Re: [PyMOL] Label size in different scenes

Vitaly, What you want is the "mdo" command. Check it out: http://www.pymolwiki.org/index.php/Mdo. We are planning to add features like frame-based settings in a future release. Cheers, -- Jason On Tue, Apr 20, 2010 at 1:09 AM, Vitaly Vostrikov wrote: > After playing around for several days,

[PyMOL] PyMOL loop

Hi again everyone, I managed to figure out how to mutate my peptide in PyMOL with non-natural amino acids, with the help of David's script. Now I'd like to create a "loop" at a particular point for a list of my residues (in .pkl text files). So, I would like PyMOL to automatically apply the mutat

[PyMOL] attaching phosphate

Hi, is it possible to attach a phosphate to a residue? I used the following commands >create Phos, elem p >show spheres, phos but I don't know how to control which amino acid the phosphate is added to. I repeated the process two different times, and the amino acid was added to the same pho

[PyMOL] Rigimol morph using only part of protein

I am trying to create a morph of a hinge region between two rigid domains. I would like to hold one domain in place and allow the other to morph from open to closed instead of a morph between the whole protein looking more like a pacman model. Any tutorials on this approach. Thanks, Patrick

Re: [PyMOL] attaching phosphate

Alaena, The easiest way is to use PyMOL's built-in Molecular Builder. Click on the "Builder" Tab from the upper control window (or see http://pymolwiki.org/index.php/Builder). It should be pretty straightforward. You can also investigate the "replace" command, with "help replace". To use it, fi

Re: [PyMOL] Label size in different scenes

Thank you, Jason. I guess I need to dig in the mailing list archive to find a bit more information on the usage of "mdo", since at this time I am rather confused at the proper application of "mview" and "mdo" for the scene transitions (aka movies). Vitaly - Original Message - From: Ja

Re: [PyMOL] Rigimol morph using only part of protein

I've not used rigimol, so at the risk of suggesting something you can't do: could you just add an align call that aligns one of the domains at each frame? On Tue, Apr 20, 2010 at 10:45 AM, Patrick Frantom wrote: > I am trying to create a morph of a hinge region between two rigid > domains. I wou

Re: [PyMOL] Label size in different scenes

Vitaly, mview just handles the position of the camera and clipping planes. mdo repeats given command(s) before the rendering of a given frame. The PyMOLWiki, the list archives and Google should offer more help. -- Jason On 4/20/10, Vitaly Vostrikov wrote: > Thank you, Jason. > > I guess I nee