[Chimera-users] savepos

Dougherty, Matthew T matthewd at bcm.edu
Wed Jun 3 06:07:29 PDT 2015


I have been automating the creation of positions using python scripts.  Something relatively simple like p001, p002, etc.

When I examine the positions using the python commands

from Midas import positions

pnames = positions.keys()

at first things appear as I would expect, but later the sequence changes relative to the index, why is that?

for example, using this to print the positions

        pnames = positions.keys()
        for pname in pnames:
          print i,pnames[i]

I get these results:

savepos p000
savepos p001
0 p000
1 p001
(as expected)

savepos p002
0 p000
1 p001
2 p002
(as expected)

savepos p003
0 p000
1 p001
2 p002
3 p003
(as expected)

savepos p004
0 p004
1 p000
2 p001
3 p002
4 p003
(not as expected)

savepos p005
0 p004
1 p005
2 p000
3 p001
4 p002
5 p003

(not as expected)

I would expect pnames[0] to correspond to the first position created, pnames[1] to the second posiiton created, etc., assuming no ~savepos used.

Want to create a situation where the default names would be pxxx, but could later be altered to more meaningful names but maintain the order of creation, or getting a session file from someone I would use their position names and tack on my default names to the end of the position list.

Matthew Dougherty
National Center for Macromolecular Imaging
Baylor College of Medicine
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