Hi, The script you use is trying to extract the atom with the name 'H' from the file. You will not find this for GLY1. This PDB file has atoms H1, H2, H3, etc, but no 'H'. Therefore you won't be able to define the N-H bond in this way. Also note that the nitrogen is not in a peptide bond, and will therefore likely to be charged and carry 2 protons. In water these protons will be exchanging very quickly and hence will be invisible in most systems.
Regards, Edward On 2 April 2013 16:18, <[email protected]> wrote: > Hi Edward, > > Thank you very much. I am a little bit confused, the pdb file > 2QFK_MONOMERHabc5.pdb have been added H by software reduce, I also check the > first residue GLY, which has 5 H atoms. Perhaps I misunderstand your > meanings, do you mean the 2QFK_MONOMERHabc5.pdb file (I have submitted > before)? Thank you. > > > Regards, > > Mengjun > > > Quoting Edward d'Auvergne <[email protected]>: > >> Hi Mengjun, >> >> This bug has now been fixed. The problem was with the very first >> residue, as the PDB file has no H atom for it. Normally this is not >> an issue because the first atom should normally not be visible in a >> nitrogen HSQC. So there are 3 ways of fixing the problem. You could >> wait until a new version of relax is released, though this could take >> a while as the next version will be the first of a brand new 3.0 >> release series. Alternatively you can check out a copy of the relax >> trunk as described in the docs >> (http://www.nmr-relax.com/manual/Latest_sources_relax_repositories.html). >> Or thirdly, you can deselect your first residue. >> >> Regards, >> >> Edward >> >> >> >> On 29 March 2013 18:03, <[email protected]> wrote: >>> >>> Hi Edward, >>> >>> Thank you so much for your suggestions. I will read it carefully. >>> >>> >>> Regards, >>> >>> Mengjun >>> >>> >>> Quoting Edward d'Auvergne <[email protected]>: >>> >>>> Hi, >>>> >>>> The best way would be to read the manual. Sebastien Morin has written >>>> a nice guide with step-by-step instructions on what you need to do in >>>> the manual. You will need to read this as there are some manual steps >>>> which relax does not automate for you which you should be aware of. >>>> You should also read Sebastien's paper on the subject >>>> (http://dx.doi.org/10.1007/s10858-009-9381-4). >>>> >>>> Regards, >>>> >>>> Edward >>>> >>>> >>>> On 28 March 2013 21:10, <[email protected]> wrote: >>>>> >>>>> >>>>> Hi Edward, >>>>> >>>>> Thanks. I have submitted the pdb file. I understand that the >>>>> consistency >>>>> test is for 2 field nmr data, for example, by comparing the J(0) at 500 >>>>> MHz >>>>> and J(0) at 700 MHz, so I loaded the two field data when using >>>>> consistency_tests.py. I am confused that if one field data is loaded in >>>>> consistency_tests.py, how can consistency_tests.py check the >>>>> consistency >>>>> between NMR data at 500 MHz and NMR data at 700 MHz? Thank you. >>>>> >>>>> With best regards, >>>>> >>>>> Mengjun >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> Quoting Edward d'Auvergne <[email protected]>: >>>>> >>>>>> Hi again, >>>>>> >>>>>> I was wondering if you have read the consistency testing part of the >>>>>> relax manual written by Sebastien Morin (the person who implemented >>>>>> this analysis). Specifically this section: >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> http://www.nmr-relax.com/manual/Consistency_testing_script_mode_relaxation_data_lo.html >>>>>> >>>>>> Note the text, "For this analysis, only data for a single field >>>>>> strength can be loaded". This may possibly be the source of some of >>>>>> your problems. >>>>>> >>>>>> Regards, >>>>>> >>>>>> Edward >>>>>> >>>>>> >>>>>> >>>>>> On 28 March 2013 20:02, Edward d'Auvergne <[email protected]> >>>>>> wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> Hi Mengjun, >>>>>>> >>>>>>> Could you also attach the PDB file? I need it to be able to run the >>>>>>> script and replicate the problem. >>>>>>> >>>>>>> Cheers, >>>>>>> >>>>>>> Edward >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 28 March 2013 16:39, anonymous <[email protected]> >>>>>>> wrote: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Additional Item Attachment, bug #20674 (project relax): >>>>>>>> >>>>>>>> File name: T1 dhp 700.txt Size:74 KB >>>>>>>> File name: T2 dhp 500.txt Size:67 KB >>>>>>>> File name: T2 dhp 700.txt Size:68 KB >>>>>>>> File name: logconsistency Size:371 KB >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________________ >>>>>>>> >>>>>>>> Reply to this item at: >>>>>>>> >>>>>>>> <http://gna.org/bugs/?20674> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Message sent via/by Gna! >>>>>>>> http://gna.org/ >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> relax (http://www.nmr-relax.com) >>>>>>>> >>>>>>>> This is the relax-devel mailing list >>>>>>>> [email protected] >>>>>>>> >>>>>>>> To unsubscribe from this list, get a password >>>>>>>> reminder, or change your subscription options, >>>>>>>> visit the list information page at >>>>>>>> https://mail.gna.org/listinfo/relax-devel >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> >>> >>> >>> >> >> > > > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-devel mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-devel _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
