[Chimera-users] multiple (redundant) distances in command line >file.txt

Olexandr Dybkov odybkov at gwdg.de
Tue Aug 4 05:44:53 PDT 2015


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 at ca/pdbSegment=A :573 at ca/pdbSegment=A
dist :453 at ca/pdbSegment=B :479 at ca/pdbSegment=B
dist :695 at ca/pdbSegment=B :395 at ca/pdbSegment=A
dist :2059 at ca/pdbSegment=B :1421 at ca/pdbSegment=B
dist :426 at ca/pdbSegment=B :944 at ca/pdbSegment=B
dist :2059 at ca/pdbSegment=B :1514 at ca/pdbSegment=D
dist :2059 at ca/pdbSegment=B :1417 at ca/pdbSegment=B
dist :1421 at ca/pdbSegment=B :2059 at ca/pdbSegment=B
dist :421 at ca/pdbSegment=C :439 at ca/pdbSegment=C
dist :453 at ca/pdbSegment=B :487 at 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

-- 
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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 at gwdg.de
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