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From: Ioannis M. <imi...@bi...> - 2016-02-29 21:54:04
|
Dear PyMOL users, I run 64-bit Windows 10. I have installed the latest PyMOL (and all other programs that are required) from: http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol PyMOL works fine. I make movies which look fine on PyMOL. Nevertheless, when I try: Menu > Save Movie As > MPEG... a pop-up error message appears: MPEG encoder missing. The FreeMOL add-ons may not be installed. Interestingly, in: "C:\Python27" where PyMOL.exe is installed, mpeg_encode.exe and mpeg_encode-x64.exe are also found. This directory is set to PATH. Have I not set PyMOL properly? Thank you in advance. Best Regards, Dr Ioannis Michalopoulos -- 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 |
|
From: Thomas H. <tho...@sc...> - 2016-02-29 13:35:26
|
Hi Timofey, See http://pymolwiki.org/index.php/ignore_case Note: The wiki page mentions 1.8.0.0 (official release), but the SVN repo had the change since 1.7.7.1 (https://sourceforge.net/p/pymol/code/4123/ ). Cheers, Thomas On 29 Feb 2016, at 06:23, Timofey Tyugashev <tyu...@ni...> wrote: > Sorry, it's actually part false alarm and part a completely different > problem. > > For false alarm:Structure retrieved by 'fetch' simply lacked residue > numbered 10, why my own file was already repaired and had it fine. > > For different problem: For some reason it turns out that 'select' is > case-sensitive and it's not actually mentioned anywhere on the wiki, so > selectors like 'resn' and 'name' simply silently failed. > Is there a way to disable it? > > 29.02.2016 17:10, Timofey Tyugashev пишет: >> If I load my own pdb file and issue a simple select command like >> 'select resi 10' it works fine, producing something like 'selection >> "sele" defined with 6 atoms'. >> However if I load the same structure using fetch command selections >> stop working, 'select resi 10' results in 'selection "sele" defined >> with 0 atoms'. >> System is Linux. PyMOL is 1.7.7.2 version from svn. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. |
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From: Timofey T. <tyu...@ni...> - 2016-02-29 11:42:03
|
If I load my own pdb file and issue a simple select command like 'select resi 10' it works fine, producing something like 'selection "sele" defined with 6 atoms'. However if I load the same structure using fetch command selections stop working, 'select resi 10' results in 'selection "sele" defined with 0 atoms'. System is Linux. PyMOL is 1.7.7.2 version from svn. |
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From: Timofey T. <tyu...@ni...> - 2016-02-29 11:20:50
|
Sorry, it's actually part false alarm and part a completely different problem. For false alarm:Structure retrieved by 'fetch' simply lacked residue numbered 10, why my own file was already repaired and had it fine. For different problem: For some reason it turns out that 'select' is case-sensitive and it's not actually mentioned anywhere on the wiki, so selectors like 'resn' and 'name' simply silently failed. Is there a way to disable it? 29.02.2016 17:10, Timofey Tyugashev пишет: > If I load my own pdb file and issue a simple select command like > 'select resi 10' it works fine, producing something like 'selection > "sele" defined with 6 atoms'. > However if I load the same structure using fetch command selections > stop working, 'select resi 10' results in 'selection "sele" defined > with 0 atoms'. > System is Linux. PyMOL is 1.7.7.2 version from svn. |
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From: Thomas H. <tho...@sc...> - 2016-02-25 18:58:26
|
Hi Carsten & Albert,
There actually is a function for getting the coordinates of a single atom. Example:
PyMOL>print cmd.get_atom_coords('first (elem O)')
Cheers,
Thomas
On 25 Feb 2016, at 09:54, Schubert, Carsten [JRDUS] <CSC...@it...> wrote:
> Albert,
>
> there is no command line tool for that purpose per se, however you can use the iterate command for that purpose.
> http://pymolwiki.org/index.php/Iterate#Example:_Get_coordinates
>
>
> There are other ways to do this but this will get you going more quickly.
>
> -----Original Message-----
> From: Albert [mailto:mai...@gm...]
