Or all the distances between less than 5-6 Angstrom from atom A. It would be nice if this could be written to a file. I'm analysing a NMR NOESY spectrum of DNA and I would like to have a list of the expected distances in typical B-DNA. Thanks, Marco Citando sette@uniroma2.it:

Dear all,

I would like to measure the distances between all atoms in a molecule, in particular between all hydrogens. I added the H but it seems to me that is possible to measure only the distance between two selected atoms and not between all atoms in a single command. How is possible to do?

Thanks for your help,

Marco

Dr.Marco Sette, Ph.D.

Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

Hi Marco, Here is a better example for your situation. Instead of looking at all distances from one atom, this would look at all distances among the specified set of atoms, in this case hydrogens. open 1zik delete solvent addh findclash element.H inter false overlap -3 hbond 0 makePseudobonds false log true (where that findclash command is all on one line even though the mail reflector will probably break it up) That finds all H pairs within 5 angstroms, I believe. That is very many pairs, even in this relatively small structure. Best Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Nov 30, 2007, at 3:47 PM, Elaine Meng wrote:

Hi Marco, Pardon the delay - at first I thought it was not possible with a command to measure multiple distances and that somebody else would have to give you a script.

However, it IS possible, but not with the "distance" command. The "findclash" command (or Find Clashes/Contacts tool) can find all clashes or contacts within some user-specified tolerance and write the results to a file. The cutoff is how much VDW overlap is present, but setting that cutoff to a negative number (with H-bond tolerance of zero) will find pairs of atoms with VDW surfaces within the cutoff distance ( its absolute magnitude). The distances between the atom centers will be greater than that, but the information written to the file or to the Reply Log includes the distances between atom centers as well as between the VDW surfaces. Just be forewarned that this may be a LOT of lines depending on your system and specified cutoff.

It's a little confusing, but here is an example:

open 1zik findclash :23.a@cg2 overlap -5 hbond 0 ignoreIntraRes true log true

will draw lines in the graphics window and send information to the Reply Log on all pairwise interactions where the VDW surface of atom CG2 in residue 23 chain A is within 5 angstroms of the VDW surface of the other atom. The lines are sorted in order of decreasing overlap:

atom1 atom2 overlap distance VAL 23.A CG2 VAL 23.B CG2 0.707 3.053 VAL 23.A CG2 LEU 19.A O 0.225 3.075 VAL 23.A CG2 VAL 23.B CB -0.631 4.391 ... VAL 23.A CG2 ARG 25.B NH1 -4.882 8.402 VAL 23.A CG2 LYS 27.B N -4.937 8.457

Including "saveFile filename" will save the information to a text file named filename. You can do exactly the same thing via the Find Clashes/Contacts GUI instead of the "findclash" command.

Here is the man page for findclash ...there are many possible keywords: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html

and for Find Clashes/Contacts: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/ findclash.html

On Nov 30, 2007, at 1:54 AM, sette@uniroma2.it wrote:

...

Or all the distances between less than 5-6 Angstrom from atom A. It would be nice if this could be written to a file. I'm analysing a NMR NOESY spectrum of DNA and I would like to have a list of the expected distances in typical B-DNA.

Thanks, Marco