Fang,
There is no relationship between ACT and PyMOL, so one wouldn't necessarily
expect them to match in terms of how they name the resulting objects. However,
I suspect there may also be a difference of intent:
Based on a quick glance at PyMOL source code, PyMOL appears to convey a
relative cell translation (based on centers of geometries), whereas ACT may be
returning the computation formula.
In other words, PyMOL attempts to inform the user as to whether the generated
symmetry-related atom selection is within the same cell as the query selection
or in one of the adjacent cells (in a translational sense). Thus in PyMOL, the
(overall) nearest mates (with respect to the center of geometry) will usually
have a translation of 00 00 00, and most of the time, nearby mates will vary +1
or -1 along a single translation.
I'm guessing ACT simply provides the symmetry operator and the effective
translation applied to generate the nearby mate. That's useful for recomputing
the mate later on, but it doesn't tell the user anything about proximity.
PyMOL's approach is unhelpful for recomputing a mate, but one can tell from the
object name alone which objects are likely to have the most extensive contacts
and how they relate in a relative sense (with respect to cell translations away
from the query selection).
Perhaps PyMOL could provide ACT-like naming through an optional setting?
Cheers,
Warren
-----Original Message-----
From: fangsh...@mbi.ucla.edu [mailto:fangsh...@mbi.ucla.edu]
Sent: Thu 9/17/2009 4:52 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Pymol Symmetry Mates Naming
Hi,all,
I am encountering a problem with symmetry mates generated by pymol. It
seems that the naming system in pymol and ccp4-supported ACT program are
not consistent. I have tested several pdbs in P4212 space group and
attempted to figure out the relationship between these two, but failed. I
appreciate it if you could hint me out.
Some comparisons are listed below.
ACT:NSYM ( number of symmetry operation) followed by number of
translations of one unit cell along x,y,z.
PYMOL: the first two digits are the symmetry operation. The next six
digits correspond to the relative integral unit cell translation xxyyzz.
I figured that the symmetry operation( the first two digits in pymol) is
off by 1 compared to the first digit in ACT, but have no idea how the last
six digits relates to the ACT
1em7.pdb
pymol ACT
01000000 21-10
02000000 3220
03000000 4010
05000000 6000
05000001 6001
-----------
1RH4.PDB
pymol ACT
000000-1 100-1
03000000 4000
01000000 20-10
-----------
178l.pdb
01000000 21-10
00000001 1001
030000-1 401-1
070000-1 8110
07000000 8111
03000000 4010
Sincerely
Fang Sheng
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