> Sent: Thursday, February 25, 2016 12:48 PM
> To: pym...@li...
> Subject: [PyMOL] how to get an atom coordinates information
>
> Hello:
>
> I would like to know the XYZ information of a specific atom. I am just wondering how can we do this? Is there any command line?
>
> thank you very much
>
> Albert
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
|
|
From: Schubert, C. [JRDUS] <CSC...@it...> - 2016-02-25 17:55:12
|
Albert, there is no command line tool for that purpose per se, however you can use the iterate command for that purpose. http://pymolwiki.org/index.php/Iterate#Example:_Get_coordinates There are other ways to do this but this will get you going more quickly. -----Original Message----- From: Albert [mailto:mai...@gm...] Sent: Thursday, February 25, 2016 12:48 PM To: pym...@li... Subject: [PyMOL] how to get an atom coordinates information Hello: I would like to know the XYZ information of a specific atom. I am just wondering how can we do this? Is there any command line? thank you very much Albert ------------------------------------------------------------------------------ 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 (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |
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From: Albert <mai...@gm...> - 2016-02-25 17:49:21
|
Hello: I would like to know the XYZ information of a specific atom. I am just wondering how can we do this? Is there any command line? thank you very much Albert |
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From: Andreas W. <4nd...@gm...> - 2016-02-25 12:48:17
|
Dear all, a colleague is interested in generating an electrostatic map of a protein containing a citrulline. Does anybody have any experience with this and could recommend any approach? Cheers, Andreas |
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From: Mohsen C. <moh...@fl...> - 2016-02-25 12:41:36
|
Hi Amin, It worked. Many Thanks Cheers Mohsen From: am...@im... [mailto:am...@im...] Sent: Thursday, 25 February 2016 10:24 PM To: pym...@li... Subject: Re: [PyMOL] Alignment of two proteins Hi. I think align 4mt1 & chain A, 3aob & chain B should work. Amin. On 2016-02-25 17:02, Mohsen Chitsaz wrote: Hi Julian, I have two homotrimer proteins, i.e. 3aob and 4mt1. I want to align chain A of 4mt1 to chain B of 3aob. How to tell Pymol to align a specific chain or part of a protein, in my case chain A of 4mt1, to a specific chain or part of another protein, in my case chain B of 3aob? Cheers Mohsen From: Mohsen Chitsaz Sent: Wednesday, 24 February 2016 11:17 PM To: 'Julian Heinrich' <ju...@jo...<mailto:ju...@jo...>> Cc: pym...@li...<mailto:pym...@li...> Subject: RE: [PyMOL] Appending a pdb file Hi Julian, Many Thanks for your help. It worked. Cheers Mohsen From: jul...@gm...<mailto:jul...@gm...> [mailto:jul...@gm...] On Behalf Of Julian Heinrich Sent: Monday, 22 February 2016 8:24 PM To: Mohsen Chitsaz <moh...@fl...<mailto:moh...@fl...>> Cc: pym...@li...<mailto:pym...@li...> Subject: Re: [PyMOL] Appending a pdb file Hi Mohsen, if you want to superimpose structures, have a look at the align command: http://pymolwiki.org/index.php/Align Cheers, Julian On Thu, Feb 18, 2016 at 10:47 PM, Mohsen Chitsaz <moh...@fl...<mailto:moh...@fl...>> wrote: Hi In order to superimpose two protein sequences, I am trying to append a pdb file to an existing protein sequence, which I have already opened in PyMol. The append function is not working in my PyMol. Could someone help me with this please. Cheers Mohsen ------------------------------------------------------------------------------ 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 (PyM...@li...<mailto:PyM...@li...>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... ------------------------------------------------------------------------------ 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 (PyM...@li...<mailto:PyM...@li...>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |
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From: <am...@im...> - 2016-02-25 12:25:04
|
