Re: [PyMOL] Quick PyMOL Autodock/Vina Plugin advice

2010-06-07 Thread Daniel Seeliger
Hi Kristina, this sometimes happens. I actually don't know why but if you set the environmental variable ADPLUGIN_NO_OUTPUT_REDIRECT it should not happen anymore. Cheers, Daniel On Monday 07 June 2010 06:50:49 pm vivat mesin wrote: > Hi Everyone, > > I am troubleshooting my Autodock/Vina Pl

Re: [PyMOL] Autodock/vina plugin for pymol on MAC

2010-06-07 Thread Daniel Seeliger
Hi, that means numpy is missing on your system. The easiest way to get rid of this problem is to upgrade to version 1.2 (I guess you're using the old 0.99). cheers, Daniel On Monday 07 June 2010 08:46:14 pm Sandip Bharate wrote: > Hello , > > > > I have problem is installing ‘Autodock/vina

[PyMOL] Autodock/vina plugin for pymol on MAC

2010-06-07 Thread Sandip Bharate
Hello , I have problem is installing ‘Autodock/vina plugin’ for pymol on Mac (Snow Leopard). I tried to install it …..i got the message that “Autodock.py plugin has been installed. Restart pymol to begin use” but it was not actually installed …the error message was…..”ImportError: No module na

[PyMOL] Quick PyMOL Autodock/Vina Plugin advice

2010-06-07 Thread vivat mesin
Hi Everyone, I am troubleshooting my Autodock/Vina Plugin installation, and I am able to write the Vina input file, but when I try to run Vina, I get an "Exception in thread" error in threading.py, autodock.py, and Tkinter.py. I have pasted the error below. If you have any advice, please let m

[PyMOL] how to save coordinate for cut DNA

2010-06-07 Thread Sangita Kachhap
Hello all I have to cut phosphodiester bond in DNA.I am able to cut it by selecting pk1 and pk2 and then deleting the bond. But I am not able to save the coordinate. When I am saving by "save molecule" and aging loading the saved molecule original molecule(Uncut DNA) is loaded. Can anybody sugg

Re: [PyMOL] help with moving objects separately

2010-06-07 Thread Jason Vertrees
Mary, The duplication idea was correct, but most likely needed to be done via the command line for flexibility: duplicating a single object of two+ chains results in an object of two+ chains. Thus, calling rotate on the new object will rotate both chains in the new object. If you want to just ro

[PyMOL] help with moving objects separately

2010-06-07 Thread Mary B. Kennedy
I am trying to create a view of a homomultimeric protein by duplicating the structure of its subunit and rotating them around a central axis. I am finding this difficult as the commands don't always behave as I expect them to. Can you tell me the best commands to use in this task. For ex