Dear Thomas, Thank you very much for your investigation.
I agree with you. PyMOL is doing right; SCALEn should be the identity matrix, or CRYST1 expanded. CRYST1 is defined to be "1 1 1 90 90 90" for structures determined by non-crystallographic methods. Thanks to the increased resolution of cryo EM, people are starting to use refinement software for crystallography. In this case, authors might submit files with CRYST1 and SCALEn based on the (pseudo-)cell used during the refinement, and annotators in PDB edit CRYST1 only, thus leading to the inconsistency. I talked to one of the authors of the structure and he said he will talk to PDB on the issue. Best regards, Takanori Nakane On 2014-05-27 14:35, Thomas Holder wrote: > Hi Takanori, > > PyMOL uses SCALEn to transform into fractional coordinates, and then > the > unit cell parameters (CRYST1) to transform back into cartesian > coordinates. The PDB spec says: "The unit cell parameters are used to > calculate SCALE". For 1VW3, CRYST1 defines a unit cube, so I assume > SCALEn should be the identity matrix, but it's not. > > You can skip this back-and-forth transformation with a setting: > > PyMOL> set pdb_insure_orthogonal, off > > I assume PyMOL is doing the right thing here. If we want to know more > about the intended interplay of CRYST1, ORIGXn and SCALEn, we might > want > to crosspost the topic to the CCP4BB list. > > Cheers, > Thomas > > Takanori Nakane wrote, On 05/24/14 03:48: >> Dear all, >> >> I noticed a strange behaviour in the handling of SCALEn >> records in PDB files. >> >> When I load 1VW3, all atomic coordinates are scaled down >> to one thousandth and therefore all atoms get connected. >> The fact that the coordinates are incorrectly transformed >> can be confirmed by saving the loaded model again. >> >> This is probably due to the presence of SCALEn records: >> >>> SCALE1 0.001000 0.000000 0.000000 0.00000 >>> SCALE2 0.000000 0.001000 0.000000 0.00000 >>> SCALE3 0.000000 0.000000 0.001000 0.00000 >> >> When they are deleted, the model can be loaded correctly. >> >> According to the PDB format specification >> http://deposit.rcsb.org/adit/docs/pdb_atom_format.html#SCALEn , >> SCALEn records should not affect real space (orthogonal) coordinates. >> >> Best regards, >> >> Takanori Nakane > > -- > Thomas Holder > PyMOL > Schrödinger, Inc. > > ------------------------------------------------------------------------------ > The best possible search technologies are now affordable for all > companies. > Download your FREE open source Enterprise Search Engine today! > Our experts will assist you in its installation for $59/mo, no > commitment. > Test it for FREE on our Cloud platform anytime! > http://pubads.g.doubleclick.net/gampad/clk?id=145328191&iu=/4140/ostg.clktrk > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ------------------------------------------------------------------------------ The best possible search technologies are now affordable for all companies. Download your FREE open source Enterprise Search Engine today! Our experts will assist you in its installation for $59/mo, no commitment. Test it for FREE on our Cloud platform anytime! http://pubads.g.doubleclick.net/gampad/clk?id=145328191&iu=/4140/ostg.clktrk _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
