Hi, It's unfortunate that this is not 100% obvious, but I know of no other way to do this while still allowing the program to be flexible. If there are any other issues, please don't hesitate to ask.
Regards, Edward 2010/1/18 Tiago Pais <[email protected]>: > Hello all, > Just to tell you that I seem to have solved issue related to multiple spins > vector extraction. I have used the following expressions: > "# Load spins > structure.load_spins(spin_id='@CA', combine_models=False, ave_pos=False) > structure.load_spins(spin_id='@CB1', combine_models=False, > ave_pos=False) > > # Set the spin name and then load the NH vectors. > spin.name(spin_id='@CA', name='CA') > structure.vectors(spin_id='@CA', attached='H*', ave=False) > spin.name(spin_id='@CB1', name='CB1') > structure.vectors(spin_id='@CB1', attached='H*', ave=False) > ....." > > I get information that the spins are all extracted and get S2 values for all > of them. > Cheers > TiagoP > > > > -----Original Message----- > From: [email protected] [mailto:[email protected]] On > Behalf Of Edward d'Auvergne > Sent: quarta-feira, 6 de Janeiro de 2010 16:42 > To: Tiago Pais > Cc: [email protected] > Subject: Re: Extracting vectors from multiple spins > > 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
