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Hi 

I have had a further dig around on this and am pretty sure that they most probably don’t come from dangle unless you have run dangle on your system

it appears that the vanilla code without a dangle run uses ccpnmr/analysis/core/ChemicalShiftBasic.py makeRandomCoilShiftList(molSystems) in the python code

This devolves down to  ccpnmr/analysis/core/MoleculeBasic.py def getRandomCoilShiftCorrectionsDict():

which cites 

  Citation

  Schwarzinger, S., Kroon, G. J. A., Foss, T. R., Chung, J., Wright, P. E., Dyson, H. J.
  "Sequence-Dependent Correlation of Random Coil NMR Chemical Shifts",
  J. Am. Chem. Soc. 123, 2970-2978 (2001)

  Values obtained from a GGXGG sequence pentapeptide.

also in ./python/ccpnmr/analysis/popups/SecStructureGraph.py which is the code for the secondary structure graph there is the following comment on the class  SecStructureGraphPopup(BasePopup):

**Display NMR Evidence for Protein Secondary Structure**

  This popup window is designed to collect together several kinds of NMR derived
  information to give a visual representation of evidence to indicate the
  regions of a protein chain with secondary structure, and what that structure
  might be. This system collects data from several sources from through-space
  (e.g. NOE) connectivity; from secondary chemical shifts; from a combined
  chemical shift index; from 3J H-Ha scalar couplings.

  The main chart lists the residue sequence of the selected chain (see
  "Options"), the predicted secondary structure of the residues and various
  types of evidence of the secondary structure. The "Sec Struc" column may be
  set manually based on the contents of the table via the [Set ...] buttons at
  the bottom, or automatically via a program like DANGLE_. In the table the
  eight through-space connectivity columns (d_aN i,i+1 to da_N i,i+2) are always
  displayed, but the other columns relating to chemical shift are optional and
  may be toggled via the top buttons. The connectivity columns are filled with a
  green colour if a given kind of connectivity is observed for a residue,
  additionally for the first three of these there is an extra distinction of
  strong (S) medium (M) and weak (W) categories. The name of a column indicates
  what kind of connectivity is present, for example d_aN i,i+1 represents the
  connection of an alpha position of one amino acid residue to the amide
  position of a residue one position further along (C-terminal) in the chain.

  The Delta-delta columns indicate secondary chemical shifts for Ca, Cb, C' and
  Ha atoms; the difference from recorded chemical shift to (sequence adjusted)
  random coil chemical shift. The random coil chemical shifts are calculated as
  specified in Schwarzinger et  al. as detailed below. These secondary chemical
  shifts are combined to give the CSI values (calculated according to the methods
  in the papers listed below) indicating the secondary structure type; -1
  indicates alpha-helix and +1 beta-strand. The last "3JHNHa" column lists any
  recorded scalar couplings between the amide and alpha hydrogens of a residue.
  These are indicative of the phi backbone angle, according to the Karplus
  relationship. These coupling values may be extracted and analysed in more
  detail using the Data Analysis : `3J H-Ha Coupling`_ system.

  The "Chart" tab shows a graphical representation of the secondary structure
  evidence data. This is the same data that is shown in the first table, it is
  merely presented differently, on a compact graphical form that may be printed
  out by making a PostScript file (right mouse menu). The order of the rows of
  data in the chart is the same order as the columns of the evidence table. The
  grey and white panels of the chart delineate the display into regions of ten
  residues. The text font used in the chart and the number or residues that
  are shown in a row, before the chart wraps back to start at the left again,
  are governed by settings in the last "Options Tab".
 are shown in a row, before the chart wraps back to start at the left again,
  are governed by settings in the last "Options Tab".

  The "Options" tab controls various aspects of how the data in the other tabs
  is displayed. The "Chain" naturally selects the sequence to use and "Shift
  List" is the source of the secondary chemical shift information. The "NOE
  Intensity Classes" section allows the user to set two values which distinguish
  between strong, medium and weak connection strength. Note that these values
  represent a peak intensity relative to the average in the peak list containing
  the connection. The lower table lists the peak lists that are used as sources
  of through-space connectivity information. The use can toggle to consider or
  reject particular peak lists by double clicking in the "Consider?" column. Any
  changes to any of these settings will be reflected one the user selects one
  of the first two tabs.

