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MOLEKEL manual

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Version 4.1

1

MOLEKEL

Version 4.1

http://www.cscs.ch/molekel/

By

Stefan Portmann

Copyright (C) 2000
-
2001 CSCS/ETHZ



Table of Content

Introduction
2


History
2


Platforms
2



Capabilities
3


Availability
3


Citation
3

License
3


Install
ation
5


Requirements

5


Unpack and install

5

Known Bugs

6

Basic Procedures

6

Every Button Explained

7


Graphics window

7



Model orientation

7



Popup menu

7


Main interface window

8



molecular models

8



bond attributes

8



quality

9



option

10



log area

10



Menu

11


Menu Load

11


Menu Geometry

12


Dipole moment

12


Labels

12


Menu Compute

13


Surface

15


Frequency

16


Menu Animate

17


Color

17


Texture

18


Menu Write

18


Menu Snapshot

19


Render

19

Various

19


Picking mode

20


File browser

20


Cancel

20


(
mkl format 24
)



(
General format: 24
)



(
KEYWORDS: 24
)

(
Index 27
)



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Version 4.1

2


Introduction

History

MOLEKEL was designed and developed at
University of Geneva

and
CSCS

/
ETHZ

by Peter F.
Flükiger in the early 90ties. The original version was based on IRIS GL and therefore only available
on SGIs. In 1998, Stefan Portmann took over the responsibility of MOLEKEL and released Version
3.0. Version 3.0 contained only minor imp
rovements and bug fixes compared to Peter F. Flükiger's
work. Version 4.0 is the first OpenGL / Mesa implementation with a completely redesigned GUI based
on the GLUT and GLUI libraries. This makes the code nearly platform independent. Version 4.0 has
abou
t the same functionality as previous versions already had, but many details could be improved, the
usage is even more convenient. Current version is 4.1.

Platforms

MOLEKEL is pretty much platform independent. The program is wr
itten in C/C++ and uses the
OpenGL / Mesa, GLUT and GLUI libraries. The OpenGL or Mesa 3D graphics library is available on
many UNIX systems, LINUX and also on WINDOWS. GLUT, the OpenGL Utility Toolkit, is a
window system independent toolkit for writing Op
enGL programs and works on X11 workstations and
Win32 PCs. GLUI is a GLUT
-
based C++ user interface library which provides controls such as
buttons, checkboxes, radio buttons, and spinners to OpenGL applications. It is window
-
system
independent, relying on
GLUT to handle all system
-
dependent issues, such as window and mouse
management. MOLEKEL as been compiled successfully on IRIX, SUN, LINUX and Win32
(mingw/gcc) systems.

Main development work was done on a SGI O2 running IRIX 6.3.

Capabilities



MOLEKEL is an interactive, three
-
dimensional molecular graphics package.



MOLEKEL represents molecules as wire frame, stick, ball
-
and
-
stick and spacefill representations.



MOLEKEL measures atom
-
atom distances, angles and torsion angl
es.



MOLEKEL can superimpose molecules.



MOLEKEL calculates and displays isosurfaces of electron and spin densities as well as
molecular orbitals from the output of various electronic structure calculation programs.



MOLEKEL uses texture mapping to c
olor code any surface according to e.g. the molecular
electrostatic potential.



MOLEKEL is able to clip any surface by a clipping plane and to render it transparent.



MOLEKEL can animate and display vibrational modes.



MOLEKEL can animate geometry op
timizations and multiple coordinate PDB and XYZ files.



MOLEKEL can display the dipole moment of a molecule



MOLEKEL can export coordinates in PDB and XYZ format in original or modified orientation.



MOLEKEL can save pictures in RGB, TIFF and JPEG fo
rmat.



MOLEKEL can render pictures at any size, i.e. larger than screen size.



MOLEKEL can automatically generate series of pictures of animations (frequencies, series of
coordinates).



Supported output file formats of electronic structure calculatio
n programs:



GAUSSIAN


GAMESS US


ADF

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Version 4.1

3



ZINDO



MOS



HONDO



PRDDO



NBO orbital coefficients together with a Gaussian logfile



MKL: Format defined to convert output of other electronic structure calculation
programs using general unix tools (aw
k, perl) to a readable format.



