Re: [PyMOL] outline in ray trace mode 2 and 3

2010-08-11 Thread piuzzi
Hi Jason, Thanks, that option works as expected. It was not referenced in pymolwiki though. Regards Quoting Jason Vertrees : > Hi Marc, > > set ray_trace_color, yourColor > > You can use named colors (eg. cyan, marine, firebrick) or hex-codes > (eg. 0xffcc00). > > Cheers, > > -- Jason > > >

Re: [PyMOL] How does PyMol add hydrogen atoms?

2010-08-11 Thread Martin Hediger
That would be really interesting to know. If there is no connectivity data provided, then my only guess is that it has some really precise bond length data to compare to. -- This SF.net email is sponsored by Make an app

[PyMOL] More DSS questions

2010-08-11 Thread Bradley Hintze
Hi, Is there more 'under the hood' to DSS? Specifically, is there a way one can see in some sort of output that a given oxygen is pointing to a given nitrogen? -- Bradley J. Hintze Graduate Student Duke University School of Medicine 801-712-8799 -

Re: [PyMOL] list of hydrogen bonds

2010-08-11 Thread Martin Hediger
I was thinking about this as well, I saw an older post on this topic http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg06211.html but it seems that the script mentioned there starts to see 'hydrogen bonds' between non-polar hydrogens and atoms up to 15 angstrom away. Can someone con

[PyMOL] movie.produce() help

2010-08-11 Thread YunHui Lisa Lin
Hi PyMOLers, I'm using the "movie.produce()" command to automate the process of saving my movie in several fragments. After saving each part, I need to clear all existing objects in order to load the next set of frames. "movie.produce" successfully saves the first movie. However, any subsequent

Re: [PyMOL] movie.produce() help

2010-08-11 Thread Jason Vertrees
Hi Lisa, This sounds like another synchronization issue. Can you try the solution here and see if it helps: http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07707.html. Also, after your initial movie is done, you can clear it out with "mset". Also check out "mclear" and "mdo".