Hi. I think align 4mt1 & chain A, 3aob & chain B should work. Amin. On 2016-02-25 17:02, Mohsen Chitsaz wrote: > Hi Julian, > > I have two homotrimer proteins, i.e. 3aob and 4mt1. I want to align chain A of 4mt1 to chain B of 3aob. How to tell Pymol to align a specific chain or part of a protein, in my case chain A of 4mt1, to a specific chain or part of another protein, in my case chain B of 3aob? > > Cheers > > Mohsen > > FROM: Mohsen Chitsaz > SENT: Wednesday, 24 February 2016 11:17 PM > TO: 'Julian Heinrich' <ju...@jo...> > CC: pym...@li... > SUBJECT: RE: [PyMOL] Appending a pdb file > > Hi Julian, > > Many Thanks for your help. It worked. > > Cheers > > Mohsen > > FROM: jul...@gm... [mailto:jul...@gm...] ON BEHALF OF Julian Heinrich > SENT: Monday, 22 February 2016 8:24 PM > TO: Mohsen Chitsaz <moh...@fl...> > CC: pym...@li... > SUBJECT: Re: [PyMOL] Appending a pdb file > > Hi Mohsen, > > if you want to superimpose structures, have a look at the align command: > > http://pymolwiki.org/index.php/Align [4] > > Cheers, > > Julian > > On Thu, Feb 18, 2016 at 10:47 PM, Mohsen Chitsaz <moh...@fl...> wrote: > >> Hi >> >> In order to superimpose two protein sequences, I am trying to append a pdb file to an existing protein sequence, which I have already opened in PyMol. The append function is not working in my PyMol. Could someone help me with this please. >> >> Cheers >> >> Mohsen >> >> ------------------------------------------------------------------------------ >> 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 [1] >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users [2] >> Archives: http://www.mail-archive.com/pym...@li... [3] > > ------------------------------------------------------------------------------ > 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 [1] > > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users [2] > Archives: http://www.mail-archive.com/pym...@li... [3] Links: ------ [1] http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 [2] https://lists.sourceforge.net/lists/listinfo/pymol-users [3] http://www.mail-archive.com/pym...@li... [4] http://pymolwiki.org/index.php/Align |
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From: Mohsen C. <moh...@fl...> - 2016-02-25 11:32:40
|
Hi Julian, I have two homotrimer proteins, i.e. 3aob and 4mt1. I want to align chain A of 4mt1 to chain B of 3aob. How to tell Pymol to align a specific chain or part of a protein, in my case chain A of 4mt1, to a specific chain or part of another protein, in my case chain B of 3aob? Cheers Mohsen From: Mohsen Chitsaz Sent: Wednesday, 24 February 2016 11:17 PM To: 'Julian Heinrich' <ju...@jo...> Cc: pym...@li... Subject: RE: [PyMOL] Appending a pdb file Hi Julian, Many Thanks for your help. It worked. Cheers Mohsen From: jul...@gm...<mailto:jul...@gm...> [mailto:jul...@gm...] On Behalf Of Julian Heinrich Sent: Monday, 22 February 2016 8:24 PM To: Mohsen Chitsaz <moh...@fl...<mailto:moh...@fl...>> Cc: pym...@li...<mailto:pym...@li...> Subject: Re: [PyMOL] Appending a pdb file Hi Mohsen, if you want to superimpose structures, have a look at the align command: http://pymolwiki.org/index.php/Align Cheers, Julian On Thu, Feb 18, 2016 at 10:47 PM, Mohsen Chitsaz <moh...@fl...<mailto:moh...@fl...>> wrote: Hi In order to superimpose two protein sequences, I am trying to append a pdb file to an existing protein sequence, which I have already opened in PyMol. The append function is not working in my PyMol. Could someone help me with this please. Cheers Mohsen ------------------------------------------------------------------------------ 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 (PyM...@li...<mailto:PyM...@li...>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |
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From: Mohsen C. <moh...@fl...> - 2016-02-24 13:19:56
|
Hi Julian, Many Thanks for your help. It worked. Cheers Mohsen From: jul...@gm... [mailto:jul...@gm...] On Behalf Of Julian Heinrich Sent: Monday, 22 February 2016 8:24 PM To: Mohsen Chitsaz <moh...@fl...> Cc: pym...@li... Subject: Re: [PyMOL] Appending a pdb file Hi Mohsen, if you want to superimpose structures, have a look at the align command: http://pymolwiki.org/index.php/Align Cheers, Julian On Thu, Feb 18, 2016 at 10:47 PM, Mohsen Chitsaz <moh...@fl...<mailto:moh...@fl...>> wrote: Hi In order to superimpose two protein sequences, I am trying to append a pdb file to an existing protein sequence, which I have already opened in PyMol. The append function is not working in my PyMol. Could someone help me with this please. Cheers Mohsen ------------------------------------------------------------------------------ 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 (PyM...@li...<mailto:PyM...@li...>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |
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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. |
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From: Thomas H. <tho...@sc...> - 2016-02-24 06:04:00
|
Hi Max,
If you send me the loop.pdb file then I'll have a look at the issue.