Supported coordinate formats:



PDB



XYZ



free format



Supported grid formats:



GAUSSIAN CUBE files



ADF TAPE41 files



MACU (MOLEKEL's format)

Availability

MOLEKEL is distributed free of
charge but is not in the public domain

(see license for details on
conditions and restrictions). Precompiled executables and object files for IRIX, SUN, LINUX and
Win32 can be downloaded from
http://www.cscs.ch/mole
kel/

. Source code is only available in the
framework of a
collaboration.
(ソースコードは共同研究の枠内でのみ利用可能である)


public domain
とは著作権が放棄された状態をさす.ここでは配布(つまりダウンロード)
については無料であるが,著作権は放棄していないと言っている.詳細は以下の
license
を参
照.)


Citation
(引用について)

Please use

the following citation in any report or publication, which includes results, especially
illustrations, obtained with MOLEKEL: MOLEKEL 4.1, P. Flükiger, H.P. Lüthi, S. Portmann, J.
Weber, Swiss Center for Scientific Computing, Manno (Switzerland), 2000
-
200
1.

MOLEKEL
を用いて得た結果,特に図を含むいかなる報告書,出版物には次のような引用文
を書いて下さい:
MOLEKEL 4.1, P. Flükiger, H.P. Lüthi, S. Portmann, J. Weber, Swiss Center for
Scientific Computing, Manno (Switzerland), 2000
-
2001


License

CSCS Binary Code License Agreement
---------------------------------------------
READ THE TERMS OF
THIS AGREEMENT AND ANY PROVIDED SUPPLEMENTAL LICENSE TERMS
(COLLECTIVELY "AGREEMENT") CAREFULLY BEFORE OPENING THE SOFTWARE
MEDIA PACKAGE. BY OPENING THE SOFTWARE MEDIA PACKAGE, YOU AGREE TO T
HE
TERMS OF THIS AGREEMENT. IF YOU ARE ACCESSING THE SOFTWARE
ELECTRONICALLY, INDICATE YOUR ACCEPTANCE OF THESE TERMS BY SELECTING
THE "ACCEPT" BUTTON AT THE END OF THIS AGREEMENT. IF YOU DO NOT AGREE TO
ALL THESE TERMS, PROMPTLY RETURN THE UNUSED SOFTWARE

TO YOUR PLACE OF
PURCHASE FOR A REFUND OR, IF THE SOFTWARE IS ACCESSED ELECTRONICALLY,
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Version 4.1

4

SELECT THE "DECLINE" BUTTON AT THE END OF THIS AGREEMENT.

1. LICENSE TO USE. CSCS grants you a non
-
exclusive and non
-
transferable license for the internal
use only of t
he accompanying software and documentation and any error corrections provided by
CSCS (collectively "Software").

2. RESTRICTIONS Software is confidential and copyrighted. Title to Software and all associated
INTELLECTUAL PROPERTY RIGHTS is retained by CSC
S and/or its licensors. Except as
specifically authorized by any Official Document from CSCS, you may not make copies of Software,
other than a single copy of Software for archival purposes. Unless enforcement is prohibited by
applicable law, you may not m
odify, decompile. No right, title or interest in or to any trademark,
service mark, logo or trade name of CSCS or its licensors is granted under this Agreement.

3. DISCLAIMER OF WARRANTY. UNLESS SPECIFIED IN THIS AGREEMENT, ALL EXPRESS
OR IMPLIED CONDITIO
NS, REPRESENTATIONS AND WARRANTIES, INCLUDING ANY
IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE
OR NON
-
INFRINGEMENT ARE DISCLAIMED, EXCEPT TO THE EXTENT THAT THESE
DISCLAIMERS ARE HELD TO BE LEGALLY INVALID.

4. LIMITATION OF LIABIL
ITY. TO THE EXTENT NOT PROHIBITED BY LAW, IN NO EVENT
WILL CSCS OR ITS LICENSORS BE LIABLE FOR ANY LOST REVENUE, PROFIT OR DATA,
OR FOR SPECIAL, INDIRECT, CONSEQUENTIAL, INCIDENTAL OR PUNITIVE DAMAGES,
HOWEVER CAUSED REGARDLESS OF THE THEORY OF LIABILITY,
ARISING OUT OF OR
RELATED TO THE USE OF OR INABILITY TO USE SOFTWARE, EVEN IF CSCS HAS BEEN
ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. In no event will CSCS's liability to you,
whether in contract, tort (including negligence), or otherwise, exceed the amo
unt paid by you for
Software under this Agreement. The foregoing limitations will apply even if the above stated warranty
fails of its essential purpose.

