Re: [PyMOL] New to PyMol. Want to extract sequence from .pse file w/ colors.

Hi Pymol Network, > > I would appreciate someones help in extracting the sequence in the viewer > above the protein. I have gone through the sequence and changed AAs to > different colors based on their position. I would ideally like to be able > to copy that sequence with the colors that they are

[PyMOL] How to tell what amino acids are in view?

Hi, Does anyone know of a way to tell which amino acids are currently in view? I am imagining something that highlights the the parts of the sequence that are visible as you rotate the molecule around. It may be much more complex than I am describing. Shane ---

[PyMOL] AttributeError: 'module' object has no attribute 'super'

AttributeError: 'module' object has no attribute 'super' I am trying to run color_by_mutation http://www.pymolwiki.org/index.php/Color_By_Mutations But I get that error. Maybe my version of Mac PyMol from 2006 doesn't have that superimpose command? How do I fix this? Thank you. Shane -

[PyMOL] fink install pymol help

I installed Fink on my mac because apparently it has pymol as a port so that I can download a newer version. According to this: http://pymol.sourceforge.net/newman/user/S0120install.html In terminal I type sudo -s apt-get *pymol install* * * But it did not work. Do you know how I could install it

Re: [PyMOL] fink install pymol help

Thanks Guys I just had to self update fink. On Thu, Mar 15, 2012 at 4:46 PM, Shane Neeley wrote: > Hi, S.S. Thanks for your help. It says, > > Failed: no package found for specification 'pymol-py27'! > > null-b88d121ba616:~ chimpsarehungry$ fink list pymol > Informa

Re: [PyMOL] fink install pymol help

I've installed all of the packages for pymol-py27 with fink. And my terminal went back to normal. Now what? How do I make PyMol an application? On Thu, Mar 15, 2012 at 5:28 PM, Shane Neeley wrote: > Thanks Guys I just had to self update fink. > > > On Thu, Mar 15, 2012 at 4:46

[PyMOL] color_by_mutation needs identical atom counts?

Hi, I am using color_by_mutations on PyMol 1.3. http://www.pymolwiki.org/index.php/Color_By_Mutations I get this error: PyMOL>run color_by_mutation.py PyMOL>color_by_mutation aav2, aav8 ExecutiveRMS-Error: Atom counts between selections don't match (30882 vs 30227) Executive: Error -- no atoms

[PyMOL] Protein Parameters?

Hi, This is unrelated to PyMol, but I just wanted to spam the community to see what they think about different protein parameters. Let me know if this sort of question is inappropriate for the forum. I have thousands of randomly generated 7 amino acid peptide sequences that are within a virus. As

[PyMOL] 60-mer virus capsid (need computing power!)

Hi, Does anyone use pymol for very large structures, such as a full virus 60-mer capsid? If so, what processing power, memory, graphics card, etc. do you need to render these large files and manipulate them without any slowing? PyMol takes about 1 minute to think after trying to spin one of these

Re: [PyMOL] 60-mer virus capsid (need computing power!)

-- and we couldn't have done that work > without our supporters. So, a special thanks goes out to them! > > Cheers, > > -- Jason > > > On Wed, Jun 13, 2012 at 2:32 PM, Shane Neeley > wrote: > > Hi, > > > > Does anyone use pymol for very large struct