Cheers,
Thomas
On 23 Feb 2016, at 09:03, Ebert Maximilian <m....@um...> wrote:
> Hi there,
>
> maybe the subject is a little bit misleading but i couldn’t find any better description. Basically I am trying to align two PDB structures, one is from the PDB directly and the other one is a file containing conformation information about a specific loop of the protein from the PDB. So I try to align this loop to the residues 211-220 of the PDB structures. My commands go like this:
>
> fetch 1g68
> load loop.pdb
> align 1g68 and chain A and n. CA+N+O+C and i. 211-220, loop
>
> instead of aligning on the 40 atoms as expected I align solely on 8, which are the N atoms. If I change the n. selection to O for instance I get ExecutiveAlign-Error: atomic alignment failed (mismatched identifiers?). This is with the macports compiled version of pymol 1.7.7.2 and the PyMOLX11Hybrid 1.7.4. However, doing exactly the same in the Macpymol version 1.7.4 it works as expected. To even make it more weird if I use Python:
>
> import __main__
> __main__.pymol_argv = [ 'pymol', ‘-qc'] # Quiet and no GUI -qc
> import pymol
> pymol.cmd.fetch('1g68’)
> pymol.cmd.load('loop.pdb’)
> pymol.cmd.align('loop', ‘1g68 and chain A and n. N+CA+O+C and i. 211-220, quiet=0)
>
> it works as well. Does anybody understands what is happening here?
>
> Thank you very much,
>
> Max
>
> PS: If you need the PDB files let me know. I don’t know if this list acceptes files
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
|
|
From: Ebert M. <m....@um...> - 2016-02-23 19:56:47
|
Hi there,
maybe the subject is a little bit misleading but i couldn’t find any better description. Basically I am trying to align two PDB structures, one is from the PDB directly and the other one is a file containing conformation information about a specific loop of the protein from the PDB. So I try to align this loop to the residues 211-220 of the PDB structures. My commands go like this:
fetch 1g68
load loop.pdb
align 1g68 and chain A and n. CA+N+O+C and i. 211-220, loop
instead of aligning on the 40 atoms as expected I align solely on 8, which are the N atoms. If I change the n. selection to O for instance I get ExecutiveAlign-Error: atomic alignment failed (mismatched identifiers?). This is with the macports compiled version of pymol 1.7.7.2 and the PyMOLX11Hybrid 1.7.4. However, doing exactly the same in the Macpymol version 1.7.4 it works as expected. To even make it more weird if I use Python:
import __main__
__main__.pymol_argv = [ 'pymol', ‘-qc'] # Quiet and no GUI -qc
import pymol
pymol.cmd.fetch('1g68’)
pymol.cmd.load('loop.pdb’)
pymol.cmd.align('loop', ‘1g68 and chain A and n. N+CA+O+C and i. 211-220, quiet=0)
it works as well. Does anybody understands what is happening here?
