Thank you very much, Edward! Vitaly
On Fri, Dec 17, 2010 at 13:03, Edward d'Auvergne <[email protected]> wrote: > Thank you for the detailed message and creating the bug report. This > is now fixed. Cheers. If you would like the changes without waiting > for a new release of relax, the new code can be checked out from the > repository by typing: > > $ svn co svn://svn.gna.org/svn/relax/1.3 relax-1.3 > > or if this doesn't work: > > $ svn co http://svn.gna.org/svn/relax/1.3 relax-1.3 > > If you already have a checked out copy, try typing: > > $ svn up > > This requires installation of the subversion program > (http://subversion.tigris.org/). > > Regards, > > Edward > > > On 17 December 2010 19:52, V.V. <[email protected]> wrote: >> Thank you, Edward! >> I have submitted the bug report (#17343). Yes, the atom name in the >> pdb file is labeled "CH2". >> >> Vitaly >> >> >> >> On Fri, Dec 17, 2010 at 11:38, Edward d'Auvergne <[email protected]> >> wrote: >>> Hi Vitaly, >>> >>> Thank you for identifying this problem. I just had a question, is the >>> atom named 'CH2' within the PDB file? If you don't mind, would you be >>> able to create a bug report for this? This would be much appreciated >>> as it would help other relax users who encounter the same problem as >>> you have found. This is not too important as it is a missing feature >>> rather than a bug but, if you could, the bug report submission page is >>> https://gna.org/bugs/?func=additem&group=relax. >>> >>> Thanks, >>> >>> Edward >>> >>> >>> >>> On 15 December 2010 02:51, V.V. <[email protected]> wrote: >>>> Hello, >>>> >>>> I am trying to create a diffusion tensor from the results file, and I >>>> am running into a following problem after >>>> "structure.create_diff_tensor_pdb" is invoked: >>>> >>>> ================ >>>> relax> structure.create_diff_tensor_pdb(scale=1.7999999999999999e-06, >>>> file='tensor.pdb', dir=None, force=True) >>>> Adding molecule 'diff_tensor' to model None (from the original >>>> molecule number None of model None) >>>> >>>> Chain A >>>> >>>> Calculating the centre of mass. >>>> RelaxWarning: Skipping the atom '#ave_mol1:2...@30' as the element name >>>> does not exist in the PDB file. >>>> ================ >>>> >>>> In the "results" file, element 30 in the atom name list is 'CH2' (Trp >>>> side chain). Also if I read the structure file with >>>> "structure.read_pdb", for each of the Trp residues I get: >>>> >>>> ================ >>>> RelaxWarning: Cannot determine the element associated with atom 'CH2'. >>>> ================ >>>> >>>> It looks like this atom was left out >>>> (http://www.mail-archive.com/[email protected]/msg06219.html). >>>> Also, if possible, could you append "OT" atom name (XPLOR format) to >>>> the oxygen list? >>>> >>>> Thank you, >>>> Vitaly >>>> >>>> _______________________________________________ >>>> 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
