Hi Olexandr. To continue past errors, you would have to use a true Python script rather than a Chimera command script. Such a script wouldn't be very complicated though, something like this: from chimera import runCommand cmds = [ "dist :540@ca/pdbSegment=A :573@ca/pdbSegment=A", "dist :453@ca/pdbSegment=B :479@ca/pdbSegment=B", "dist :695@ca/pdbSegment=B :395@ca/pdbSegment=A", "dist :2059@ca/pdbSegment=B :1421@ca/pdbSegment=B", "dist :426@ca/pdbSegment=B :944@ca/pdbSegment=B", "dist :2059@ca/pdbSegment=B :1514@ca/pdbSegment=D", "dist :2059@ca/pdbSegment=B :1417@ca/pdbSegment=B", "dist :1421@ca/pdbSegment=B :2059@ca/pdbSegment=B", "dist :421@ca/pdbSegment=C :439@ca/pdbSegment=C", "dist :453@ca/pdbSegment=B :487@ca/pdbSegment=B", ] for cmd in cmds: try: runCommand(cmd) except: # ignore errors pass You would put the above in a file whose name ends in ".py" (preserving the indentation, which matters in Python) and run it simply by opening the file with the "open" command. --Eric Eric Pettersen UCSF Computer Graphics Lab On Aug 4, 2015, at 5:44 AM, Olexandr Dybkov wrote:

Dear UCSF Chimera team,

I am trying to measure and draw multiple distances by pasting into the command line respective commands. As outcome I would like to have: 1. the dashed lines between each pair of atoms that I am checking 2. the distances shown above/on the lines 3. a log or a file with all the distances checked (one line per each distance command I executed)

For example, dist :540@ca/pdbSegment=A :573@ca/pdbSegment=A dist :453@ca/pdbSegment=B :479@ca/pdbSegment=B dist :695@ca/pdbSegment=B :395@ca/pdbSegment=A dist :2059@ca/pdbSegment=B :1421@ca/pdbSegment=B dist :426@ca/pdbSegment=B :944@ca/pdbSegment=B dist :2059@ca/pdbSegment=B :1514@ca/pdbSegment=D dist :2059@ca/pdbSegment=B :1417@ca/pdbSegment=B dist :1421@ca/pdbSegment=B :2059@ca/pdbSegment=B dist :421@ca/pdbSegment=C :439@ca/pdbSegment=C dist :453@ca/pdbSegment=B :487@ca/pdbSegment=B and so on

Resulting in Distance between #50 LYS 540 CA and #50 LYS 573 CA: 13.0 Distance between #35 LYS 453.B CA and #35 LYS 479.B CA: 22.7 Distance between #35 LYS 695.B CA and #50 LYS 395 CA: 8.8 Distance between #35 LYS 2059.B CA and #35 LYS 1421.B CA: 20.5 Distance between #35 LYS 426.B CA and #35 LYS 944.B CA: 25.7 Distance between #35 LYS 2059.B CA and #53 LYS 1514.T CA: 115.7 Distance between #35 LYS 2059.B CA and #35 LYS 1417.B CA: 15.2 Distance monitor already exists

That is, 8 out of 10 distances were checked. Since the 8th line was a swap of atom1 and atom2 of 4th, the Chimera Error window popped up and execution of further commands was stopped

Similarly, the execution is interrupted if: - one or both atoms are missing - one or both atoms are present in multiple copies - if such distance was checked already

Is there a way to ignore/skip this kind of check points and just report such cases in the log? I used to do this in pymol and the python script reported all distances (even redundant) and errors (atom 1 or/and atom 2 are missing) without stopping. At the end I had a txt file with exactly one line for each command. It would be nice to have the same functionality in UCSF Chimera as well.

Thank you very much for your help!

Kind regards, Olexandr

-- ----------------------------------------------------------------- Dr. Olexandr Dybkov

Max-Planck-Institute for Biophysical Chemistry Department of Cellular Biochemistry Am Fassberg 11 37077 Göttingen Germany Tel. ++49-551-201 1979 Fax ++49-551-201 1197 email: odybkov@gwdg.de ----------------------------------------------------------------

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