[Chimera-users] Problems with reproducing 'write relative' output

Dan McNamara dem at g.ucla.edu
Wed Mar 25 00:52:17 PDT 2015


Hi all,

I am encountering a strange inconsistency with the 'relative' option for
the "write" command. Searching for similar problems on the mailing list
came up short, so I thought I'd ask about it.

To put it briefly, I run chimera with --nogui and perform ~780,000 total
matches in which I write out new coordinates using 'relative.' My issue
lies in automating this process with .com scripts, which creates different
results from typing out the exact same commands into the command line of
the GUI. This has been plaguing me for a year or so, and most recently I
can cite using version 1.10.1 (build 40427).

Below is a small example to illustrate my operations. The "B-new_#.pdb"
output files will contain different coordinates if they originate from
automated runs or manual execution.

This problem is sporadic and I cannot narrow down the source of the
discrepancy. From best I can tell, there are occasionally output files from
automation (e.g. B-new_#.pdb) that are in the correct coordinate reference
frame. However, many (most?) are not and it is a big obstacle.

I hope that someone may have some insight on this problem.

/////////// example ///////////
open A.pdb
open B.pdb
open C.pdb

##write out selection from #0 [this file is always consistent]
select #0:...
write selected relative 0 #0 A-new.pdb

##move #2 onto #0
match #2:... #0:...
##move #1 onto #2
match #1:... #2:...

##write out selection from #1 and save it in its new position relative to
#0 [inconsistent]
select #1:...
write selected relative 0 #1 B-new_1.pdb
~select all

##move #1 slightly
match #1:... #2:...+1

##write out selection from #1 and save it in its new position relative to
#0 [inconsistent]
select #1:...
write selected relative 0 #1 B-new_2.pdb
~select all

##move #1 slightly more
match #1:... #2:...+2

##write out selection from #1 and save it in its new position relative to
#0 [inconsistent]
select #1:...
write selected relative 0 #1 B-new_3.pdb
/////////// example ///////////

Best,
Dan McNamara
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