[PyMOL] util.ss error

Hi all I am trying to assign secondary structure for a pdb file and get the following error: PyMOL>util.ss util.ss: WARNING: This is not a "correct" secondary structure util.ss: assignment algorithm! Please use only as a last resort. util.ss: initiating secondary structure assignment on 224 r

[PyMOL] residues deviate from protein secondary catoon representation

Dear pymol users, I am trying to show some residues in sticks while the whole protein is in cartton representation. However I find that some residues do not attach to the cartoon at all. I understand that the secondary cartoon is an approximation along the backbone. Is there a way that I can show

[PyMOL] show residues forming hydrogen bonds with each other

Hi, I have the following task to do and wonder if anyone can show a simple way to do it. I want to show the residues forming intermolecular hydrogen bonds between two proteins. dist protein A, protein B, 3.5 Then I want to show those residues that form hydrogen bonds with each other. How do I

[PyMOL] pymol on os x.3

Hi, I recently installed pymol 0.93 on panther. It turns out that all menus on the viewr are missing. I wonder if this is normal in the new pymol. Thanks. Yunfeng

[PyMOL] play gif movie in powerpoint

Hi, I use "convert" to generate a gif file from series of png files produced by pymol. However I cannot get the ideal speed in powerpoint as seen using safari. It seems too jumpy in powerpoint. Does anybody have the same problem? Thanks. Eric ### Research Associ

[PyMOL] pymol + gromacs trajectories

Hi, I wonder if people can give a summary of how pymol makes movies out of gromacs trr (or xtc) files without having to use all the individual frame pdb files. Thanks! Eric

Re: [PyMOL] pymol + gromacs trajectories

Thank you, Bruno and Tsjerk. I found both approaches work very well. Eric Frankly, with Pymol, people don't as far as I know. What I usually do is determine for the first frame of the individual pdb files (obtained with trjconv -sep) the orientation, viewing point and appearance. This I save

[PyMOL] blinking pictures on sgi4DIRIX646

Hi, I have pymol 0.97 installed on a sgi workstation. However it keeps the old picture when I move the molecule, which seems like a long time delay. I wonder if people have similar experience. Eric

Re: [PyMOL] blinking pictures on sgi4DIRIX646

It is indeed a Octane with IRIX64 6.5. Date: Thu, 25 Nov 2004 09:50:51 -0800 (PST) From: Nat Echols To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] blinking pictures on sgi4DIRIX646 Hi, I have pymol 0.97 installed on a sgi workstation. However it keeps the old picture when I move th