  **Caveats & Tips**

  The most accurate secondary structure prediction currently available in
  CCPN comes from the embedded DANGLE_ program. Although DANGLE has a separate
  graphical interface its secondary structure predictions, if committed, will be
  visible in this system via the displayed secondary structure classification.

  Regions of a polypeptide backbone with stable secondary structure will tend to
  show more near-sequence ("short range") though-space connectivities than
  unstructured, flexible  regions; commonly termini and loops. Naturally
  alpha-helices will tend to show i to i+3 and i to i+4 connections, due to the
  periodicity of the helix. Beta strand regions will often show i to i+2
  connectivity by lack i to i+3 and i to i+4, given that stands are extended
  conformations.

  **References**

  Secondary chemical shifts:

  *Schwarzinger, S., Kroon, G. J. A., Foss, T. R., Chung, J., Wright, P. E., Dyson, H. J.
  "Sequence-Dependent Correlation of Random Coil NMR Chemical Shifts",
  J. Am. Chem. Soc. 123, 2970-2978 (2001)*

  Chemical Shift Index

  *Wishart DS, Sykes BD.
  The 13C chemical-shift index: a simple method for the identification of protein
  secondary structure using 13C chemical-shift data.
  J Biomol NMR. 1994 Mar;4(2):171-80.*

  *Wishart DS, Sykes BD, Richards FM.
  The chemical shift index: a fast and simple method for the assignment of protein
  secondary structure through NMR spectroscopy.
  Biochemistry. 1992 Feb 18;31(6):1647-51.*

  .. _DANGLE: DanglePopup.html
  .. _`3J H-Ha Coupling`: CalcHnHaCouplingPopup.html


This also suggest that dangle would be a lot better. I am not sure either of these are state of the art any more and I would most probably use The Mulder method (https://pubs.acs.org/doi/abs/10.1021/ja105656t) excepting special circumstances 

I hope that helps…

regards
Gary

On 9 Jan 2019, at 00:00, CCPNMR automatic digest system <[log in to unmask]> wrote:

There are 4 messages totaling 644 lines in this issue.

Topics of the day:

 1. Secondary Structure Chart (3)
 2. Certificate Verify Issue when Updating

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Date:    Tue, 8 Jan 2019 04:20:59 +0000
From:    Niko Loening <[log in to unmask]>
Subject: Secondary Structure Chart

Can somebody explain to me what values are used as the baseline for calculating the secondary chemical shifts for Cb's in the Secondary Structure Chart? The references in the documentation only refer to Ca/Co/N/HN/Ha chemical shifts. I've got a suspicion that the values that CCPN has, at least for proline, are incorrect.

In my case, I've got a (mostly) disordered protein with proline Cb shifts between 32.0 and 32.1 for the five prolines. These values are very close to the random coil chemical shift values reported by Wishart (J. Bionmr, 5 (1995) 67-81) and also very close to the BMRB average value (31.9 ppm). However, the secondary chemical shift reported by CCPN analysis is a whopping -2.7 for these residues. Other Cb shifts are not wildly off, so its not a referencing problem on my part, and I'm very sure these prolines are in the trans conformation based on their Cb and Cg shifts.

In fact, when I use CCPN to generate a set of predicted random coil chemical shifts (Data Analysis -> Measurement Lists -> Make Random Coil Chemical Shift List) I find that the resulting list seems to have some rather different values for the following residues compared to the results published by Wishart in 1995.

Asp (Co, Ca, and Cb)
Glu (Cb and maybe Co)
Gly (Co)
Pro (Co and Cb)

There also might be deviations for Cys, Phe, Tyr, and Thr but my protein doesn't have those amino acids so I couldn't check them easily. Of course, things have progressed in the 20 years since Wishart published his results so CCPN might be using newer data or a more sophisticated algorithm. But, based on what I'm seeing, I still think there are some mistakes in CCPN's data.

