[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 "/home/jose

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 c

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] Se

[PyMOL] CAVER resolved (sort of)

BS"D 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 a

Re: [PyMOL] Pymol build from source

Dear Joseph, On Tue, 07 Jul 2009 11:00:10 +0200, Andre Joseph 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 launch pymol

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 tr

Re: [PyMOL] unexpected EOF while parsing

Thanks. It works now. Original message >Date: Tue, 7 Jul 2009 18:11:56 +0200 >From: Tsjerk Wassenaar >Subject: Re: [PyMOL] unexpected EOF while parsing >To: jo...@uchicago.edu, pymol-users > >Hi Jouko, > >You were writing a python script. Now Pymol API can handle basic >Python, bu

[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 sphere

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, po

Re: [PyMOL] CAVER resolved (sort of)

On Jul 7, 2009, at 5:48 AM, Harry M. Greenblatt wrote: > BS"D > > 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 t

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 py

Re: [PyMOL] Pymol build from source

Robert & Joseph: I just updated and tested both of the distutils and autotools open-source build systems to match the current source -- you should be good to go. please "svn update" and retry Cheers, Warren > -Original Message- > From: Robert Campbell [mailto:robert.campb...@queensu.ca]