Thank you very much,
Max
PS: If you need the PDB files let me know. I don’t know if this list acceptes files |
|
From: Sanishvili, R. <rsa...@an...> - 2016-02-23 13:38:07
|
Dear Colleagues, We are pleased to announce the 9th annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Title: CCP4 crystallographic school: From data collection to structure refinement and beyond Dates: June 21 through 29, 2016 Site: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises Data collection workshop the first three days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Crystallographic computation workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on, interactive trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 21. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Registration fees: The registration fee for the selected participants is $400 for the academic and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the reservations at economical lodging at the Argonne Guest House. The workshop will cover all other expenses. We hope to see you at the school, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsa...@an... |
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From: Robert H. <ha...@st...> - 2016-02-22 15:43:08
|
Ioannis, I suggest using the CIF file from EBI instead: http://www.ebi.ac.uk/pdbe/static/entry/download/1hho-assembly-1.cif.gz It looks good to me -- just one model. For reference, the RCSB site is using Jmol and is simply loading 1HHO itself and constructing the assembly *in situ *using the symmetry operators in that file, not reading the assembly file. PyMOL must have a simple way to do that as well. Right? Or do you have to load the assembly file? There is no mistake in the PDB assembly file. Jmol also reads that just fine, but as you point out, it is in the form of two models, for reasons I do not understand. It looks to me like when the PDB assembly file is created, each BIOMT transformation is put into a separate model. This is NOT what EBI does when they create the analogous mmCIF assembly file. A totally different multi-model (NMR solution) issue has been noticed with CIF assembly files from EBI. [e.g. http://www.ebi.ac.uk/pdbe/static/entry/download/2lev-assembly-1.cif.gz] In that case, there are 20 models, and the atom ordering ens up by chain, not be model, so that the coordinates for each "model" are scattered throughout the file, which seems quite odd to me. And I notice that RCSB also creates a PDB assembly file for 2lev, but in that case only one model is produced, and it is just the first NMR model. So this is still an imperfect design all around. In both cases, I my opinion, there are design flaws. Don't know that you can call that a bug.... Bob Hanson |
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From: Ioannis M. <imi...@bi...> - 2016-02-22 14:55:34
|
This approach does not seem to work. On Monday 22 of February 2016 05:53:14 Thomas Holder 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 -- 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 |
|
From: Thomas H. <tho...@sc...> - 2016-02-22 14:19:15
|
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. |
|
From: Ioannis M. <imi...@bi...> - 2016-02-22 12:45:10
|
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 > >> > >> ------------------------------------------------------------------------- > >> --->> > >> > -- 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 (PyM...@li...) > >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > >> > Archives: http://www.mail-archive.com/pym...@li... > >> > >> -- > >> 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 > >> > >> > >> ------------------------------------------------------------------------- > >> ----- 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 (PyM...@li...) > >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > >> Archives: http://www.mail-archive.com/pym...@li... > > > > -------------------------------------------------------------------------- > > ---- 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 (PyM...@li...) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pym...@li... -- 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 |
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From: Ezra P. <ezr...@rc...> - 2016-02-22 11:17:48
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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 >> > >> > >> > >> ---------------------------------------------------------------------------- >> > -- 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 (PyM...@li...) >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> > Archives: http://www.mail-archive.com/pym...@li... >> >> -- >> 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 >> >> >> ------------------------------------------------------------------------------ >> 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
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From: Spencer B. <spe...@gm...> - 2016-02-22 10:05:01
|
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 > > > > > > > ---------------------------------------------------------------------------- > > -- 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 (PyM...@li...) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pym...@li... > > -- > 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 > > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
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From: Julian H. <ju...@jo...> - 2016-02-22 09:54:27
|
Hi Mohsen, if you want to superimpose structures, have a look at the align command: http://pymolwiki.org/index.php/Align Cheers, Julian On Thu, Feb 18, 2016 at 10:47 PM, Mohsen Chitsaz < moh...@fl...> wrote: > Hi > > > > In order to superimpose two protein sequences, I am trying to append a pdb > file to an existing protein sequence, which I have already opened in PyMol. > The append function is not working in my PyMol. Could someone help me with > this please. > > > > Cheers > > Mohsen > > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
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From: Jame R.Ketudat-C. <ca...@su...> - 2016-02-22 09:42:02
|
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
>
>
> ----------------------------------------------------------------------------
> -- 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 (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
--
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
|
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From: Ioannis M. <imi...@bi...> - 2016-02-21 20:56:18
|
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 |