From: James D. <J.D...@ve...> - 2011-12-14 23:50:34
|
Dear All, I am currently having a problem with the distance command when applied to merged objects. The real case is actually when I remove a ligand from a binding site and merge in a new ligand. But as a simple example, I think I can demonstrate with the following: >frag ala, ala1 >frag ala, ala2 >translate [4,0,0], ala2 >label all, ID >distance d1, ala1 & ID 3, ala2 & ID 0 This creates a distance object fine. But if I now merge the two objects into a new object: >create new, ala1 | ala2 >disable ala1 | ala2 and manually create two single atom selections corresponding to the original ID 3 and ID 0 atoms (using atom select mode and renaming the selections to give 'sele1' and 'sele2'): >distance d2, sele1, sele2 gives me a distance between ID 0 and 3 both on what used to be ala2, and not between the two selected atoms! Am I doing something wrong with 'create'? I don't recall having a problem with this sort of operation until maybe ~ 6 months ago... I am using rev 3971 under Windows. Any help/advice greatly appreciated. Kind regards James ______________________________________________________________________ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or pos...@ve.... Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the "Company address and registration details" link at the bottom of the page.. ______________________________________________________________________ |
From: Troels E. L. <tl...@gm...> - 2011-12-15 08:04:40
|
Hi James. I think it is because you create a object, which have identical ID's in the object. new: 2x ID 7, 2x 5 and so on. hide label, all label new, index hide label, all label new, id either use the index, to make selections alter the chain name for one of the fragments, before creation or so. /T Troels Emtekær Linnet Slotsvej 2 4300 Holbæk Mobil: +45 60210234 2011/12/15 James Davidson <J.D...@ve...> > ** > Dear All, > > I am currently having a problem with the distance command when applied to > merged objects. The real case is actually when I remove a ligand from a > binding site and merge in a new ligand. But as a simple example, I think I > can demonstrate with the following: > > >frag ala, ala1 > >frag ala, ala2 > >translate [4,0,0], ala2 > >label all, ID > >distance d1, ala1 & ID 3, ala2 & ID 0 > > This creates a distance object fine. But if I now merge the two objects > into a new object: > > >create new, ala1 | ala2 > >disable ala1 | ala2 > > and manually create two single atom selections corresponding to the > original ID 3 and ID 0 atoms (using atom select mode and renaming the > selections to give 'sele1' and 'sele2'): > > >distance d2, sele1, sele2 > > gives me a distance between ID 0 and 3 both on what used to be ala2, and > not between the two selected atoms! > > > Am I doing something wrong with 'create'? I don't recall having a problem > with this sort of operation until maybe ~ 6 months ago... I am using rev > 3971 under Windows. Any help/advice greatly appreciated. > > Kind regards > > James > > ______________________________________________________________________ > PLEASE READ: This email is confidential and may be privileged. It is > intended for the named addressee(s) only and access to it by anyone else is > unauthorised. If you are not an addressee, any disclosure or copying of the > contents of this email or any action taken (or not taken) in reliance on it > is unauthorised and may be unlawful. If you have received this email in > error, please notify the sender or pos...@ve.... Email is not > a secure method of communication and the Company cannot accept > responsibility for the accuracy or completeness of this message or any > attachment(s). Please check this email for virus infection for which the > Company accepts no responsibility. If verification of this email is sought > then please request a hard copy. Unless otherwise stated, any views or > opinions presented are solely those of the author and do not represent > those of the Company. > > The Vernalis Group of Companies > Oakdene Court > 613 Reading Road > Winnersh, Berkshire > RG41 5UA. > Tel: +44 118 977 3133 > > To access trading company registration and address details, please go to > the Vernalis website at www.vernalis.com and click on the "Company > address and registration details" link at the bottom of the page.. > ______________________________________________________________________ > > > ------------------------------------------------------------------------------ > Cloud Computing - Latest Buzzword or a Glimpse of the Future? > This paper surveys cloud computing today: What are the benefits? > Why are businesses embracing it? What are its payoffs and pitfalls? > http://www.accelacomm.com/jaw/sdnl/114/51425149/ > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
From: Thomas H. <sp...@us...> - 2011-12-15 12:27:59
|
