Makes sense. I've been looking at different approaches to editing the Tinker
file back to the base format. My present goal is to view Tinker dynamics arc
files, which are concatenated, augmented xyz format. Strangely, and
unfortunately, Tinker's translation to pdb (xyzpdb.exe in Windows) produces a
Jmol unreadable file:
HEADER spentane.xyz MM3 parameters
COMPND
SOURCE
HETATM 1 C 1 1 -0.554 1.439 -0.145
HETATM 2 C 1 1 -0.461 -0.005 0.353
HETATM 3 C 1 1 -1.752 -0.749 0.002
HETATM 4 C 1 1 0.726 -0.700 -0.317
HETATM 5 C 1 1 2.027 -0.033 0.133
HETATM 6 H 5 1 -0.693 1.443 -1.226
HETATM 7 H 5 1 -1.400 1.934 0.332
HETATM 8 H 5 1 0.365 1.969 0.105
HETATM 9 H 5 1 -0.322 -0.009 1.434
HETATM 10 H 5 1 -1.891 -0.745 -1.079
HETATM 11 H 5 1 -1.686 -1.778 0.356
HETATM 12 H 5 1 -2.598 -0.254 0.479
HETATM 13 H 5 1 0.740 -1.752 -0.032
HETATM 14 H 5 1 0.632 -0.618 -1.400
HETATM 15 H 5 1 2.014 1.019 -0.152
HETATM 16 H 5 1 2.122 -0.114 1.216
HETATM 17 H 5 1 2.873 -0.528 -0.344
CONECT 1 2 6 7 8
CONECT 2 1 3 4 9
CONECT 3 2 10 11 12
CONECT 4 2 5 13 14
CONECT 5 4 15 16 17
CONECT 6 1
CONECT 7 1
CONECT 8 1
CONECT 9 2
CONECT 10 3
CONECT 11 3
CONECT 12 3
CONECT 13 4
CONECT 14 4
CONECT 15 5
CONECT 16 5
CONECT 17 5
END
The third line "SOURCE" appears to be the culprit. I've not seen that in pdb
files previously; apparently, neither has Jmol. When it is removed, the
resulting file LOADs in Jmol, but with all atoms colored carbon gray.
Regards,
George
________________________________
From: Robert Hanson [[email protected]]
Sent: Monday, January 20, 2014 7:43 PM
To: [email protected]
Subject: Re: [Jmol-users] Tinker xyz files as Jmol input
We won't be able to read a "Tinker" file. It's not an "xyz" file. It's its own
format, and apparently it has no header with which to identify itself. So if we
do write a reader, it will never load these files directly. More likely it
would read them with a prefix such as:
load tinker::out.xyz
On Mon, Jan 20, 2014 at 2:31 PM, Whitwell, George
<[email protected]<mailto:[email protected]>> wrote:
Hi,
I've been loading Tinker's version of .xyz files into Jmol with unexpected
connections displayed.
Jmol writes a file with number of atoms followed by a blank line and a 4 column
atom format (symbol, x, y, z - 5 dec places).
17
C -0.55370 1.43900 -0.14471
C -0.46130 -0.00500 0.35261
C -1.75150 -0.74880 0.00170
C 0.72611 -0.69990 -0.31680
C 2.02730 -0.03280 0.13331
H -0.69280 1.44280 -1.22580
H -1.39970 1.93400 0.33220
H 0.36540 1.96880 0.10530
H -0.32230 -0.00880 1.43360
H -1.89060 -0.74500 -1.07940
H -1.68571 -1.77750 0.35590
H -2.59750 -0.25380 0.47851
H 0.73950 -1.75180 -0.03150
H 0.63160 -0.61830 -1.39960
H 2.01390 1.01910 -0.15200
H 2.12180 -0.11440 1.21610
H 2.87330 -0.52781 -0.34360
Tinker reads and writes additional information: some text in the first line (no
blank before atoms) and 6 columns (#, symbol, x, y, z - 6 dec places, FF type)
plus connection info for each atom.
17 spentane.xyz MM3 parameters
1 C -0.553700 1.439000 -0.144710 1 6 8 7 2
2 C -0.461300 -0.005000 0.352610 1 4 1 3 9
3 C -1.751500 -0.748800 0.001700 1 10 2 11 12
4 C 0.726110 -0.699900 -0.316800 1 14 13 5 2
5 C 2.027300 -0.032800 0.133310 1 17 4 15 16
6 H -0.692800 1.442800 -1.225800 5 1
7 H -1.399700 1.934000 0.332200 5 1
8 H 0.365400 1.968800 0.105300 5 1
9 H -0.322300 -0.008800 1.433600 5 2
10 H -1.890600 -0.745000 -1.079400 5 3
11 H -1.685710 -1.777500 0.355900 5 3
12 H -2.597500 -0.253800 0.478510 5 3
13 H 0.739500 -1.751800 -0.031500 5 4
14 H 0.631600 -0.618300 -1.399600 5 4
15 H 2.013900 1.019100 -0.152000 5 5
16 H 2.121800 -0.114400 1.216100 5 5
17 H 2.873300 -0.527810 -0.343600 5 5
In my observations, Jmol (14.0.1 applet) displays various incorrect connections
for the Tinker files, either bonding atoms that shouldn't be or not bonding
atoms that should be. The file listed above gives me one methyl group all
disconnected. What am I missing?
Thanks,
George Whitwell
NC Wesleyan College
------------------------------------------------------------------------------
CenturyLink Cloud: The Leader in Enterprise Cloud Services.
Learn Why More Businesses Are Choosing CenturyLink Cloud For
Critical Workloads, Development Environments & Everything In Between.
Get a Quote or Start a Free Trial Today.
http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
_______________________________________________
Jmol-users mailing list
[email protected]<mailto:[email protected]>
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
CenturyLink Cloud: The Leader in Enterprise Cloud Services.
Learn Why More Businesses Are Choosing CenturyLink Cloud For
Critical Workloads, Development Environments & Everything In Between.
Get a Quote or Start a Free Trial Today.
http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
