excellent work, Eric. Note that I've added several more examples at
http://www.stolaf.edu/people/hansonr/jmol/test/proto/altloc.htm
and will expand that as needed.
Eric Martz wrote:
1ALX seems a bona-fide example of altLocs, but is unusual in having four, or
even five, altLocs for some atoms. It also has sequence microheterogeneity,
marked by insertion codes in column 27, and described in the remarks. The one
thing that seems inconsistent is that each of the four altLocs A,B,C,D for
MOH519 (methanol) have 50% occupancy, totalling 200%. This I don't understand.
MOH519 has five altLocs A,B,C,D,E each with 40% occupancy.
1ALX displays just fine in the 10.x. Basically it is a set of solvent
molcule options around double-stranded DNA. One can select each
different option using
conformation 0;wireframe on
or select them one by one with
conformation 1;wireframe on
conformation 2;wireframe on
conformation 3;wireframe on
etc.
There are always PDB files that are illegally formatted. Already I see such
cases for altLoc, thanks to Jaim's list below. The most common case appears to
be when numeral portions of 4-character atom names are incorrectly allowed to
spill into column 17 (see 1B0Q below).
well, nothing we can do about that, I think...
Not all numerals in column 17 are formatting errors, however. 1AAC uses numerals
for genuine alternate locations. It is (almost) consistent in using 1,2, or in a
few cases 1,2,3, for altLocs. HOH270 has four alternate locations. The last 3
are marked 2,3,4 but strangely, the first is not marked 1 in column 17. Here is
another rare case where Jmol's display will be incorrect if Jmol strictly obeys
the altLoc formatting rules.
Jmol takes numbers, numerals, anything there. Order is insignificant.
1B0Q is a minimized average NMR result. The hydrogens on CG1 of VAL10 have
numbers that spill into column 17:
ATOM 169 3HG11VAL
10 -7.765 -5.241 -4.992
1.00
0.00 H
ATOM 170 3HG12VAL
10 -8.357 -6.210 -6.346
1.00
0.00 H
ATOM 171 3HG13VAL
10 -7.189 -6.908 -5.228
1.00
0.00 H
But these three hydrogens do not represent altLocs for one atom; they are the
three H's on the sidechain methyl. So, when the altLoc characters are 1, 2, 3
one can be suspicious that they are bogus.
fortunately, "conformation 0" would just display them all.
1D2L also has such bogus altLoc numerals.
2BSG (alpha carbons only) stands out because only "A" occurs in column 17 (no
"B"). Three VAL residues have A in column 17, but these are not altLoc's. What
they signify is unclear to me, even after inspection of the PDB header.
2MB5 is myoglobin with carbon monoxide bound to the heme iron. Both the carbon
and oxygen in the CO are given altLocs A & B, although the coordinates for
carbons A and B are identical! The oxygens are in different positions. (Atom
serial numbers 2567-2570.) These atoms have occupancies of 58% and 42% (total
100%) confirming that these are genuine altLocs. (However I find it puzzling
that the carbon is between the iron and the oxygen -- does this make chemical
sense?)
Absolutely. :CO: binds on carbon to metals. Nice structure.
restrict none; conformation 1; wireframe 0.15
restrict none; conformation 2; wireframe 0.15
work as expected.
I think what we are seeing is that it is quite possible, particularly
with heteroatoms -- HOH and such -- to have a different number of
atoms in different altloc sets. That's fine. They can be displayed
together or individually; one has total control.
OK, I'm convinced my altloc/conformation idea works for any of these.
Obviously some data are not true "conformations", but many are. In the
case where this is just different solvent position/solvent number
options, I think you just have to realize that that is what it is, and
not worry about it. In many of these cases, a nice display is probably
conformation 0; color altloc
so that all the optional positions are displayed color coded. But
there are all sorts of other options I can think of -- small stars
could be nice for the water in variable positions
select solvent and not *%; color altloc;
spacefill off;wireframe off;stars 0.3
So the selection business is very flexible.
So far so good?
Bob
-Eric Martz
From: Jaime Prilusky <[EMAIL PROTECTED]>
Subject: altLocation preliminary results
To: [EMAIL PROTECTED] (Eric Martz)
Date: Mon, 15 May 2006 15:09:51 +0300 (IDT)
Dear Eric,
The extraction of altLocation data goes slow, and on top of that,
our server was down for several hours due to a UPS replacement.
The complete results should be ready in a couple of days.
First, I run most of the non-X-RAY entries, and here's the result:
1hb5 CRYO-ELECTRON_MICROSCOPY 0.00 27273 A=01461 B=01461
1hb9 CRYO-ELECTRON_MICROSCOPY 0.00 36364 A=01948 B=01948
1ia0 CRYO-ELECTRON_MICROSCOPY 15.00 9606 A=00083 B=00083
1suv CRYO-ELECTRON_MICROSCOPY 0.00 20612 A=00040 B=00040
2bsg CRYO-ELECTRON_MICROSCOPY 15.00 1089 A=00003
2c8i CRYO-ELECTRON_MICROSCOPY 0.00 1165 A=00074 B=00074
1iu6 NEUTRON_DIFFRACTION 1.60 847 A=00046 B=00046
1l2k NEUTRON_DIFFRACTION 1.50 2717 A=00147 B=00147
1v9g NEUTRON_DIFFRACTION 1.80 531 A=00011 B=00011
1vcx NEUTRON_DIFFRACTION 1.50 896 A=00047 B=00047
1wq2 NEUTRON_DIFFRACTION 2.40 2140 A=00105 B=00105
2mb5 NEUTRON_DIFFRACTION 1.80 2851 A=00002 B=00002
3ins NEUTRON_DIFFRACTION 1.50 1978 A=00094 B=00094
1b0q NMR 0.00 175 1=00001 2=00001 3=00001
1j6t NMR 0.00 10673 A=00099 B=00075
1ln6 NMR 0.00 4242 A=00001 B=00001
1o4x NMR 0.00 4727 A=00072 B=00072 C=00015
1mw4 NMR_010 0.00 20740 A=00097 B=00097
1f8p NMR_017 0.00 10030 1=00002 2=00002
1bhi NMR_020 0.00 11780 1=00020 2=00020
1d2l NMR_020 0.00 12620 1=00646 2=00684 3=00266
1eww NMR_020 0.00 24580 1=00001 2=00001 3=00001
1osl NMR_020 0.00 61219 A=01636 B=01636 C=01080
>From the X-RAY processed entries so far, a few that might interest you,
that have more than 3 altLocations.
1aac X-RAY_DIFFRACTION 1.31 1019 1=00063 2=00063 3=00004 4=00001
1al4 X-RAY_DIFFRACTION 1.13 956 A=00232 B=00238 C=00034 D=00012
1alx X-RAY_DIFFRACTION 1.20 866 A=00153 B=00138 C=00038 D=00012
E=00006
Jaim
--
Dr Jaime Prilusky | [EMAIL PROTECTED]
Head of Bioinformatics ISPC |
R&D Bioinformatics and Data Management |
Weizmann Institute of Science | fax: 972-8-9344113
76100 Rehovot - Israel | tel: 972-8-9344959
info URL http://bip.weizmann.ac.il/staff/jaime_prilusky.html
OCA is at http://bip.weizmann.ac.il/oca/
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