Hi James, I can confirm this, looks like a recently introduced bug. Correct result with pymol-1.4.1 Wrong result with pymol-1.5.0b1 Troels is right, if you alter the IDs you can work around the bug. alter ala2, ID=ID+100 But AFAIK only `index` is a unique atom property in PyMOL, so still I would consider this a bug. Cheers, Thomas On 12/15/2011 12:23 AM, James Davidson wrote: > Dear All, > I am currently having a problem with the distance command when applied > to merged objects. The real case is actually when I remove a ligand from > a binding site and merge in a new ligand. But as a simple example, I > think I can demonstrate with the following: >>frag ala, ala1 >>frag ala, ala2 >>translate [4,0,0], ala2 >>label all, ID >>distance d1, ala1 & ID 3, ala2 & ID 0 > This creates a distance object fine. But if I now merge the two objects > into a new object: >>create new, ala1 | ala2 >>disable ala1 | ala2 > and manually create two single atom selections corresponding to the > original ID 3 and ID 0 atoms (using atom select mode and renaming the > selections to give 'sele1' and 'sele2'): >>distance d2, sele1, sele2 > gives me a distance between ID 0 and 3 both on what used to be ala2, and > not between the two selected atoms! > Am I doing something wrong with 'create'? I don't recall having a > problem with this sort of operation until maybe ~ 6 months ago... I am > using rev 3971 under Windows. Any help/advice greatly appreciated. > Kind regards > James > > ______________________________________________________________________ > PLEASE READ: This email is confidential and may be privileged. It is > intended for the named addressee(s) only and access to it by anyone else > is unauthorised. If you are not an addressee, any disclosure or copying > of the contents of this email or any action taken (or not taken) in > reliance on it is unauthorised and may be unlawful. If you have received > this email in error, please notify the sender or > pos...@ve.... Email is not a secure method of communication > and the Company cannot accept responsibility for the accuracy or > completeness of this message or any attachment(s). Please check this > email for virus infection for which the Company accepts no > responsibility. If verification of this email is sought then please > request a hard copy. Unless otherwise stated, any views or opinions > presented are solely those of the author and do not represent those of > the Company. > > The Vernalis Group of Companies > Oakdene Court > 613 Reading Road > Winnersh, Berkshire > RG41 5UA. > Tel: +44 118 977 3133 > > To access trading company registration and address details, please go to > the Vernalis website at www.vernalis.com and click on the "Company > address and registration details" link at the bottom of the page.. > ______________________________________________________________________ -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: Jason V. <jas...@sc...> - 2011-12-16 19:22:51
|
James, > I am currently having a problem with the distance command when applied to > merged objects. The real case is actually when I remove a ligand from a > binding site and merge in a new ligand. But as a simple example, I think I > can demonstrate with the following: The problem is in the create command. We'll try to fix it soon. Cheers, -- Jason On Wed, Dec 14, 2011 at 6:23 PM, James Davidson <J.D...@ve...> wrote: > Dear All, > > I am currently having a problem with the distance command when applied to > merged objects. The real case is actually when I remove a ligand from a > binding site and merge in a new ligand. But as a simple example, I think I > can demonstrate with the following: > >>frag ala, ala1 >>frag ala, ala2 >>translate [4,0,0], ala2 >>label all, ID >>distance d1, ala1 & ID 3, ala2 & ID 0 > > This creates a distance object fine. But if I now merge the two objects > into a new object: > >>create new, ala1 | ala2 >>disable ala1 | ala2 > > and manually create two single atom selections corresponding to the original > ID 3 and ID 0 atoms (using atom select mode and renaming the selections to > give 'sele1' and 'sele2'): > >>distance d2, sele1, sele2 > > gives me a distance between ID 0 and 3 both on what used to be ala2, and not > between the two selected atoms! > > > Am I doing something wrong with 'create'? I don't recall having a problem > with this sort of operation until maybe ~ 6 months ago... I am using rev > 3971 under Windows. Any help/advice greatly appreciated. > > Kind regards > > James > > ______________________________________________________________________ > PLEASE READ: This email is confidential and may be privileged. It is > intended for the named addressee(s) only and access to it by anyone else is > unauthorised. If you are not an addressee, any disclosure or copying of the > contents of this email or any action taken (or not taken) in reliance on it > is unauthorised and may be unlawful. If you have received this email in > error, please notify the sender or pos...