5. Termination. This Agreement is effective until terminated. You may terminate this Agreement at
any

time by destroying all copies of Software. This Agreement will terminate immediately without
notice from CSCS if you fail to comply with any provision of this Agreement. Upon Termination, you
must destroy all copies of Software.

6. Severability. If any p
rovision of this Agreement is held to be unenforceable, this Agreement will
remain in effect with the provision omitted, unless omission would frustrate the intent of the parties, in
which case this Agreement will immediately terminate.

7. Integration. Th
is Agreement is the entire agreement between you and CSCS relating to its subject
matter. It supersedes all prior or contemporaneous oral or written communications, proposals,
representations and warranties and prevails over any conflicting or additional t
erms of any quote, order,
acknowledgment, or other communication between the parties relating to its subject matter during the
term of this Agreement. No modification of this Agreement will be binding, unless in writing and
signed by an authorized represen
tative of each party.


For inquiries please contact:

Centro Svizzero di Calcolo Scientifico (CSCS)

Swiss Federal Institute of Technology

Via Cantonale,

Galleria 2

CH
-
6928 Manno

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Version 4.1

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Switzerland


Installation

Requirements



Screen resolution of at least 768 x 1024 pixels

Unpack and install

コンパイルされた実行形式配布物には以下のファイルが含まれている:

molekel/bin/molekel

the molekel script: adjust paths depending on your installation
molekel/bin/molekel*.arch

the molekel executable: platform dependent

molekel/lib/LICENSE

license information

molekel/lib/README

this i
nstruction

molekel/lib/atoms.data

text file with atom type data

molekel/lib/help.txt

currently a dummy

molekel/lib/ms

the executable of Connolly's molecular surface program




Unzip and unpack molekel*.tar.gz (
gzip
-
cd molekel*.tar.gz | tar
-
xvf
-
)
to anywhere.

either



move the files in
molekel/bin

to
/usr/local/bin
, then
rehash
.


move the folder
molekel/lib

to
/usr/local/lib/molekel
.

or



adjust the paths in the script molekel



add the location of the script to the path, rehash, or define an a
lias.



On Win9x/NT unpack the distribution to any place. Copy glut*.dll from the GLUT distribution to the
C:
¥
WINDOWS
¥
SYSTEM32 folder for a general installation or to the folder where molekel lives.

To relink with other versions of third party objects or
shared objects of other packages do the
following:



Unzip and unpack molekel
-
objects*.tar.gz (gzip
-
cd molekel
-
objects*.tar.gz | tar
-
xvf
-
) to
anywhere.



cd to molekel/objects.



copy the Makefile of your platform (e.g. "cp Makefile
-
objects.sgi
-
n32 Make
file"), adjust the
paths in the Makefile.

(

n32 : with new 32 bits compiler,
-
o32 : with old 32 bits compiler )



type "make", the executable "glutmolekel" will be generated.



rename glutmolekel appropriately (e.g. molekel*.sgi
-
n32).



Some libraries

which might not be on your system by default are required to relink MOLEKEL:



OpenGL (
http://www.opengl.org/

): check with your vendor if available for your system

or Mesa: can be downloaded from
http://www.mesa3d.org/


If OpenGL is available for your system, performance is usually better compared to Mesa.



GLUT, the OpenGL Utility Toolkit: can be downloaded from
http://rea
lity.sgi.co
m/mjk/glut3/glut3.html




MUI

: is part of the GLUT distribution



GLUI (Version 2.1): can be downloaded from
http://www.cs.unc.edu/~
rademach/gl
ui/


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Version 4.1

6

GLUI is distributed under the GNU Lesser General Public License (
http://www.gn
u.org/copyleft/lesser.html

)



libtiff: can be downloaded from
http://www.libtiff.org/tiff
-
v3.5.5.tar.gz




libjpeg: can be downloaded from
ftp://ftp.uu.net/graphics/jpeg




libimage: can be downloaded from
https://toolbox.sgi.com/toolbox/src/haeberli/libim
age/index.html#dl

(only needed if "
-
limage" is present in your Makefile)


Known Bugs



If MOLEKEL crashes on Win32 systems a restart is most li
kely required to be able to use any
GLUI/GLUT application again. For some reasons the content of GLUT windows will be messed
up after a crash.

