[PyMOL] Getting surface residues
Hi Pymolers. How would you get a list of surface residues the fastest way? Like: [3-10], [14-18] I have a rough structure from crystallography, and have made a trypsin digest and mass spec analysis. And I see fragments which have been post-trans modified. Now I am interested in matching if those fragments are surface exposed or internal. What tools does pymol have to find out if the residues are surface exposed? Or is there another easy tool? Best Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Getting surface residues
Hi Troels, I've been using http://www.pymolwiki.org/index.php/FindSurfaceResidues at some point. Seems to work well enough. Otherwise you could go through the PISA server at http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html But I don't remember how exactly I would get the surface residues out from that. mvh Folmer 2012/10/31 Troels Emtekær Linnet tlin...@gmail.com Hi Pymolers. How would you get a list of surface residues the fastest way? Like: [3-10], [14-18] I have a rough structure from crystallography, and have made a trypsin digest and mass spec analysis. And I see fragments which have been post-trans modified. Now I am interested in matching if those fragments are surface exposed or internal. What tools does pymol have to find out if the residues are surface exposed? Or is there another easy tool? Best Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Folmer Fredslund -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Getting surface residues
Dear Troels, Personally I don't use PyMol for this problem. Rather I use the application NACCESS (http://www.bioinf.manchester.ac.uk/naccess/) and choose a total relative solvent accessibility of at least 5% (Miller, S. et al, 1987, J Mol Biol 196, 641–656) to assess whether a residue is at the protein surface or not. The relative solvent accessibilities are listed in 5th column of the NACCESS .rsa output file. Best Abdullah On 31 Oct 2012, at 07:11, Troels Emtekær Linnet tlin...@gmail.com wrote: Hi Pymolers. How would you get a list of surface residues the fastest way? Like: [3-10], [14-18] I have a rough structure from crystallography, and have made a trypsin digest and mass spec analysis. And I see fragments which have been post-trans modified. Now I am interested in matching if those fragments are surface exposed or internal. What tools does pymol have to find out if the residues are surface exposed? Or is there another easy tool? Best Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ---@ Abdullah Kahraman, PhD Aebersold - Malmstroem Group Institute of Molecular Systems Biology ETH Zurich HPT C75 Wolfgang-Pauli-Str. 16 8093 Zurich Switzerland http://www.imsb.ethz.ch/researchgroup/malars/people/abdullah_kahraman abdul...@imsb.biol.ethz.ch work: +41-(0)44-633 66 71 mobile: +41-(0)76-317 0305 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] visualise NOEs
Hi Krisztina, check the attached script (strongly modified). It doesn't use a regex anymore, but uses a split function which takes parentheses into account. Also it doesn't parse name and resi, but passes the selection string directly to PyMOL (which understands most of CNS selection syntax!). Your example selects segidA, since PyMOL will strip off whitespace from the segid, you might need something like this to fix it before calling plot_noe: PyMOL alter all, segi=segi.rjust(4) Hope that helps. Cheers, Thomas On 10/31/2012 04:36 PM, Krisztina Feher wrote: Dear All thanks to Thomas for the modfication on the plot_noe.py. It turns out that the CNS .tbl file can have different formats, the one I used only includes residue ID and atom name, but soemtimes it also inlcudes segment ID as well, see on the attached file. How do I have to modify the noe_regex pattern so that it is recognised? Thanks in advance, regards, Krisztina -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen plot_noe.py Description: application/chimera -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Getting surface residues
Thanks! Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234 2012/10/31 Abdullah Kahraman abdul...@imsb.biol.ethz.ch Dear Troels, Personally I don't use PyMol for this problem. Rather I use the application NACCESS (http://www.bioinf.manchester.ac.uk/naccess/) and choose a total relative solvent accessibility of at least 5% (Miller, S. et al, 1987, *J Mol Biol* 196, 641–656) to assess whether a residue is at the protein surface or not. The relative solvent accessibilities are listed in 5th column of the NACCESS .rsa output file. Best Abdullah On 31 Oct 2012, at 07:11, Troels Emtekær Linnet tlin...@gmail.com wrote: Hi Pymolers. How would you get a list of surface residues the fastest way? Like: [3-10], [14-18] I have a rough structure from crystallography, and have made a trypsin digest and mass spec analysis. And I see fragments which have been post-trans modified. Now I am interested in matching if those fragments are surface exposed or internal. What tools does pymol have to find out if the residues are surface exposed? Or is there another easy tool? Best Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ---@ Abdullah Kahraman, PhD Aebersold - Malmstroem Group Institute of Molecular Systems Biology ETH Zurich HPT C75 Wolfgang-Pauli-Str. 16 8093 Zurich Switzerland http://www.imsb.ethz.ch/researchgroup/malars/people/abdullah_kahraman abdul...@imsb.biol.ethz.ch work: +41-(0)44-633 66 71 mobile: +41-(0)76-317 0305 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Angle between two structure upon alignment
Dear user Can you please help me in finding the angle between two structure upon alingment. I have aligned two structure and one structure is not perfectly aligned on other. There is domain of two structure tilting outward upon alignment. IS there any way to find the angle between two structure. Thanks in advances. -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
