[PyMOL] CAVER question

BSD Dear All, I addressed this question to the CAVER contact address, but it bounced. I downloaded and tested the latest CAVER plugin on Linux and it worked fine. I also wanted to test this under OSX, but the readme file says that one needs JRE 1.6, and the latest upgrade to JRE on

Re: [PyMOL] pymol question

Hi, You can draw a CGO circle in the yz plane using: x1,y1,z1 = -0.1, 0, 0 # start point r1,g1,b1 = 1,0,0 # color (red) x2,y2,z2 = 0.1, 0, 0 # end point r2,g2,b2 = 1,1,0 # color (yellow) radius = 10 cmd.load_cgo( [ 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2, b2 ], cylinder1 ) To

[PyMOL] Pymol build from source

Dear Delano Scientific support I've been fetching source code from the sourceforge repositories yesterday. I've no error or warning during ./configure, make or make install steps. However, when I launch pymol, I've the following error: Traceback (most recent call last): File

Re: [PyMOL] unexpected EOF while parsing

Hi Jouko, I think you went through the Python and Pymol tutorials a bit too fast ;) You're writing a Python script to be loaded with 'run'. That means you have to adhere to Python API and can't use the Pymol specific language. E.g. you can't use 'png pdb', but have to use 'cmd.png(pdb)' in which

Re: [PyMOL] unexpected EOF while parsing

Jouko, Try to use the cmd.load(pdb) command instead of load pdb Apparently, the load statement takes a file name as argument, not a variable, whereas the api call (cmd.load) can handle variables. Best, Grégori -Original Message- From: jo...@uchicago.edu [mailto:jo...@uchicago.edu]

[PyMOL] CAVER resolved (sort of)

BSD Dear All, Scott Dixon pointed out that you can optionally get JRE 1.6 for OSX from the Apple website. I did this, and CAVER succeeded (but see below). One does have to make sure to use Java Preferences utility in the utilities folder to make sure JRE 1.6 (i.e., J2SE 6.0) is used

Re: [PyMOL] unexpected EOF while parsing

Thanks to you and Gregori Gerebtzoff, I can now load the pdb, color the image, and save it as a picture. However I can only do that for the first cross section. I am still getting the unexpected EOF error. I did have the line indented after the loop. I think that maybe when I copied and pasted

[PyMOL] thanks for the help

thanks for the help everyone. I'll try these ideas out. thanks again!Benjamin -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new

Re: [PyMOL] Pymol build from source

Dear Joseph, On Tue, 07 Jul 2009 11:00:10 +0200, Andre Joseph andrejos...@gmail.com wrote: Dear Delano Scientific support I've been fetching source code from the sourceforge repositories yesterday. I've no error or warning during ./configure, make or make install steps. However, when I

Re: [PyMOL] unexpected EOF while parsing

Hi Jouko, You were writing a python script. Now Pymol API can handle basic Python, but it's not a one-to-one Python interpreter. To include blocks you have to do more than indentation. You have to put a slash in front of the for statement and end all but the of the blocks with a backslash. When

Re: [PyMOL] unexpected EOF while parsing

Thanks. It works now. Original message Date: Tue, 7 Jul 2009 18:11:56 +0200 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [PyMOL] unexpected EOF while parsing To: jo...@uchicago.edu, pymol-users pymol-users@lists.sourceforge.net Hi Jouko, You were writing a python script.

[PyMOL] is this how i would write a coding sequence?

I'm trying to use a suggestion another pymol user sent to create a sphere of a specific size in a pdb file. Is this the correct coding? I have no experience doing any kind of programming so I am not sure if I did this right. I put the text I entered in in red if that helps anything.bencreate

Re: [PyMOL] is this how i would write a coding sequence?

Aha! I knew there was a better way of doing this, but I was stuck on a machine that only had an old version of PyMOL. Assuming you're using PyMOL 1.0 or newer, you can just use pseudoatom. To create a sphere of radius 10.0 at the xyz position (50.0,60.0,12.0), just do this: pseudoatom mysphere,

Re: [PyMOL] CAVER resolved (sort of)

On Jul 7, 2009, at 5:48 AM, Harry M. Greenblatt wrote: BSD Dear All, Scott Dixon pointed out that you can optionally get JRE 1.6 for OSX from the Apple website. I did this, and CAVER succeeded (but see below). One does have to make sure to use Java Preferences utility in the

Re: [PyMOL] unexpected EOF while parsing

To include blocks you have to do more than indentation. You have to put a slash in front of the for statement and end all but the of the blocks with a backslash. Actually, nowadays you can just wrap Python blocks with the statements: python and python end. For example: # example pymol