[PyMOL] NVIDIA Quadro 600

Hi all, I would like to ask whether it is nvidia quadro 600 compatible with pymol 3d stereo on windows 7? Do you have any experiemce with this card? Thank you for help Smith     -- Keep Your Developer Skills Current with

[PyMOL] Pymol and Gromacs XTC

Dear all, I think there is no easy way of reading Gromacs xtc trajectories into PyMOL, At least in the version compiled for Debian, which I don't think includes the vmd plugins. I should have probably asked about this before, but now I just coded a little script that loads xtc in pymol. It has

Re: [PyMOL] NVIDIA Quadro 600

Yes, you can do nvidia 3d vision with this card under win 7 (not linux!) with a 120Hz LCD monitor or a 120Hz DLP projector. On Wed, Feb 8, 2012 at 2:03 AM, wrote: > Hi all, > > I would like to ask whether it is nvidia quadro 600 compatible with pymol 3d > stereo on windows 7? Do you have any exp

[PyMOL] One liner for getting amino acid sequence from pdb file

Hi. I have a pdb file, which is a modelled structure from another sequence. I want to check the amino acid sequence in the structure. Does anyone know a one-liner in pymol which will extract the sequence in one-letter code? best Troels

Re: [PyMOL] One liner for getting amino acid sequence from pdb file

print cmd.get_fastastr('all') Cheers, Thomas On 02/08/2012 03:24 PM, Troels Emtekær Linnet wrote: > Hi. > > I have a pdb file, which is a modelled structure from another sequence. > > I want to check the amino acid sequence in the structure. > Does anyone know a one-liner in pymol which will e

Re: [PyMOL] One liner for getting amino acid sequence from pdb file

Thanks! I put it on the wiki: http://pymolwiki.org/index.php/Get_fastastr Cheers 2012/2/8 Thomas Holder > print cmd.get_fastastr('all') > > Cheers, > Thomas > > > On 02/08/2012 03:24 PM, Troels Emtekær Linnet wrote: > >> Hi. >> >> I have a pdb file, which is a modelled structure from another

Re: [PyMOL] Pymol and Gromacs XTC

Hi Raúl, the pymol 1.2r1 package in Ubuntu (lucid) loads xtc files fine, it has the VMD plugins enabled. As far as I know this is the same package as in debian (at least in squeeze, http://packages.debian.org/squeeze/pymol). If you compile from source, you can apply the attached patch. Cheer

Re: [PyMOL] One liner for getting amino acid sequence from pdb file

Hi Troels, cmd.save("filename.fasta") will save the sequence of your PDB file in a file in fasta format. Then you could open the file and put the content in a list. cheers, Osvaldo -- Forwarded message -- > From: "Troels Emtekær Linnet" > To: "pymol-users@lists.sourceforge.net

[PyMOL] Change default read position of .pymolrc and .pymolrc.py

Hi. We have builded svn pymol at our unilabs linux computers. Is there a way to tell pymol it should look for .pymolrc and .pymolrc.py other places than the users home library? Or can you run the commands in these files in another way? Best Troels ---

Re: [PyMOL] Update Selection From Frames

Takanori, I've tried the following: for a in range(1,8): cmd.mdo(a,"hide sphere; select test, input_object_name & c. b & i. 19 around 4 & resn HOH; show sphere, test") where "HOH" is the residue name for water (so I want to know only the waters within a 4 Angstrom radius of residue number 19). H

Re: [PyMOL] Change default read position of .pymolrc and .pymolrc.py

Hi Troels, you can put a file named $PYMOL_PATH/run_on_startup.py If you want to know what happens in detail, have a look at pymol/invocation.py and in particular at pymol.invocation.get_user_config(). Hope that helps. Cheers, Thomas Troels Emtekær Linnet wrote, On 02/08/12 19:30: > Hi

Re: [PyMOL] Update Selection From Frames

Hi Sean, try the attached example script, hope you manage to modify it for your needs. Cheers, Thomas Sean Law wrote, On 02/08/12 19:34: Takanori, I've tried the following: for a in range(1,8): cmd.mdo(a,"hide sphere; select test, input_object_name & c. b & i. 19 around 4 & resn HOH; sh

[PyMOL] label position

Dear all, I want label a few distances independently with my own labels. I set a label in the form label /wt//A/THR`254/CA, "10.0"+ u"\u00c5".encode('utf-8') which I can move independently using the set label positio command. If I incorporate a second label and try to change the position with t

Re: [PyMOL] label position

Christian, > I want label a few distances independently with my own labels. I set a label > in the form > label  /wt//A/THR`254/CA, "10.0"+ u"\u00c5".encode('utf-8') > which I can move independently using the set label positio command. > If I incorporate a second label and try to change the positi