Paul Emsley]

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.

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

[Gert Vriend]

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 > 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 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
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 Email :
nwmoria...@lbl.gov
Fax   : 510-486-5909   Web 
: CCI.LBL.gov 


On Thu, Mar 23, 2017 at 8:39 PM, Alex Lee
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.

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

[Pavel Afonine]

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  wrote:

> 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
>> "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.
>>
>> Well, you can always AWK out 3 residues and run procheck on them,
> something like:
>
>   awk '$1~/ATOM/ && $5~/B/ && $6~/^6[567]/' /a/pdb/pdb2h88.ent >w.pdb
>   procheck w.pdb 1.8
> followed by:
>   gs w_01.ps
> or:
>   ps2pdf w_01.ps
>   acroread !$
>
> (The AWK command will have to be tweaked if fields run together in the
>   pdb due to large numbers or alt. conformations for these three residues)
>
> I agree such a feature would be useful in coot. Sometimes you want to
> know if an outlier is just outside or way outside, or if it is halfway
> between two allowed regions, and with large, low-quality structures it is
>  hard to find the residue in the crowded rama plot.
> Clickable points in the R plot fills the bill going one way, now
> highlighting
> points corresponding to selected residue would be the other half.
> eab
>

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

[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 "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.


Well, you can always AWK out 3 residues and run procheck on them,
something like:

  awk '$1~/ATOM/ && $5~/B/ && $6~/^6[567]/' /a/pdb/pdb2h88.ent >w.pdb
  procheck w.pdb 1.8
followed by:
  gs w_01.ps
or:
  ps2pdf w_01.ps
  acroread !$

(The AWK command will have to be tweaked if fields run together in the
  pdb due to large numbers or alt. conformations for these three residues)

I agree such a feature would be useful in coot. Sometimes you want to
know if an outlier is just outside or way outside, or if it is halfway
between two allowed regions, and with large, low-quality structures it is
 hard to find the residue in the crowded rama plot.
Clickable points in the R plot fills the bill going one way, now highlighting
points corresponding to selected residue would be the other half.
eab


w_01.pdf
Description: Adobe PDF document

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

[Pavel Afonine]

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  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  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 
>> 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 <(510)%20486-5709> Email : nwmoria...@lbl.gov
>>> Fax   : 510-486-5909 <(510)%20486-5909>   Web  : CCI.LBL.gov
>>>
>>> On Thu, Mar 23, 2017 at 8:39 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
 "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.


>>>
>>
>

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

[Xiao Lei]

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  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 
> 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 <(510)%20486-5709> Email : nwmoria...@lbl.gov
>> Fax   : 510-486-5909 <(510)%20486-5909>   Web  : CCI.LBL.gov
>>
>> On Thu, Mar 23, 2017 at 8:39 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
>>> "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.
>>>
>>>
>>
>

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

[Pavel Afonine]

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  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 <(510)%20486-5709> Email : nwmoria...@lbl.gov
> Fax   : 510-486-5909 <(510)%20486-5909>   Web  : CCI.LBL.gov
>
> On Thu, Mar 23, 2017 at 8:39 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
>> "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.
>>
>>
>

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

[Nigel Moriarty]

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 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909   Web  : CCI.LBL.gov

On Thu, Mar 23, 2017 at 8:39 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 "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.
>
>

[ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

[Alex Lee]

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.