Dear all, Thank you for your informative answers.
For various reasons, I am not yet willing to move to cif. Indeed remark 285 of the 1hho header: http://www.rcsb.org/pdb/files/1HHO.pdb?headerOnly=YES reads: REMARK 285 REMARK 285 THE ENTRY COORDINATES REMARK 285 ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME. Rasmol 2.7.5.2 displays both states of the biological structure, but, unfortunately, it does not recognise the secondary structure elements of the second state. The fact that Rasmol and the three html embedded viewers in the PDB page: http://www.rcsb.org/pdb/explore/jmol.do?structureId=1HHO&bionumber=1 display the second state, means that Pymol is the one that has the issue, as Ezra mentioned. As PyMOL's failure to recognise non-standard crystal frames is a major issue, I think I have to report it to PyMOL developers. How do I do a bug report on PyMOL 1.8.0.0? I just joined your emailing list and I am not sure how to do that. Thank you in advance. Best Regards, Ioannis On Monday 22 of February 2016 05:53:08 Ezra Peisach wrote: > 1hho does have a non-standard crystal frame. (see remark 285) > > If you load the assembly PDB file in rasmol - it displays properly. Pymol > is having the issue. > > However, if you fetch the cif file in pymol, and ask it to display the > assembly - it does the right thing. > > set assembly, 1 > fetch 1hho > > > Ezra > > On Mon, Feb 22, 2016 at 5:04 AM, Spencer Bliven <spencer.bli...@gmail.com> > > wrote: > > This looks like a bug in the PDB's file, and you should definitely let > > them know about it. It's a particularly weird case since the second model > > doesn't correspond to any of the valid crystallographic operators. > > Probably > > it is a problem with the very non-standard crystal frame specified by the > > SCALE matrix in the PDB file. These are always problematic, to the point > > that some tools (e.g. EPPIC <http://eppic-web.org>) will ignore them > > completely. > > > > While waiting for the PDB to fix the file, you can generate the biological > > unit from the symmetry operators using: > > > > fetch 1hho, async=0 > > symexp sym, 1hho, 1hho, 2 > > > > -Spencer > > > > On Mon, Feb 22, 2016 at 10:19 AM, Jame R.Ketudat-Cairns <cai...@sut.ac.th> > > > > wrote: > >> Dear Ioannis, > >> > >> I was wondering about that, too. Given the prominence of hemoglobin > >> > >> structure and oxygen binding in Biochemistry education, the 1 HHO > >> structure > >> seems to be a bad biological structure to calculate incorrectly. I guess > >> an email to the PDB might be in order (if it is intentional, they could > >> at > >> least explain it in that case). > >> > >> Best Regards, > >> > >> Jim > >> > >> ________________________________________ > >> From: Ioannis Michalopoulos <imicha...@bioacademy.gr> > >> Sent: Monday, February 22, 2016 4:05 PM > >> To: Jame R.Ketudat-Cairns > >> Subject: Re: [PyMOL] PyMOL split_states error on [PDB: 1hho] > >> > >> Dear Jim, > >> > >> Thank you for your prompt answer which worked perfectly. I was writing a > >> tutorial for my students and I found many incorrectly calculated > >> biological > >> units. I wonder if we should complain to PDB about it, or wait and see > >> what > >> PyMOL can do about it, first. > >> > >> Best Regards, > >> > >> Ioannis > >> > >> On Monday 22 of February 2016 02:09:05 you wrote: > >> > Dear Ioannis, > >> > > >> > The 1HHO biological unit seems to be calculated incorrectly (just > >> > >> spun > >> > >> > around the y-axis 180 degrees). I found that the symexp command works > >> > >> for > >> > >> > this: symexp sym, 1hho, (1hho), 1 > >> > Best Regards, > >> > > >> > Jim > >> > > >> > ________________________________________ > >> > From: Ioannis Michalopoulos <imicha...@bioacademy.gr> > >> > Sent: Monday, February 22, 2016 3:39 AM > >> > To: pymol-users@lists.sourceforge.net > >> > Subject: [PyMOL] PyMOL split_states error on [PDB: 1hho] > >> > > >> > Dear PyMOL users, > >> > > >> > I run PyMOL 1.8.0.0 for Windows. > >> > > >> > I loaded the biological assembly of 1HHO: > >> > > >> > http://www.rcsb.org/pdb/files/1HHO.pdb1.gz > >> > > >> > When I tried: > >> > > >> > split_states 1hho > >> > >> > PyMOL failed to produce the proper tetramer that is seen at: > >> http://www.rcsb.org/pdb/explore/jmol.do?structureId=1HHO&opt=3&bionumber= > >> 1 > >> > >> > Instead PyMOL shows a weird tetramer. Is it a bug? This approach works > >> > fine on other cases eg 1SVC. Is there any other way to do it? > >> > > >> > Thank you in advance. > >> > > >> > Best Regards, > >> > > >> > Ioannis > >> > -- > >> > Dr Ioannis Michalopoulos > >> > Staff Research Scientist - Associate Professor Level > >> > Centre of Systems Biology > >> > > >> > Tel: +30 210 6597 127 > >> > Fax: +30 210 6597 545 > >> > Email: imicha...@bioacademy.gr > >> > _________________________________________________ > >> > Biomedical Research Foundation, Academy of Athens > >> > Soranou tou Efessiou 4, 115 27 Athens, Greece > >> > >> ------------------------------------------------------------------------- > >> --->> > >> > -- Site24x7 APM Insight: Get Deep Visibility into Application > >> > >> Performance > >> > >> > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > >> > Monitor end-to-end web transactions and take corrective actions now > >> > Troubleshoot faster and improve end-user experience. Signup Now! > >> > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 > >> > _______________________________________________ > >> > 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 > >> > >> -- > >> Dr Ioannis Michalopoulos > >> Staff Research Scientist - Associate Professor Level > >> Centre of Systems Biology > >> > >> Tel: +30 210 6597 127 > >> Fax: +30 210 6597 545 > >> Email: imicha...@bioacademy.gr > >> _________________________________________________ > >> Biomedical Research Foundation, Academy of Athens > >> Soranou tou Efessiou 4, 115 27 Athens, Greece > >> > >> > >> ------------------------------------------------------------------------- > >> ----- Site24x7 APM Insight: Get Deep Visibility into Application > >> Performance APM + Mobile APM + RUM: Monitor 3 App instances at just > >> $35/Month > >> Monitor end-to-end web transactions and take corrective actions now > >> Troubleshoot faster and improve end-user experience. Signup Now! > >> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 > >> _______________________________________________ > >> 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 > > > > -------------------------------------------------------------------------- > > ---- Site24x7 APM Insight: Get Deep Visibility into Application > > Performance APM + Mobile APM + RUM: Monitor 3 App instances at just > > $35/Month > > Monitor end-to-end web transactions and take corrective actions now > > Troubleshoot faster and improve end-user experience. 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