Re: exportRe: export|
Hi, the PDC was intended for proteins only so far. Furthermore the assumption was that peak are related to some ordinal number. e.g. the residue number. The user has no format restrictions in giving peak names. On the other side, if peak names contain a number the PDC extracts the number and uses it for example to generate the histogram display, say T1 vs. sequence. If the user provides false annotations the histogram generation will fail. In the example I have sent the peaks came from TopSpin, someone did the annotation there. I personally annotate like ALA-4 but others do lile ALA [4] or ALA/4. The PDC can also read annotation from BMRB or XEASY peaklist files. As it comes to to areas in the PDC where the PDB file is utilized, e.g. display of T1 on the 3D structure it is assumed that the annotation fits to the PDB file. A mapping of names as you describe is not done in the PDC. If you prefer a certain type of annotation we can at least suggest this to the user. Best regads, Peter On 1/25/2011 3:41 PM, Edward d'Auvergne wrote: 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. 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