[PyMOL] install Pymol 1.5 on Linux Mint 13

2013-09-12 Thread Vitali Stanevich
Hi, I'm trying to install PyMOL-v1.5.0.4-Linux-x86_64 on Linux Mint 13. After successful unpacking, sh-ing and copying into /usr/local/bin/pymol I tried to execute Pymol from the terminal, but error came out: vitali@vs-Think ~/install/pymol $ pymol /home/vitali/install/pymol/pymol.exe: 1:

Re: [PyMOL] 1.5 version runs slow with large objects

2012-02-16 Thread Vitali Stanevich
card? Cheers, -- Jason On Tue, Feb 14, 2012 at 5:27 PM, Vitali Stanevich stanev...@wisc.edu wrote: Hi, I recently installed a new version of licensed pymol 1.5. It works ok with small molecules (25 kDa). But, unfortunately, I found that after I load relatively large molecules (60

Re: [PyMOL] 1.5 version runs slow with large objects

2012-02-16 Thread Vitali Stanevich
, you need the use_shaders setting turned on. Cheers, -- Jason On Thu, Feb 16, 2012 at 2:09 PM, Vitali Stanevich stanev...@wisc.edu wrote: Jason, I did install latest driver for a card (295.20) from nvidia site. The problem still exists. Any other suggestions? Thanks, Vitali

[PyMOL] 1.5 version runs slow with large objects

2012-02-14 Thread Vitali Stanevich
Hi, I recently installed a new version of licensed pymol 1.5. It works ok with small molecules (25 kDa). But, unfortunately, I found that after I load relatively large molecules (60 kDa) everything really slows down, movements become somewhat abrupt and etc. At the same time, I can open this

Re: [PyMOL] query

2011-11-21 Thread Vitali Stanevich
these residues, but is there any way to depict these hydrogen bonds also and the distances? Dr. Jayashree Ramana http://www.juit.ac.in/bio/jsr.php -- *From:* Vitali Stanevich stanev...@wisc.edu *To:* rjayashree13-scie...@yahoo.co.in rjayashree13-scie...@yahoo.co.in

Re: [PyMOL] query

2011-11-20 Thread Vitali Stanevich
check this out: http://www.pymolwiki.org/index.php/InterfaceResidues if you want faster and easier, but less reliable (in my opinion) way, you can analyze your .pdb with PISA: http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html vitali On Sun, Nov 20, 2011 at 1:51 AM,

Re: [PyMOL] Movie to export

2011-11-09 Thread Vitali Stanevich
have a look at this link: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Morph_with_Chimera disregard morph part. you can modify script to contain frames instead of states. i installed ffmpeg from repositories on ubuntu and don't remember any issues with kodecs. vitali On Wed, Nov

Re: [PyMOL] Movie to export

2011-11-09 Thread Vitali Stanevich
one more thing: ffmpeg script at that link didn't work for me so i had to modify it like that ffmpeg -f image2 -qscale 5 -r 24 -b 9600 -i image%d.png movie.mpg On Wed, Nov 9, 2011 at 11:22 PM, Vitali Stanevich stanev...@wisc.eduwrote: have a look at this link: http://strucbio.biologie.uni