Hi, I am getting a "non-positive definite" error when following the mrc refmac5 Tutorial:
https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/tutorials/refmac_tutorial/files/part_2.html#prepare_tls I'm using the same data recommended by the tutorial and am following the tutorial with no deviations -see error below. Am I misinterpreting the SKTTLS summary, is this a binary problem, a data problem, tutorial problem... Any guidance would be appreciated. Best wishes, Reza #### SKTTLS SUMMARY #### # Total number of bonds between residues: 491 # Number of bonds beyond 95th percentile for any residual: 0 # Number of bonds beyond 99th percentile for any residual: 0 # NOTE: bonds beyond 99th %ile are included in the 95th %ile count # Percentiles are from REFMAC segmented TLS refinements in PDB as of Sept. 2009 # Residuals are calculated for each bond between residues; one additional # residual is calculated for each alternate atom in such bonds, from the first # C or O3' to the alternate atom. # Extreme residuals may indicate problems with the ADPs for the two atoms in the bond: # -- ADPs differ by more than usual, which may be due to misassignment of TLS # segment boundaries, or # -- something went wrong during refinement - maybe the residual B bottomed out # at 2.0? - or # -- one or both atoms have non-positive definite ADP, in which case CCuij is # given the arbitrary extreme value of zero - regardless of how # similar the two ADPs are. # Statistics for residuals in this structure: # # RESIDUAL MEAN SIGMA WORST # CCuij 0.9993 0.0009 0.9945 # RSIMU 0.0313 0.0211 0.1235 # RDELU 0.0305 0.0255 0.1402 # Statistics for anisotropy (ratios of smallest to largest eigenvalue) # for anisotropic positive-definite atoms in this structure: # # NUMBER # CHAIN TYPE MEAN SIGMA OF ATOMS # Protein 0.6586 0.0830 3950 # Nucleic Acid 0.0000 0.0000 0 # Other nonsolvent 0.0000 0.0000 0 #### END OF SKTTLS SUMMARY #### Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 ________________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Dmytro Guzenko <dmytro.guze...@pharm.kuleuven.be> Sent: Monday, April 10, 2017 6:29 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: Re: [ccp4bb] Structure comparison Gert, There is nothing wrong with suggesting 45 softwares, as one of those may do exactly what a person needs and save loads of time. Besides, comparing protein structures locally need not involve any superposition method. I would say comparing torsion angles/distances between atoms is a more common solution to this problem. There are still cutoffs and weights to consider of course. Approaches vary on how to handle those (e.g. theoretical or through validation), but I seriously doubt your response constitutes 'case closed'. Kind regards, Dmytro. On 10/04/17 12:06, Gert Vriend wrote: > Rather then now start mentioning yet 45 other 3D superposition > softwares, I think a pointer to the Wikipedia should suffice: > > https://en.wikipedia.org/wiki/Structural_alignment > > The Russian Doll effect (if you align more residues the comparison stats > get worse) is best explained (my opinion) by the CATH people (Orengo > group), and Arthur Lest is the only one (still, I think) who has been > thinking extensively about the cutoff question. > > Greetings > Gert > >>>> From: Reza Khayat >>>> Sent: Sunday, April 9, 2017 6:07 PM >>>> To: CCP4 bulletin board >>>> Subject: Structure comparison >>>> >>>> Hi, >>>> >>>> I have refined several structures of a protein from different space >>>> groups and would like to compare them to one another. Is there a >>>> program/software suite that would provide an objective comparison >>>> of the structures and identify regions where the structures are >>>> sufficiently different from one another to warrant a closer look? I >>>> think the most important aspect of the analysis would be defining a >>>> threshold (possibly based on resolution and structure statistics) >>>> that would identify sufficient difference between structures. Thanks. >>>> >>>> Best wishes, >>>> Reza >>>> >>>> Reza Khayat, PhD >>>> Assistant Professor >>>> City College of New York >>>> Department of Chemistry >>>> New York, NY 10031 > > Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het > handelsregister onder nummer 41055629. > The Radboud university medical center is listed in the Commercial > Register of the Chamber of Commerce under file number 41055629.