もし,
Win32
システムで
MOLEKEL
が異常終了した場合は,再び
GLUI/GLUT application

MOLEKEL
を含む)を利用するためにコンピュータの再起動が大概必要になるだろう.
ある理由から
crash
した後は
GLUT windows
の表示が乱れるようである.


Basic Procedures



MOLEKEL
は分子を描画する
graphics window
とログを表示する
scrollable

main
interface wind
ow
から成り立っている.主たる操作は左マウスボタンを
graphics window
でクリックして現れる
popup menu
で行う.



Rotation
,
translation

scaling

は左と中央(もし有れば)のマウスボタンを
SHIFT
,

CONTROL

ALT keys
を同時に押すことで行う.矢印キーも使える.



Output of electronic structure calculation programs

coordinate files

popup menu

"Load" subm
enu
によって読み込まれる.
MOLEKEL

isosurfaces
を表示するために,
Gaussian jobs

"GFPRINT"

"POP=REG"

"POP=FULL" keywords
を用いて実行する必要
がある.



Geometrical parameters

(bond dist., angles...)

popup menu

"Geometry" submenu
からオ
プションを指定して得ることができる.これらの機能のどれか1つを選択すれば
picking
mode
に入る.
picking mode


SHIFT key
と左マウスボタンを押すことで分子を回転で
きる.中央マウスボタンを押すか
popup menu

"Done picking"
を選ぶと
picking mode

ら出ることができる.



Superimpose

two molecules:
popup menu

"Geometry" submenu
から
"Match"
を選択し,
matching
させる原子を順番に(
first atom first molecule, first atom second molecule, second
atom f
irst molecule, second atom second molecule...;

pick
する.中央マウスボタンを押すか
popup menu

"Done picking"
を選ぶと
picking mode
から出ることができる.



Isosurfaces

popup menu

"Compute" submenu
で生成できる.
Grid data

surface files

popup menu

"Surface"
を選択し,開いた
popup

window "
S
urface"
からロードできる.
"Sur
face" popup window

surfaces
についての詳細な制御ができる.



Color code a surface

according to the molecular electrostatic potential: surface (e.g. electron
density)
をつくり,
popup menu

"Compute" submenu
から
"MEP"
を選択し,そして
"Dot
surface"
を選択して
"ok"
をクリックする.他の物性に対する
color code
については
surfac
e"
popup window
からその物性の
grid file
を読み込み,
"grid value"
を選択する.



Series of structures

from geometry optimizations and from coordinate files containing multiple
structures

popup menu

"Animate"
で動画として表示できる.

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Vibrational normal modes

popup menu

"Frequencies"
で表示と動画がで
きる.



Coordinates

popup menu

"Write" submenu

export
できる.



Pictures


popup menu

"Snapshot"
で保存できる.用いた
TIFF library
に依存して
LZW
compression
はサポートされていない(
see possible message in the terminal window
).
"Render"
メニューを使って指定した大きさで保存する.



Colors

popup menu

"Color"
で変更できる.
popu
p menu

"Texture"
を用いて種々の対
象によって異なった
textures
を割り当てることができる.



Close all
全ての
popup windows
はもはや必要でなくなれば適当なボタン

("cancel")
で閉
じることができる.けっして適当なフレーム領域をダブルクリックしたり,ウィンドウ
マネージャのオプションを用いてどんなウィンドウも閉じてはいけない.それをやれば
まさにそれ1つのウィンドウが閉じるのではなく
application
が閉じるからである


Every Button Explained

Graphics window

Model orientation


回転:

x
-
,
y
-

axis


分子の中心付近

左マウスボタン
を押してマウスを動かす.

あるいはキーボードの
矢印キー
を使う.

z
-
axis


分子の中心から離れたところ

左マウスボタン
を押してマウスを動かす.

あるいはキーボードの
<Ctrl>
キー

左右矢印キー
を使
う.


並進:

x
-
,
y
-

axis


中央マウスボタン
を押す.

