Re: [PyMOL] Creating of chmeric protein

2012-01-29 Thread James Starlight
Hi Jordan! Thank you for so detailed explanation Indeed I've noticed that so simple operation is very routine in pymol :( Now I'm looking for good easy-to-use modelling software wich is free for accademical users. I'd like that this soft would have good graphical interphace and flexibility lik

Re: [PyMOL] Editing of the pdb structure

2012-01-29 Thread Tim Schulte
Dear James, I agree with Joao, for fast and dirty minimisation you might try the program Chimera or VegaZZ. If you just wanna have an energy-minimized small molecule the Prodrg server is the way to go. Cheers, Tim Von: João Rodrigues [anar...@gmail.com] Gesendet:

[PyMOL] Open .pdb / .pml files in ubuntu/mint

2012-01-29 Thread Troels Emtekær Linnet
Hi guys. Ehh. I have a newly installed Mint 12 box with gnome 3. I have that annoying thing, that when I click a text .pdb files, it opens with gedit. Then I can right click and select .pdb files to open with pymol. But when I then click a .txt file, it opens it with pymol. Grrr... I know its so

Re: [PyMOL] Open .pdb / .pml files in ubuntu/mint

2012-01-29 Thread Jordan Willis
Hmm, Have you tried putting a .txt and .pdb file on your desktop. Right click either one and click Properties. There is an Open With tab. It should say "Open this file and other .txt files with" and then you can select gedit. Conversely do the same for .pdb files. Jordan On Jan 29, 2012, a

Re: [PyMOL] Open .pdb / .pml files in ubuntu/mint

2012-01-29 Thread Jordan Willis
Oh duh, You are saying the .pdb is read as a "plain text file" You would then have to add a new mime type ".pdb" to the source XML file that gnome reads in /usr/share/mime/packages/freedesktop.org.xml http://library.gnome.org/admin/system-admin-guide/stable/mimetypes-source-xml.html.en Sorry