Hi all, The bug seems to be that the "pdb_insure_orthogonal" setting is only applied to the first model. Turning the setting off shows the correct assembly:
set pdb_insure_orthogonal, off load 1hho.pdb1 If "pdb_insure_orthogonal" is on, PyMOL will apply the SCALE transformation, which might be necessary to correctly line up with the corresponding electron density map. Ioannis, you can file bug reports on https://sf.net/p/pymol/bugs/ but reporting a bug here on the pymol-users list is equally effective :) Cheers, Thomas On 22 Feb 2016, at 04:44, Ioannis Michalopoulos <imicha...@bioacademy.gr> wrote: > 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 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ 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