あるいは
<SHIFT>
キー

左マウスボタン
を押しながらマウスを動かす.

あるいは
<SHIFT>
キー

矢印キー
を使う.

z
-
axis


<SHIFT>
キー

中央マウスボタン
を押しながらマウスを
動かす.

あるいは
<SHIFT><Alt>

左マウスボタン
を押しながらマ
ウスを上下に動かす.

あるいは
< Ctrl >
キー

<Alt>
キー
?)と
上下矢印キー
を使
う.


ズーム:

<Ctrl>
キー

中央マウスボタン
を押しながらマウスを動
かす.

あるいは
<
SHIFT><Ctrl>

左マウスボタン
を押しながら
マウスを上下に動かす.

あるいは
<Ctrl>
キー

上下矢印キー
を使う.

ズームはいつも全ての分子に適用される(個々の分子には
できない)

Popup menu

Press right mouse button

in the
graphics window.

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Version 4.1

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Main interface window

molecular models

分子の表示モデルを選択する(選択された複数の分子で,
異なったモデルで表示できる)
:



wire model



sticks



ball&stick



spacefill




multiplebonds


ball&stick
モデルが選択されているとき,
single,
double and triple bonds
を区別して表示する

bond attributes






del bond

delete an existing bond:

del bond
をクリックし
(picking mode
に入る;そのことが
main interface
window

log area
に表示される
)
,消去する
bonds

pick
する
(
左マウスボタンで
)
.中央マウスボタ
ンあるいは
popup menu

Done picking
をクリック
して
picking mode
を抜ける.



add bond

add a new bond:

a
dd bond
をクリックし
(picking mode
に入る;そのことが
main interface
window

log area
に表示される
)
,新しい
bond
で結合する2つの
atoms

pick
する
(
左マ
ウスボタンで
)
.中央マウスボタンあるいは
popup menu

Done picking
をクリックして
picking mode
を抜ける.



mod to single
,
mod to double
,
mod to triple


modify an existing bond to a single, d
ouble or triple bond respectively
: click
mod to
*
をク
リックし
(picking mode
に入る;そのことが
main interface window

log area
に表示され

)
,変更する
bonds

pick
する
(
左マウスボタンで
)
.中央マウスボタンあるいは
popup
menu

Done picking
をクリックして
picking mode
を抜ける.



own bond color

display bonds with a separate color (
ball&stick

only).

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Version 4.1

9



vdW scale
-
factor


modify ball size (

ball&stick

only
).



bond
-
thickness


modify stick size (

wire model
,

sticks

and
ball&stick
).


manipulate all

全ての原子を一緒に
rotate and translate
させる.
surface clip

move rot clip

active
ならば,
1つの分子の全ての
clip
された面が一
緒に
rotate and translate
する.


switch mol


step one molecule further in the list of molecules and make this molecule the active molecule.


delete mol


delete the active molecule (no undo).


pick mol


make a specific molecule the active molecule: click
pick mo
l

(you enter picking mode; annotated in
the log area of the
main interface window

), pick the molecule (left mouse button) to become the
active molecule, you are exiting picking mode automatically.


quality

choose between thre
e quality levels:
high
,
medium

and
low
; performance of redisplaying the main
graphics window increases with lower quality.



depthcue
: enable depthcueing; objects further away will be rendered darker. You can modify the
depthcue range in the popup
option w
indow

launched from the
main interface window

with
option
. Moving the object along the z
-
axis, can also help to achieve the desired result.



texture
: enables to use texture in general. If the performance of redisplaying is unsatisfying on
your computer, d
isabling texture mapping will help.



smooth line
: enable line smoothing; makes lines and letters looking nicer, might slow down
redisplaying.


center

redefine center of rotation of one molecule: click
center

(picking mode
に入る;そのことが
main
interface window

log area
に表示される
)
,新しい回転の中心としたい
atoms

pick
する
(left
mouse button)
.複数の原子を
pick
した場合,全ての
pick
された原子の幾何中心を回転の中
心として設定される.設定を確認し,中央マウスボタンあるいは
popup menu

Done picking
をクリックして
picking mode
を抜ける.


reset


reset active molecule to its original orien
tation, has no influence on the scaling factor.


spin


enters spinning mode: a rotation defined with a mouse motion well be applied continuously. Stop
spinning by clicking
spin

again.