So, what algorithm is CCPN using to predict random coil chemical shifts? Is there a way to correct this?

Thanks,

Niko Loening

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Date:    Tue, 8 Jan 2019 14:58:26 +0100
From:    John Kirkpatrick <[log in to unmask]>
Subject: Re: Secondary Structure Chart

Hi Niko,

I was a bit curious about this, so I had a dig around.  It seems that the 
random-coil shifts (and secondary-structure shifts) are coming from the DANGLE 
code, which is using random-coil shifts from J. Biomol. NMR 18, 43-48 (2000). 
These were measured in 8 M urea at pH 2, so I suspect the low pH accounts for the 
big discrepancies for Glu and Asp (I also see similar differences).  For the 
proline Cb, it looks as if it is the random-coil shift for the cis geometry (34.8 
ppm) that is being used rather than that for the trans (32.22 ppm); I guess this 
means there could be a bug somewhere, since both the cis and trans values are 
present in the reference table.

Cheers
John


On 08/01/2019 05:20, Niko Loening wrote:
Can somebody explain to me what values are used as the baseline for
calculating the secondary chemical shifts for Cb's in the Secondary Structure
Chart? The references in the documentation only refer to Ca/Co/N/HN/Ha
chemical shifts. I've got a suspicion that the values that CCPN has, at least
for proline, are incorrect.

In my case, I've got a (mostly) disordered protein with proline Cb shifts
between 32.0 and 32.1 for the five prolines. These values are very close to
the random coil chemical shift values reported by Wishart (J. Bionmr, 5 (1995)
67-81) and also very close to the BMRB average value (31.9 ppm). However, the
secondary chemical shift reported by CCPN analysis is a whopping -2.7 for
these residues. Other Cb shifts are not wildly off, so its not a referencing
problem on my part, and I'm very sure these prolines are in the trans
conformation based on their Cb and Cg shifts.

In fact, when I use CCPN to generate a set of predicted random coil chemical
shifts (Data Analysis -> Measurement Lists -> Make Random Coil Chemical Shift
List) I find that the resulting list seems to have some rather different
values for the following residues compared to the results published by Wishart
in 1995.

Asp (Co, Ca, and Cb) Glu (Cb and maybe Co) Gly (Co) Pro (Co and Cb)

There also might be deviations for Cys, Phe, Tyr, and Thr but my protein
doesn't have those amino acids so I couldn't check them easily. Of course,
things have progressed in the 20 years since Wishart published his results so
CCPN might be using newer data or a more sophisticated algorithm. But, based
on what I'm seeing, I still think there are some mistakes in CCPN's data.

So, what algorithm is CCPN using to predict random coil chemical shifts? Is
there a way to correct this?

Thanks,

Niko Loening

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Date:    Tue, 8 Jan 2019 17:08:19 +0000
From:    Wayne Boucher <[log in to unmask]>
Subject: Re: Secondary Structure Chart

Indeed, the code is using the “BMRB” “reference” data in data/ccp/nmr/NmrReference directory to determine the random coil values. I’ve asked Tim if he remembers where those come from.

Wayne

On 8 Jan 2019, at 13:58, John Kirkpatrick <[log in to unmask]> wrote:

Hi Niko,

I was a bit curious about this, so I had a dig around.  It seems that the random-coil shifts (and secondary-structure shifts) are coming from the DANGLE code, which is using random-coil shifts from J. Biomol. NMR 18, 43-48 (2000). These were measured in 8 M urea at pH 2, so I suspect the low pH accounts for the big discrepancies for Glu and Asp (I also see similar differences).  For the proline Cb, it looks as if it is the random-coil shift for the cis geometry (34.8 ppm) that is being used rather than that for the trans (32.22 ppm); I guess this means there could be a bug somewhere, since both the cis and trans values are present in the reference table.

