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Re: [PyMOL] PyMOL split_states error on [PDB: 1hho]
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From: Thomas H. <tho...@sc...> - 2016-02-24 06:31:20
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This is fixed in SVN rev 4150. Cheers, Thomas On 22 Feb 2016, at 05:53, Thomas Holder <tho...@sc...> wrote: > 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 <imi...@bi...> 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 <spe...@gm...> >>> >>> 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 <ca...@su...> >>>> >>>> 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 <imi...@bi...> >>>>> 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 <imi...@bi...> >>>>>> Sent: Monday, February 22, 2016 3:39 AM >>>>>> To: pym...@li... >>>>>> 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: imi...@bi... >>>>>> _________________________________________________ >>>>>> Biomedical Research Foundation, Academy of Athens >>>>>> Soranou tou Efessiou 4, 115 27 Athens, Greece > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. |
