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.david...@vernalis.com> 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 postmas...@vernalis.com. 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 (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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Learn Windows Azure Live! Tuesday, Dec 13, 2011 Microsoft is holding a special Learn Windows Azure training event for developers. It will provide a great way to learn Windows Azure and what it provides. You can attend the event by watching it streamed LIVE online. Learn more at http://p.sf.net/sfu/ms-windowsazure _______________________________________________ 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
