Dear Edward,
I'm back in the office, let me now reply to the various points:
Used integrals: The PDC offers 4 options. These are (and written
like this into the output):
- peak intensities
- area integral
- peak shape integral
- deconvoluted peak integral (x) where x is: lorentzian or gaussian
or fixed gauss/lorentz or variable gauss/lorentz
"peak volumes" ? Was this used in one of the older output files ?
Default values: I'm not quite sure what you mean. The PDC has
default values for all settings. The the TopSpin
parameter files of the spectra are read and information is taken
from there if available. Then The user gets
everything on display and can change. Whatever he does latest,
counts and is save if the user uses the save option.
However, at the very end I do not check whether the settings
correspond to the default values or not and I do not
indicate this in the export. I think noe of the Bruker software does
something like this.
Concerning the peaks used there are various options like
- automatically picked peaks
- peaks from peaklist.xml at spectrum
- peaks from xxxx where xxx is a peaklist.xml of any other spectrum
Peak positions/annotations can be done/modified in the PDC but
initially the ones contained in the loaded
peaklist.xml are used. These files also contain a tag for 'type'
which can be one out of seven types (auto,
manual, etc.). I have not imported all this information into the PDC
since I assumed the peaklists are deposit
separately into BMRB. If the user modifies peaks in the PDC he can
update peaklist.xml on disk.
PDC info: I would guess (tentatively) it should read like:
# Protein Dynamics Center software.
SOFTWARE['rotein Dynamics Center'] = ?? // this I don't understand this field
SOFTWARE['rotein Dynamics Center'].name = "Protein Dynamics Center"
SOFTWARE['rotein Dynamics Center'].authors = "Bruker BioSpin GmbH"
SOFTWARE['rotein Dynamics Center'].url = "" class="moz-txt-link-rfc2396E" href="http://www.bruker-biospin.com">"http://www.bruker-biospin.com"
SOFTWARE['rotein Dynamics Center'].tasks = ["relaxation analysis"]
Best regards,
Peter
On 2/18/2011 10:38 AM, Edward d'Auvergne wrote:
Hi,
I've just about finished implementing the Bruker Protein Dynamic
Centre (PDC) file reading and had a few questions. The first is for
peak height vs. peak volume. Am I correct to assume that the 2
entries in the PDC file are:
Used integrals: peak intensities
Used integrals: peak volumes
Would you also have a list of default values for the PDC file? How
can I differentiate between user who has properly entered the
experimental info vs. someone who is slack and has left everything to
the default values? I would like to read the info for BMRB deposition
only if the user has set it.
As for the spectrum name, this is not needed for relax or the
subsequent BMRB deposition. Another thing for BMRB deposition is that
I can have the PDC software info added automatically to the NMR-STAR
file. For this I would need to add some information. For example for
relax, we have the code:
# relax software.
SOFTWARE['relax'] = Software_store()
SOFTWARE['relax'].name = "relax"
SOFTWARE['relax'].authors = "The relax development team"
SOFTWARE['relax'].url = "" class="moz-txt-link-rfc2396E" href="http://nmr-relax.com">"http://nmr-relax.com"
SOFTWARE['relax'].tasks = ["data processing"]
Would you have a preference for the name, authors, url, and task name?
The software can also be associated with a reference which will be
added to the BMRB, if you have one for the PDC.
Cheers,
Edward
On 29 January 2011 06:20, Neidig, Klaus-Peter
<Klaus-Peter.Neidig@xxxxxxxxxxxxxxxxx> wrote:
Hi Michael,
good point. Yes, the PDC reads a sequence file if available (needed for display purposes)
This, including the sequence itself is contained in the sample section.
The PDC also reads a PDB file that includes protons. It is needed to calculate the diffusion tensor
and it is optionally used for display purposes. I will add the name of the pdb file to the sample section
Actually, the spectrum name is also not contained in the output. Should I add that as well ?
Alternatively, I could add the name of the PDC project file. This is a xml file containing everyting that
is relevant as part of a project. So far, in the header section, I only mention the name of a method/project.
However, the project file is only available if the user stored his work as a project which is optional.
Best regards,
Peter
PS: We see on TV that after the big flood in Queensland there now also a lot of water in Victoria. I hope
you are not affected.
