Hi, If you load the PDB file, you need to then need to execute structure.load_spins() for 'CA' and 'CB' separately. Not all atoms of the PDB file are treated as spin systems, you must manually specify these. There should be in the save file spin containers, i.e. XML elements starting and ending with spin desc="Spin container" name="CA" num="???"> and </spin> respectively. Only then will you be able to say that protons are attached to these spins.
Regards, Edward 2010/1/6 Tiago Pais <[email protected]>: > Well, the spins of interest are also present in the pdb file previously > loaded. > > -----Original Message----- > From: [email protected] [mailto:[email protected]] On > Behalf Of Edward d'Auvergne > Sent: quarta-feira, 6 de Janeiro de 2010 16:17 > To: Tiago Pais > Cc: [email protected] > Subject: Re: Extracting vectors from multiple spins > > Hi, > > This is strange, it should work! Could you file a bug report for > this? If you include data for one or two spins that can reproduce > this, and the script that was used, I should be able to sort out what > is happening very quickly. Though maybe it's just in the script. If > you have the 'CA' and 'CB' spins loaded, the structure.vectors() call > should work. Are these spins loaded into the program before calling > structure.vectors()? > > Cheers, > > Edward > > > > 2010/1/4 Tiago Pais <[email protected]>: >> I have tried that before but it doesn't work - there's the spin.name > issue. >> When it is running the second spin there is a warning message: >>>RelaxWarning: The spin ':140&:w...@cd1' is already named. Set the force flag >> to rename >> It goes like this for all the residues and then it stops: >>>The attached atom is not a proton. >>> >>>RelaxError: No vectors could be extracted. >> >> Cheers >> TiagoP >> >> >> -----Original Message----- >> From: Edward d'Auvergne [mailto:[email protected]] >> Sent: segunda-feira, 4 de Janeiro de 2010 10:46 >> To: Tiago Pais >> Cc: [email protected] >> Subject: Re: Extracting vectors from multiple spins >> >> Hi, >> >> You could try something such as: >> >> relax> structure.vectors(spin_id='@CA', attached='H1', ave=False) >> >> and: >> >> relax> structure.vectors(spin_id='@CB', attached='H2', ave=False) >> >> if that is how the atoms are named. Hope this helps. >> >> Regards, >> >> Edward >> >> >> >> 2009/12/17 Tiago Pais <[email protected]>: >>> Hello guys, >>> >>> Does anyone know if it is possible to extract vectors for multiple spins >> in >>> the same run? >>> >>> Lets say I would like to extract vectors for example from Ca to H1 and Cb >> to >>> H2. For the proton attached I imagine one can use the “*” character but >> for >>> the spin itself I don’t see how it can be done. >>> >>> If anyone has any idea, please reply. >>> >>> Cheers >>> >>> Tiago P >>> >>> >>> >>> ************************************** >>> >>> Tiago Pais, PhD. student >>> >>> Cell Physiology & NMR >>> >>> Instituto de Tecnologia Química e Biológica-Oeiras >>> >>> >>> >>> _______________________________________________ >>> relax (http://nmr-relax.com) >>> >>> This is the relax-users 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-users >>> >>> >> >> > > > _______________________________________________ > relax (http://nmr-relax.com) > > This is the relax-users 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-users > _______________________________________________ relax (http://nmr-relax.com) This is the relax-users 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-users