@ve.... Email is not a > secure method of communication and the Company cannot accept responsibility > for the accuracy or completeness of this message or any attachment(s). > Please check this email for virus infection for which the Company accepts no > responsibility. If verification of this email is sought then please request > a hard copy. Unless otherwise stated, any views or opinions presented are > solely those of the author and do not represent those of the Company. > > The Vernalis Group of Companies > Oakdene Court > 613 Reading Road > Winnersh, Berkshire > RG41 5UA. > Tel: +44 118 977 3133 > > To access trading company registration and address details, please go to the > Vernalis website at www.vernalis.com and click on the "Company address and > registration details" link at the bottom of the page.. > ______________________________________________________________________ > > ------------------------------------------------------------------------------ > Cloud Computing - Latest Buzzword or a Glimpse of the Future? > This paper surveys cloud computing today: What are the benefits? > Why are businesses embracing it? What are its payoffs and pitfalls? > http://www.accelacomm.com/jaw/sdnl/114/51425149/ > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Jason V. <jas...@sc...> - 2011-12-16 22:08:11
|
James, This bug is now fixed in the open-source code (commit 3974) and will be fixed in the next beta build of Incentive PyMOL. Cheers, -- Jason On Wed, Dec 14, 2011 at 6:23 PM, James Davidson <J.D...@ve...> wrote: > Dear All, > > I am currently having a problem with the distance command when applied to > merged objects. The real case is actually when I remove a ligand from a > binding site and merge in a new ligand. But as a simple example, I think I > can demonstrate with the following: > >>frag ala, ala1 >>frag ala, ala2 >>translate [4,0,0], ala2 >>label all, ID >>distance d1, ala1 & ID 3, ala2 & ID 0 > > This creates a distance object fine. But if I now merge the two objects > into a new object: > >>create new, ala1 | ala2 >>disable ala1 | ala2 > > and manually create two single atom selections corresponding to the original > ID 3 and ID 0 atoms (using atom select mode and renaming the selections to > give 'sele1' and 'sele2'): > >>distance d2, sele1, sele2 > > gives me a distance between ID 0 and 3 both on what used to be ala2, and not > between the two selected atoms! > > > Am I doing something wrong with 'create'? I don't recall having a problem > with this sort of operation until maybe ~ 6 months ago... I am using rev > 3971 under Windows. Any help/advice greatly appreciated. > > Kind regards > > James > > ______________________________________________________________________ > PLEASE READ: This email is confidential and may be privileged. It is > intended for the named addressee(s) only and access to it by anyone else is > unauthorised. If you are not an addressee, any disclosure or copying of the > contents of this email or any action taken (or not taken) in reliance on it > is unauthorised and may be unlawful. If you have received this email in > error, please notify the sender or pos...@ve.... Email is not a > secure method of communication and the Company cannot accept responsibility > for the accuracy or completeness of this message or any attachment(s). > Please check this email for virus infection for which the Company accepts no > responsibility. If verification of this email is sought then please request > a hard copy. Unless otherwise stated, any views or opinions presented are > solely those of the author and do not represent those of the Company. > > The Vernalis Group of Companies > Oakdene Court > 613 Reading Road > Winnersh, Berkshire > RG41 5UA. > Tel: +44 118 977 3133 > > To access trading company registration and address details, please go to the > Vernalis website at www.vernalis.com and click on the "Company address and > registration details" link at the bottom of the page.. > ______________________________________________________________________ > > ------------------------------------------------------------------------------ > Cloud Computing - Latest Buzzword or a Glimpse of the Future? > This paper surveys cloud computing today: What are the benefits? > Why are businesses embracing it? What are its payoffs and pitfalls? > http://www.accelacomm.com/jaw/sdnl/114/51425149/ > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: James D. <J.D...@ve...> - 2011-12-16 22:44:53
|
Hi Jason, > This bug is now fixed in the open-source code (commit 3974) > and will be fixed in the next beta build of Incentive PyMOL. That was quick work - thanks! Kind regards James ______________________________________________________________________ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or pos...@ve.... Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the "Company address and registration details" link at the bottom of the page.. ______________________________________________________________________ |