Dr. Klaus-Peter Neidig
Software Development / Head of Analysis Group
Bruker BioSpin GmbH
Silberstreifen
76287 Rheinstetten, Germany
Phone: +49 721 5161-6447
Fax: +49 721 5161-6480
Peter.Neidig@xxxxxxxxxxxxxxxxx
www.bruker.com
Bruker BioSpin GmbH: Sitz der Gesellschaft/Registered Office: Rheinstetten, HRB 102368 Amtsgericht Mannheim
Geschäftsführer/Managing Directors: Jörg Laukien, Dr. Bernd Gewiese, Dr. Gerhard Roth
Diese E-Mail und alle Anlagen können Betriebs- oder Geschäftsgeheimnisse, oder sonstige vertrauliche Informationen enthalten. Sollten Sie diese E-Mail irrtümlich erhalten haben, ist Ihnen eine Kenntnisnahme des Inhalts, eine Vervielfältigung oder Weitergabe der E-Mail und aller Anlagen ausdrücklich untersagt. Bitte benachrichtigen Sie den Absender und löschen/vernichten Sie die empfangene E-Mail und alle Anlagen. Vielen Dank.
This message and any attachments may contain trade secrets or privileged, undisclosed or otherwise confidential information. If you have received this e-mail in error, you are hereby notified that any review, copying or distribution of it and its attachments is strictly prohibited. Please inform the sender immediately and delete/destroy the original message and any copies. Thank you.
________________________________________
From: Michael Bieri [michael.bieri@xxxxxxxxxxxxx]
Sent: Saturday, January 29, 2011 1:00 AM
To: Edward d'Auvergne
Cc: Neidig, Klaus-Peter; Neidig, Klaus-Peter; relax-devel@xxxxxxx
Subject: Re: export
Hi
I think there is everything we will need. The important parameters
(x-nucleus, spectrometer frequencies) are given. I also think that the
fact that PDC is for proteins only facilitates the import (as the
assignment is the residue number).
Peter, do you use a structure file for the calculations? If so, it would
be nice to store the PDB identifier and relax can automatically download
it from the net (or find it on the hard drive).
The rest will be straight forward.
Cheers
Michael
Am 26.01.2011 01:41, schrieb Edward d'Auvergne:
Hi,
Thanks. This is looking pretty good, and the version number should
really help with any future changes and automatic parsing of the
files. Michael, can you see anything missing or that would be useful
to have in the PDC file?
The only thing that still worries me a little is the name of the
peaks. Is this a free format? For example, what if a user would like
to use the Trp side chain NH data as well? Or if a natural abundance
13C relaxation data set is collected? Or what do RNA/DNA people, or
even small molecule people, do? In relax we will need to match what is
in the PDC file into some 'spin sequence' consisting of hierarchies of
molecules, residues, and spins that the user defines through a
sequence file or PDB file. So this might be the hardest part to
implement in reading the PDC file.
Cheers,
Edward
P.S. It's better to attach files to the task (http://gna.org/task/?7180).
On 25 January 2011 14:44, Dr. Klaus-Peter Neidig
<peter.neidig@xxxxxxxxxxxxxxxxx> wrote:
Hi,
in the mean I have made a few small changes to the PDC export, e.g. I added a version ID
which allows you to check it. Below I have made a little document and also attached a sample
T1 export file.
Maybe you can have a look at it and comment on it if needed. We can still add more changes.
I plan a PDC 1.1.5 within the next 2-3 weeks that should include the changes. Form then on it
should stay constant as long as possible.
Best regards,
Peter
On 1/11/2011 4:13 PM, Edward d'Auvergne wrote:
Happy new year!
The reading of the PDC files is not implement yet as we had to work
out which sections and information were required. Now that most
things are sorted out for the relaxation times with the error scaling,
time to rate conversion, etc., relax will most likely just read this
section. I.e. walk to the results 'SECTION" and then read that
converting to relaxation rates and removing the scaling. How is the
peak name defined though? What about side chain TRP NH peaks? This
should not take long at all, though Michael and I are quite busy
finishing the relax GUI at the moment. Additional information would
be parsed from the PDC header and 'sample information' section. I'll
answer more of your questions below:
On 24 December 2010 07:58, Dr. Klaus-Peter Neidig
<peter.neidig@xxxxxxxxxxxxxxxxx> wrote:
Dear Edward& Michael,
I wish you some nice holidays and a good start into the new year.
The last time I had sent you examples of the PDC ouput. I would assume that you can easily
read it via Python and that your Python programs are flexible. I will make sure that the format
stays in its essential components, i.e. values are tab separated and the sections start with
the keywords used so far.
