COOT not "connected" to PHENIX

From: Yuri <yuri.pompeu
Date: 25 October 2011 22:02
I installed the version with python embedded in coot
And it works!!
Thanks a lot!!

On Tue, 25 Oct 2011 11:41:38 -0700, Nathaniel Echols wrote:

On Tue, Oct 25, 2011 at 11:40 AM, Yuri > wrote:

Now here comes the stupid question...
How do I fix it?
Install a different coot version or is it something in my architecture?

Install a different Coot.  If you're downloading from Paul Emsley's
page, you need a package with "python" in the file name.  I have no
idea whether the Linux binaries distributed by CCP4 have Python or not
(the Mac version definitely does).

-Nat

--
Yuri Pompeu

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From: Paul Emsley
FYI, from version 0.7, I will not distribute binaries without python.

Paul.

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From: Tim Gruene

Grand - with every python script one has to distribute a specific python
version. More food for my prejudice against python ;-)
Tim

- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen


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From: Ed Pozharski
... and with every program one has to distribute binaries for every
platform... more food for my prejudice against software ;-)

This really is not about python, it's about distributing with or without
dependencies.  And you are absolutely right about that: for example,
ccp4-6.2.0 comes with python2.6.7 embedded, and, if one goes with
defaults and downloads coot with it, python2.6 in coot's lib folder.
Same with phenix - you get python2.7 with it and python2.4 with
pymol0.99 that comes with it.  By the way, I already have another pymol
that I compiled myself (1.4) and the one from ubuntu repositories (1.2).
Except for the latter, each carries its own copy of whichever python it
needs.  Every single python avatar takes 50-100Mb of space, which is
fortunately not in short supply.

This is why the right way to distribute *nix software is to distribute
software itself and ask the end-user to get all the dependencies (not
that hard these days).  It is fully understood, of course, that people
that do this for living find it more troublesome to deal with me whining
about how their software is screwing up my matplotlib than to just give
me another python copy. What's an extra 50Mb between friends ;-)

Cheers,

Ed.

--
"I'd jump in myself, if I weren't so good at whistling."
                              Julian, King of Lemurs

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From: Jaime Jensen
I experienced this same issue a while ago. When I attempt to reinstall coot using Fink (instructions on Bill Scott's coot page), I receive this error in Terminal:

WARNING: While resolving dependency "nose-py27" for package "numpy-py27-1.5.1-1", package "nose-py27" was not found.
Reading build dependency for numpy-py27-1.5.1-1...
WARNING: While resolving dependency "nose-py27" for package "numpy-py27-1.5.1-1", package "nose-py27" was not found.
Can't resolve dependency "nose-py27" for package "numpy-py27-1.5.1-1" (no
matching packages/versions found)
Exiting with failure.


I had originally downloaded ccp4-6.2.0 (Mac version), and experienced no problems until I tried to open coot from PHENIX. Any suggestions on how to resolve this issue?


Jaime

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From: Pavel Afonine
Hi,

it is a wonderful idea, apart from two tiny nuances: 1) many have no idea about what the command line is, and 2) asking users going through the trouble of installing dependencies will scare them away from the software. Personally, I do not use programs that do not work right out of the box or take more than a minute to make it run. 

So, I would rather let the majority use whatever works, and let a few gurus count versions of Python in various software and how much space they take.

Pavel