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 > 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.. > ______________________________________________________________________ -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ 10 Tips for Better Server Consolidation Server virtualization is being driven by many needs. But none more important than the need to reduce IT complexity while improving strategic productivity. Learn More! http://www.accelacomm.com/jaw/sdnl/114/51507609/ _______________________________________________ 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