May I ask if you in what detail you read other keywords ?
Example:
The section with the integrals looks like:
SECTION: used integrals
Mixing time [s]: 0.01 0.03 .........
Would you suffer if I changed Mixing time into Mixing times ? Or do you just read a token up to : ?
We wouldn't need to read this section in relax as we know how to
convert the relaxation values and errors to the correct form. But to
find the relevant data, a fixed tag name would be useful. relax would
be able to handle changes, as long as the PDC file has version
information in it and the change occurs between different versions.
Then we can search for 'Mixing time [s]' in version 'x' and 'Mixing
times' in version 'y'.
The reason why I'm asking that someone looked through export and report and found such minor
differences. Other examples are that in between the tab separated title lines of the tables, e.g.
the title line Peak name F1[ppm] F2[ppm] .... sometimes additional spaces are contained,
sometimes 2, sometimes 3.
In relax, the amount of spacing does not matter. It should not matter
- the only case where it does is the retarded PDB format. Parsers
should be able to handle this if written properly, just split the line
up by whitespace.
Do you evaluate these title lines at all or just the relevant table that follows ?
This title line would be skipped. Can it be that the user can change
which columns are shown? For example can they rearrange these
columns, or say not show the F1 and F2 columns? If these columns are
variable, then we would have to read that line.
Early next year we should write down which parts of the output must no be changed by myself
to avoid conflicts.
It would be nice to have these files versioned so that automatic
parsers can handle any future changes. That would make things much
easier.
Cheers,
Edward
.
--
Dr. Klaus-Peter Neidig
Software Development / Head of Analysis Group
Bruker BioSpin GmbH
Silberstreifen
76287 Rheinstetten, Germany
Phone: +49 721 5161-6447
Fax: +49 721 5161-6480
Peter.Neidig@xxxxxxxxxxxxxxxxx
www.bruker.com
________________________________
Bruker BioSpin GmbH: Sitz der Gesellschaft/Registered Office: Rheinstetten, HRB 102368 Amtsgericht Mannheim
Geschäftsführer/Managing Directors: Jörg Laukien, Dr. Bernd Gewiese, Dr. Gerhard Roth
Diese E-Mail und alle Anlagen können Betriebs- oder Geschäftsgeheimnisse, oder sonstige vertrauliche Informationen enthalten. Sollten Sie diese E-Mail irrtümlich erhalten haben, ist Ihnen eine Kenntnisnahme des Inhalts, eine Vervielfältigung oder Weitergabe der E-Mail und aller Anlagen ausdrücklich untersagt. Bitte benachrichtigen Sie den Absender und löschen/vernichten Sie die empfangene E-Mail und alle Anlagen. Vielen Dank.
This message and any attachments may contain trade secrets or privileged, undisclosed or otherwise confidential information. If you have received this e-mail in error, you are hereby notified that any review, copying or distribution of it and its attachments is strictly prohibited. Please inform the sender immediately and delete/destroy the original message and any copies. Thank you.
.
--
|
Dr. Klaus-Peter
Neidig
Software Development / Head of Analysis
Group
|
Bruker
BioSpin GmbH
Silberstreifen
76287 Rheinstetten,
Germany
|
Phone:
+49
721 5161-6447
Fax:
+49 721 5161-6480
|
|
|
Bruker
BioSpin GmbH: Sitz der Gesellschaft/Registered Office:
Rheinstetten,
HRB 102368 Amtsgericht Mannheim
Geschäftsführer/Managing
Directors: Jörg Laukien, Dr. Bernd Gewiese, Dr.
Gerhard Roth
Diese
E-Mail und alle Anlagen können Betriebs- oder
Geschäftsgeheimnisse,
oder sonstige vertrauliche Informationen enthalten.
Sollten Sie diese
E-Mail irrtümlich erhalten haben, ist Ihnen eine
Kenntnisnahme des
Inhalts, eine Vervielfältigung oder Weitergabe der
E-Mail und aller
Anlagen ausdrücklich untersagt. Bitte benachrichtigen
Sie den Absender
und löschen/vernichten Sie die empfangene E-Mail und
alle Anlagen.
Vielen Dank.
This message and any attachments may contain trade
secrets or
privileged, undisclosed or otherwise confidential
information. If you
have received this e-mail in error, you are hereby
notified that any
review, copying or distribution of it and its
attachments is strictly
prohibited. Please inform the sender immediately and
delete/destroy the
original message and any copies.
Thank you. |
|
Re: export