Cheers
John


On 08/01/2019 05:20, Niko Loening wrote:
Can somebody explain to me what values are used as the baseline for
calculating the secondary chemical shifts for Cb's in the Secondary Structure
Chart? The references in the documentation only refer to Ca/Co/N/HN/Ha
chemical shifts. I've got a suspicion that the values that CCPN has, at least
for proline, are incorrect.
In my case, I've got a (mostly) disordered protein with proline Cb shifts
between 32.0 and 32.1 for the five prolines. These values are very close to
the random coil chemical shift values reported by Wishart (J. Bionmr, 5 (1995)
67-81) and also very close to the BMRB average value (31.9 ppm). However, the
secondary chemical shift reported by CCPN analysis is a whopping -2.7 for
these residues. Other Cb shifts are not wildly off, so its not a referencing
problem on my part, and I'm very sure these prolines are in the trans
conformation based on their Cb and Cg shifts.
In fact, when I use CCPN to generate a set of predicted random coil chemical
shifts (Data Analysis -> Measurement Lists -> Make Random Coil Chemical Shift
List) I find that the resulting list seems to have some rather different
values for the following residues compared to the results published by Wishart
in 1995.
Asp (Co, Ca, and Cb) Glu (Cb and maybe Co) Gly (Co) Pro (Co and Cb)
There also might be deviations for Cys, Phe, Tyr, and Thr but my protein
doesn't have those amino acids so I couldn't check them easily. Of course,
things have progressed in the 20 years since Wishart published his results so
CCPN might be using newer data or a more sophisticated algorithm. But, based
on what I'm seeing, I still think there are some mistakes in CCPN's data.
So, what algorithm is CCPN using to predict random coil chemical shifts? Is
there a way to correct this?
Thanks,
Niko Loening
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Date:    Tue, 8 Jan 2019 12:57:31 -0700
From:    Leanna Marquart <[log in to unmask]>
Subject: Re: Certificate Verify Issue when Updating

Hi Edward,

Was there ever a fix for this license issue?
Lisa and I never got it working after all this time.

Thanks for your help,
Leanna

————————
Leanna Marquart
M.S. Student
Chemistry Department
Boise State University




On Nov 29, 2018, at 4:28 AM, Micael Silva <[log in to unmask]> wrote:

Hello Edward,

I am currently user of CcpNmr v2.4 and for assignment purposes, I am trying to install the CcpNmr v3.0.b2 (MacOS X)

Thanks for the fix for certificate error, indeed the update worked. However I have the same error as Lisa: 

ERROR: invalid licence for Analysis-V3 version number "3.0.b2"

Can you send me new licence?  The available one (in the website) is only until April 2018.

Micael Silva
PhD Student
(Bio)Structure and Interactions by NMR
NOVA University of Lisbon

****
Micael Simões Silva
MolBioS PhD Student ITQB - UNL
(Bio) Molecular Structure and Interactions by NMR Group UCIBIO@REQUIMTE
Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa
2829-516 Caparica, Portugal
Institutional E-mail: [log in to unmask] <mailto:[log in to unmask]>
Website: http://www.linkedin.com/in/micaels <http://www.linkedin.com/in/micaels>
De: CcpNmr software mailing list <[log in to unmask] <mailto:[log in to unmask]>> em nome de Lisa Warner <[log in to unmask] <mailto:[log in to unmask]>>
Enviado: 7 de novembro de 2018 22:35
Para: [log in to unmask]
Assunto: Re: Certificate Verify Issue when Updating

Hi Ed,

Thanks for all your help. Leanna and I both have tried the FixCertificateUpdate.tar with or without Licence3.0.b3.tar and we still end up with the same error message:

ERROR: invalid licence for Analysis-V3 version number "3.0.b2"
Aborting program

We were curious about .b2 vs. .b3?


Thanks -- Lisa 

On Tue, Nov 6, 2018 at 3:09 AM Edward Brooksbank <[log in to unmask] <mailto:[log in to unmask]>> wrote:
Hello Leanna,

sorry to everyone for the problems.

Please find attached a fix for the certificate errors, this is due in part to the migration to a new server.

Copy the file to the root of your install, possibly /AnalysisV3 or /ccpnmr_v3
and untar with:

tar xzf FixCertificateUpdate.tgz

Regards
Ed

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