[PyMOL] Importing simplejson in pymol on OSX

2012-07-24 Thread Matthew Baumgartner
Hi, I wrote a short script that I am going to use in pymol. I need to parse a json file and then display the contents in some manner. It works just fine in Ubuntu 12.04, but when I try it on OSX, it doesn't work. The problem that I am having is that when I try `import simplejson` or `import js

Re: [PyMOL] Tagging di-sulfide bonds in trial version of pymol

2012-07-24 Thread Thomas Holder
On 07/24/2012 05:54 PM, Arjun Sharma wrote: > Any idea on how to tag/label di-sulfide bonds in protein in the > Macpymol (trial version). For some reason I am unable to use the > disulfide label option provided in the dropdown menu of the program. How about something like this: select disulfide,

[PyMOL] Tagging di-sulfide bonds in trial version of pymol

2012-07-24 Thread Arjun Sharma
Hi, Any idea on how to tag/label di-sulfide bonds in protein in the Macpymol (trial version). For some reason I am unable to use the disulfide label option provided in the dropdown menu of the program. -- Live Security

Re: [PyMOL] sequence file extraction

2012-07-24 Thread Robert Campbell
Hi Thomas, On Tue, 2012-07-24 12:57 EDT, Thomas Holder wrote: > Hi Stefano, > > this is a known bug and it has not been fixed yet. A workaround is to > only save one object at a time to fasta format. > > See bug report: > http://sourceforge.net/tracker/?func=detail&aid=3466472&group_id=4546

Re: [PyMOL] sequence file extraction

2012-07-24 Thread Jason Vertrees
Hi Vaheh, Thanks for pointing this out. I just fixed this, am testing, and will push the changes shortly. Cheers, -- Jason On Tue, Dec 27, 2011 at 11:15 AM, Oganesyan, Vaheh wrote: > I'm using ver. 1.4.1 and it looks like PyMOL recently lost the ability to > extract the sequence info. > I'm

Re: [PyMOL] sequence file extraction

2012-07-24 Thread Thomas Holder
Hi Stefano, this is a known bug and it has not been fixed yet. A workaround is to only save one object at a time to fasta format. See bug report: http://sourceforge.net/tracker/?func=detail&aid=3466472&group_id=4546&atid=104546 Cheers, Thomas On 07/24/2012 12:08 PM, Stefano Marzi wrote: > I

Re: [PyMOL] sequence file extraction

2012-07-24 Thread Stefano Marzi
I have got the same problem with pymol 1.5.0.4 and restarting the computer is not fixing it. Any help please? Thanks Stefano Le 27/12/2011 20:19, Oganesyan, Vaheh a écrit : > Never mind. After restarting the computer fasta file is being written. > > Vaheh > > > > > -Original Message-