[PyMOL] Still need help with fetch and pymol 1.7

2014-01-20 Thread Lapolla, Suzanne M (HSC)
I am posting this again as I have still not figured out why I am unable to fetch or use the pdb plugin loader with pymol 1.7 I have cut/copied/pasted the error msg I get below. I have tried uninstalling and reinstalling python 2.7.6 as well as python 1.7 (I have windows 64 bit --so I tried the

Re: [PyMOL] Still need help with fetch and pymol 1.7

2014-01-20 Thread David Hall
I think there's a bug in python's code, not pymol's In the file that it describes at the end ( C:\Python27\lib\mimetypes.py ) , you should change line 250 from: except UnicodeEncodeError: to except (UnicodeEncodeError,UnicodeDecodeError): keeping the indentation in the file and so on. Then the

Re: [PyMOL] PyMOL v1.7 Released

2014-01-20 Thread Michael Banck
Hi, On Tue, Jan 14, 2014 at 05:11:51PM -0600, Jason Vertrees wrote: We are happy to announce the release of PyMOL v1.7.0.0! Congrats! One thing though: the open-source splash image has not been updated for 1.7 and still says 1.6.x. Michael

Re: [PyMOL] Still need help with fetch and pymol 1.7

2014-01-20 Thread Lapolla, Suzanne M (HSC)
Thank you thank you! I will try that later today--I do appreciate the help. Did I say thank you yet? Suzanne From: David Hall [li...@cowsandmilk.net] Sent: Monday, January 20, 2014 8:34 AM To: Lapolla, Suzanne M (HSC) Cc: pymol-users@lists.sourceforge.net

Re: [PyMOL] PyMOL v1.7 Released

2014-01-20 Thread Jason Vertrees
Michael, Nice catch—we'll fix it. Thanks for letting us know. Cheers, -- Jason On Mon, Jan 20, 2014 at 9:11 AM, Michael Banck mba...@gmx.net wrote: Hi, On Tue, Jan 14, 2014 at 05:11:51PM -0600, Jason Vertrees wrote: We are happy to announce the release of PyMOL v1.7.0.0! Congrats!

[PyMOL] Pymol, number and label the helices

2014-01-20 Thread Gefei Chen
Hi guys, I am now preparing some proteins structure figures, and I think Pymol is a good program. But now something happened to me, my protein just has 5 helices, and I want to number and label the helices as H1, H2 …and H5 in the figure with using Pymol directly (not photoshop), but I am

[PyMOL] mutagenesis wizard data file loading

2014-01-20 Thread Michael Banck
Hi, I noticed that the mutagenesis wizard uses PYMOL_PATH/data to locate the chempy sidechains, however, PYMOL_DATA would be more appropriate if the data is not installed alongside the pymol modules. The attached patch fixes this. Michael --- ./modules/pymol/wizard/mutagenesis.py.orig

Re: [PyMOL] Pymol, number and label the helices

2014-01-20 Thread Jason Vertrees
Gefei, Please read about labels (http://www.pymolwiki.org/index.php/Label; and http://www.pymolwiki.org/index.php/Category:Labeling) and pseudoatoms ( http://www.pymolwiki.org/index.php/Pseudoatom). These should help you label what you need to. Cheers, -- Jason On Mon, Jan 20, 2014 at 9:57

Re: [PyMOL] Still need help with fetch and pymol 1.7

2014-01-20 Thread Lapolla, Suzanne M (HSC)
Just wanted to say that your fix did solve my problem. Thanks again! From: David Hall [li...@cowsandmilk.net] Sent: Monday, January 20, 2014 8:34 AM To: Lapolla, Suzanne M (HSC) Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Still need help

Re: [PyMOL] mutagenesis wizard data file loading

2014-01-20 Thread Jason Vertrees
Michael, I think you're right. We'll make and push the changes. Cheers, -- Jason On Mon, Jan 20, 2014 at 10:40 AM, Michael Banck mba...@gmx.net wrote: Hi, I noticed that the mutagenesis wizard uses PYMOL_PATH/data to locate the chempy sidechains, however, PYMOL_DATA would be more