Hello, I am trying to measure distances between atoms using the Tools -> Structure Analysis -> Distances routine. Chimera is requesting that two atoms must be selected in the main graphics window for this to work. I can't figure out how to select the atoms. Can someone help me? John
Hi John, There are several ways to select atoms, but I guess you mean "picking" them from the screen. By default, picking two atoms would be done with Ctrl-click on the first atom, then Shift-Ctrl-click on the second. The shift is needed to add to the selection instead of replacing it. How to select is described here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html> and in the getting started tutorial <http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html#MenuMouse
Or, if you are looking at the Distances tool, you could press its Help button to see its man page, which lists the ways to add the measurement and includes links to the selection page. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 19, 2010, at 5:02 AM, Beale, John wrote:
Hello, I am trying to measure distances between atoms using the Tools -> Structure Analysis -> Distances routine. Chimera is requesting that two atoms must be selected in the main graphics window for this to work. I can’t figure out how to select the atoms. Can someone help me? John
Le 19 janv. 2010 à 19:50, Elaine Meng a écrit :
Hi John, There are several ways to select atoms, but I guess you mean "picking" them from the screen. By default, picking two atoms would be done with Ctrl-click on the first atom, then Shift-Ctrl-click on the second. The shift is needed to add to the selection instead of replacing it.
How to select is described here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html>
and in the getting started tutorial <http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html#MenuMouse>
Or, if you are looking at the Distances tool, you could press its Help button to see its man page, which lists the ways to add the measurement and includes links to the selection page.
I hope this helps, Elaine
Hi, Now that we're here... Is it possible to pick just one atom and show the distances of surrounding atoms within a certain radius. I'm not talking about zone selection, just showing distances (as the usual pseudo-bonds) up to a fixed or user-defined radius. If the possibility does not exist, it would be nice to have. Best, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombardia@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2
Hi Miguel, There is no user interface one-step to do exactly that, but here are a couple of ideas: (a) if you are handy with python, you could get a list of the atoms within a zone of "atom1" and then loop through that list, creating their distance measurements to "atom1" (b) here is what I'd do, as a nonprogrammer: instead use "Find Clashes/ Contacts" (under Tools... Structure Analysis) or the command equivalent, "findclash". It can write out a list of atom pairs meeting your criteria, their distances, and their VDW overlaps (which can be negative, corresponding to when the VDW spheres of a pair of atoms are not overlapping but separated by space). The cutoff you give this tool is actually the VDW overlap rather than the distance, but if it is really distances you care about, you can set the cutoff VDW overlap generously to include the distances you want, then sort the output by the distances. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash...
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> For example, the findclash command in the following: open 2gbp preset apply int 2 show ligand z<8 focus findclash :bgc@o1 overlap -1.0 hbond 0.0 log true ... finds all atoms in other residues interacting with BGC atom O1 (with their VDW surfaces within 1 Angstrom) and writes the following information to the Reply Log: Allowed overlap: -1 H-bond overlap reduction: 0 Ignore contacts between atoms separated by 4 bonds or less Ignore intra-residue contacts 8 contacts atom1 atom2 overlap distance BGC 310.A O1 ASP 154.A OD1 0.231 2.649 BGC 310.A O1 ASN 256.A ND2 -0.005 3.105 BGC 310.A O1 ARG 158.A NH2 -0.154 3.254 BGC 310.A O1 ASP 154.A CG -0.272 3.612 BGC 310.A O1 ASN 91.A ND2 -0.275 3.375 BGC 310.A O1 HOH 319.A O -0.677 3.597 BGC 310.A O1 HOH 379.A O -0.782 3.702 BGC 310.A O1 ASP 154.A CB -0.887 4.227 The last column is the distance. There are also options for saving the information to a file, whether pseudobonds should be drawn and their linewidth and color, etc. The graphical interface "Find Clashes/ Contacts" has the same capabilities. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 20, 2010, at 12:02 AM, Miguel Ortiz Lombardia wrote:
Hi, Now that we're here... Is it possible to pick just one atom and show the distances of surrounding atoms within a certain radius. I'm not talking about zone selection, just showing distances (as the usual pseudo-bonds) up to a fixed or user-defined radius. If the possibility does not exist, it would be nice to have. Best, -- Miguel
Dear Elaine, Thank you for the procedures that you suggest. They are indeed useful! Best regards, Miguel Le 20 janv. 2010 à 19:00, Elaine Meng a écrit :
Hi Miguel, There is no user interface one-step to do exactly that, but here are a couple of ideas:
(a) if you are handy with python, you could get a list of the atoms within a zone of "atom1" and then loop through that list, creating their distance measurements to "atom1"
(b) here is what I'd do, as a nonprogrammer: instead use "Find Clashes/Contacts" (under Tools... Structure Analysis) or the command equivalent, "findclash". It can write out a list of atom pairs meeting your criteria, their distances, and their VDW overlaps (which can be negative, corresponding to when the VDW spheres of a pair of atoms are not overlapping but separated by space). The cutoff you give this tool is actually the VDW overlap rather than the distance, but if it is really distances you care about, you can set the cutoff VDW overlap generously to include the distances you want, then sort the output by the distances. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
For example, the findclash command in the following:
open 2gbp preset apply int 2 show ligand z<8 focus findclash :bgc@o1 overlap -1.0 hbond 0.0 log true
... finds all atoms in other residues interacting with BGC atom O1 (with their VDW surfaces within 1 Angstrom) and writes the following information to the Reply Log:
Allowed overlap: -1 H-bond overlap reduction: 0 Ignore contacts between atoms separated by 4 bonds or less Ignore intra-residue contacts
8 contacts atom1 atom2 overlap distance BGC 310.A O1 ASP 154.A OD1 0.231 2.649 BGC 310.A O1 ASN 256.A ND2 -0.005 3.105 BGC 310.A O1 ARG 158.A NH2 -0.154 3.254 BGC 310.A O1 ASP 154.A CG -0.272 3.612 BGC 310.A O1 ASN 91.A ND2 -0.275 3.375 BGC 310.A O1 HOH 319.A O -0.677 3.597 BGC 310.A O1 HOH 379.A O -0.782 3.702 BGC 310.A O1 ASP 154.A CB -0.887 4.227
The last column is the distance. There are also options for saving the information to a file, whether pseudobonds should be drawn and their linewidth and color, etc. The graphical interface "Find Clashes/Contacts" has the same capabilities. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 20, 2010, at 12:02 AM, Miguel Ortiz Lombardia wrote:
Hi, Now that we're here... Is it possible to pick just one atom and show the distances of surrounding atoms within a certain radius. I'm not talking about zone selection, just showing distances (as the usual pseudo-bonds) up to a fixed or user-defined radius. If the possibility does not exist, it would be nice to have. Best, -- Miguel
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-- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombardia@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2
participants (3)
-
Beale, John -
Elaine Meng -
Miguel Ortiz Lombardia