Re: [PyMOL] nucleic acid (one or two letter) residue names

that's true, residue names should be right-justified. http://www.wwpdb.org/documentation/format32/sect1.html Residue nameOne of the standard amino acid or nucleic acids, as listed below, or the non-standard group designation as defined in the HET dictionary. Field is

Re: [PyMOL] nucleic acid (one or two letter) residue names

Hi, On Wed, May 18, 2011 at 6:00 AM, Thomas Holder spel...@users.sourceforge.net wrote: that's true, residue names should be right-justified. This is a bug. Please file it on our open-source bug tracker http://sourceforge.net/tracker/?group_id=4546atid=104546. I will fix it when I get the

Re: [PyMOL] nucleic acid (one or two letter) residue names

Hi Pascal, On 05/18/2011 04:46 PM, Pascal Auffinger wrote: Thanks, could you do that and provide a binary ? I can't provide a binary, sorry. Or alternatively, could you post precisely which line to change to what ? Or change it in the source code so that we could download an updated

Re: [PyMOL] nucleic acid (one or two letter) residue names

On 05/18/2011 05:01 PM, Jason Vertrees wrote: This is a bug. Please file it on our open-source bug tracker http://sourceforge.net/tracker/?group_id=4546atid=104546. I will fix it when I get the chance. Bugs item #3304003

Re: [PyMOL] PyMOL-users Digest, Vol 60, Issue 7

Hi PyMOL Community, I have a trajectory file loaded into PyMOL but I would like to play the movie in reverse order. Is there a way to achieve this within PyMOL? I know that I could do this by outputting the states as PNG files and then reversing them in an external program but I would like

Re: [PyMOL] PyMOL-users Digest, Vol 60, Issue 7

On 05/18/2011 06:50 PM, Sean Law wrote: Hi PyMOL Community, I have a trajectory file loaded into PyMOL but I would like to play the movie in reverse order. Is there a way to achieve this within PyMOL? If you have 100 states, type: mset 100-1 See also: http://www.pymolwiki.org/index.php/Mset

[PyMOL] change transparency for only a selection

Hello list, I would like to change the stick_transparency for a selection but it doesn't seem to work. I am using the xyz file from the wiki: http://www.pymolwiki.org/index.php/Visualizing_a_computed_structure_-_a_commented_example and the attached script. What am I doing wrong? Thanks

Re: [PyMOL] change transparency for only a selection

Hi Nick, Sticks are bonds. For that we use set_bond not set. Try: set_bond stick_transparency, 0.8, rest set_bond stick_transparency, 0.0, sel_01 Cheers, -- Jason On Wed, May 18, 2011 at 1:39 PM, Nicolas Bock nicolasb...@gmail.com wrote: Hello list, I would like to change the

Re: [PyMOL] change transparency for only a selection

Hi Nick, On Wed, 2011-05-18 11:39 EDT, Nicolas Bock nicolasb...@gmail.com wrote: Hello list, I would like to change the stick_transparency for a selection but it doesn't seem to work. I am using the xyz file from the wiki:

Re: [PyMOL] change transparency for only a selection

Hi Jason, thanks, that works! nick On 05/18/11 12:08, Jason Vertrees wrote: Hi Nick, Sticks are bonds. For that we use set_bond not set. Try: set_bond stick_transparency, 0.8, rest set_bond stick_transparency, 0.0, sel_01 Cheers, -- Jason On Wed, May 18, 2011 at 1:39 PM,

[PyMOL] movie: interpolate between different states

Hi, can pymol interpolate between states in a movie? Suppose I have coordinates of a docking process with several states, and I would like to animate that process, but smoothly. I would madd 1 x15 madd 2 x15 . . . but would like pymol to interpolate in those 15 frames between state 1 and 2,

Re: [PyMOL] nucleic acid (one or two letter) residue names

Hi Thomas, Thanks for submitting the bug. I've modified and applied the patch and pushed the code. It's fixed. Cheers, -- Jason On Wed, May 18, 2011 at 11:43 AM, Thomas Holder spel...@users.sourceforge.net wrote: On 05/18/2011 05:01 PM, Jason Vertrees wrote: This is a bug.  Please file it

Re: [PyMOL] movie: interpolate between different states

Hi Nick, You can use the smooth command (http://www.pymolwiki.org/index.php/Smooth) on the structure of choice. Incentive PyMOL comes with a molecular morpher called rigimol that morphs a starting structure into an ending structure. I suggest trying the smooth command first if you already have

Re: [PyMOL] movie: interpolate between different states

Hi Jason, I have the incentive version, but how do I use rigimol? I can't find documentation for it on the documentation webpage. The link from http://pymol.org/dsc/dokuwiki/doku.php?id=ips=rigimol seems to be dead. Thanks, nick On 05/18/11 15:20, Jason Vertrees wrote: Hi Nick, You can

[PyMOL] change atom coordiates?

Hello, can I selectively change coordinates of particular atoms in a state? It seems that alter_state is not able to do that, since the expression (at least according to the help text) seems to apply to the x-coordinate of all atoms in the state for instance. The result of cmd.get_model() might

Re: [PyMOL] change atom coordiates?

Hi Nicolas, can I selectively change coordinates of particular atoms in a state? Yes, you just need to properly select that atom. It seems that alter_state is not able to do that, since the expression (at least according to the help text) seems to apply to the x-coordinate of all atoms in