Re: [PyMOL] Spheres for metal ions
Hi Gary, On Tue, 20 May 2008 12:12:43 +0200, Gary Hunter wrote: > I am displaying pdb files of metalloenzymes, and like to show the metal ions > as spheres. > I select the metal and use show>spheres > Fine > Somehow recently I must have done something to reset the vdw radius of > manganese (MN in the pdb), as Mn atoms now display as small spheres (a > little larger than solvent as nb_spheres). > They were fine originally (!) and other metal atoms display at correct sizes > (much bigger than my Mn). > What could I have done? > > A global edit of sphere_scale etc. simply changes all. > I reset the setting>edit_all using the dialog as a check too. > I can use: > Alter name MN, vdw=vdw*2 > Rebuild > > Or whatever, but I have to do it for each pdb file I read in now (if it has > a Mn atom). > Could I have messed with the vdw value in some way? > > Is there a way to actually check the values being used for vdw radii? You can get the vdw radii for any items (say you have a selection called "metals") with: iterate metals, print chain, resn,resi,vdw which will print the chain ID, residue name, residue number and van der Waals radius for each. Of course, this only applies to the vdw radius that is assigned after you read in the PDB file. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 http://pldserver1.biochem.queensu.ca/~rlc
Re: [PyMOL] Spheres for metal ions
Gary Hunter wrote: I am displaying pdb files of metalloenzymes, and like to show the metal ions as spheres. I select the metal and use show>spheres Fine Somehow recently I must have done something to reset the vdw radius of manganese (MN in the pdb), as Mn atoms now display as small spheres (a little larger than solvent as nb_spheres). They were fine originally (!) and other metal atoms display at correct sizes (much bigger than my Mn). What could I have done? A global edit of sphere_scale etc. simply changes all. I reset the setting>edit_all using the dialog as a check too. I can use: Alter name MN, vdw=vdw*2 Rebuild Or whatever, but I have to do it for each pdb file I read in now (if it has a Mn atom). Could I have messed with the vdw value in some way? Is there a way to actually check the values being used for vdw radii? Thanks Gary Prof. Gary J. Hunter, Department of Physiology and Biochemistry, University of Malta, Msida, MSD 06, Malta. phone: +356 2340 2917 phone: +356 21316655 (secretary), Fax: +356 21310577 Gary, You will normally have to manually adjust the ionic radius of metal ions to correctly render them. For starters, PDB files are not always good at distinguishing between atoms and ions; second, there is no single "ionic radius" for metal ions, as their effective radius depends on coordination number. (For example, zinc has different ionic radii for 4- and 5-coordinate compounds. A simple way to adjust radii globally by element is: alter elem zn, vdw=0.74 rebuild (This would set zinc in a protein structure to 0.74A, the appropriate value for a four-coordinate metal environment.) There are many databases out there for obtaining ionic radii. For example, see http://abulafia.mt.ic.ac.uk/shannon/ . Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu
[PyMOL] Subject: Displaying multiple models from 1 pdb file
Gary,
Sorry to hear you couldn't get CE to work for you. If you have time, please
email me (personally or via the PyMOLWiki) and let me know what frustrations
you had. I'd like to make it more user friendly.
To quickly answer your question about visualizing the true-CE results use
split_states:
# (1) load the CE result file
load /path/to/ceResults.txt
# (2) call split_states to show the other molecule
split_states ceResults
HTH,
-- Jason
--
Jason Vertrees, PhD (javer...@{utmb,cs.dartmouth}.edu)
http://www.best.utmb.edu/
http://www.pymolwiki.org/
[PyMOL] Spheres for metal ions
I am displaying pdb files of metalloenzymes, and like to show the metal ions as spheres. I select the metal and use show>spheres Fine Somehow recently I must have done something to reset the vdw radius of manganese (MN in the pdb), as Mn atoms now display as small spheres (a little larger than solvent as nb_spheres). They were fine originally (!) and other metal atoms display at correct sizes (much bigger than my Mn). What could I have done? A global edit of sphere_scale etc. simply changes all. I reset the setting>edit_all using the dialog as a check too. I can use: Alter name MN, vdw=vdw*2 Rebuild Or whatever, but I have to do it for each pdb file I read in now (if it has a Mn atom). Could I have messed with the vdw value in some way? Is there a way to actually check the values being used for vdw radii? Thanks Gary Prof. Gary J. Hunter, Department of Physiology and Biochemistry, University of Malta, Msida, MSD 06, Malta. phone: +356 2340 2917 phone: +356 21316655 (secretary), Fax: +356 21310577