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Version 4.1

10

fullscreen


make the
graphics window

fullscreen. To return to normal mo
de press the <ESC
>

key. You can
popup the
main interface window

also in fullscreen mode from the
popup menu

.


option



projection
: choose between an orthogonal and a perspective
(遠近法)
projection
(投影図)
.



window size
: set the window size to specific values.



depthcue range
: set the depthcue range along the z
-
axis.



molecular properties
:



transparent spacefill
: render balls of the spacefill representation transparent to make the
s
tick representation underneath visible.



hide hydrogens
: do not display hydrogens



backbone only
: connect and display only CA atoms of amino acids. Works only with
PDB files.



idle
: enables GLUI idle function. This makes the spinners really spinning, i.
e
. while pressing on
the spinner arrow with the left mouse button, the value of the spinner increases or decreases
continuously until the mouse button is released again. This is of course very nice, but the
required GLUI idle function takes quite some CPU
resources even if MOLEKEL is doing
nothing than waiting for the next command. With disabled GLUI idle function, the spinner
changes its value by a certain value for each mouse click or by pressing the left mouse button
and moving the mouse up or down.


log area

actual molecule
: tells you which is currently your active molecule.
log info
: scrollable information
area; click with the left mouse button into the area and move the mouse up or down. Clicking with the
left mouse button

into the top or bottom area of the log area lets you step through the informations.

help


This launches Netscape with the manual from MOLEKEL's home page. Not implemented on Win32.


info


gives you version and license information.


quit


quit MOLEKEL.

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Menu

popup menu

gives you main control.

Menu Load

load coordinate and log files.



xyz
: load xyz coordinate file; atoms are recognized either by their element
symbol or element number. Select
the appropriate format of your file in the
popup
xyz format window

. Only lines which comply with the selected
format are read.





multiple structure xyz
: load xyz coordinate file containing multiple
structures. Fo
rmat corresponds to the
babel xyz format (http://www.eyesopen.com/babel.html)

.



pdb
: load pdb coordinate file; only lines containing ATOM and HETATM are read.



multiple structure pdb
: load pdb coordinate

file containing multiple structures.



gaussian log
: load data from a gaussian log file. To make full use of MOLEKEL run your
gaussian jobs with the "
GFPRINT
" and "
POP=FULL
" or "
POP=REG
" option and set the "
#P
"
print level.



gaussian cube
: load coordinat
es from a gaussian cube file. To load the actual cube data see the
popup
surface window

.



nbo orb
: load orbital coefficients from a NBO calculation (as implemented in gaussian). Use the
keyword "PLOT" in NBO to write out the various orbital coefficients
. Load the regular gaussian
logfile first and then change the already read in molecular orbital coefficients with this option to
be able to display natural bond orbitals.



gamess (us) log
: load data from a gamess log file. US version is tested best, PC G
amess and UK
version seem also to work.



hondo
: load data from a hondo log file, the punch file is also required.



adf
: load data from a adf log file, the TAPE21 file is also required. To display orbitals or the
electron density you need to have instal
led the adf utilities densf and dmpkf locally. The cube
grids are generated via the TAPE41 file with these tools. Define the environmental variable
ADFBIN pointing to the location of the utilities. To use adf2.x set MOLEKEL_ADF2x (csh:
"setenv MOLEKEL_ADF2
x" is enough) before starting MOLEKEL. TAPE21 are binary files!
They need to be transferred from platform to platform in ascii format using dmpkf and udmpkf.



mos
: load data from a mos log file (program of H. Baumann, ETHZ).



prddo
: load data from a pr
ddo/m log file.



zindo
: load data from a zindo log file. You can read in the occupation of a particular excited state
by replacing the line, e.g.

*************** STATE 5 ***************


by

*************** STATe 5 ***************


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in the output file to

read in e.g. state 5.



mkl
: load data from a MOLEKEL file. The format was defined to be able to convert any program
output into a readable format using e.g. (awk, perl...) (extension.mkl).

The mkl format description can be found under mkl format at the e
nd of this document.

Menu Geometry



Atom
: dump atom information to the terminal: Select
Atom

(you enter picking mode; annotated
in the log area of the
main interface window
), pick the atoms (left mouse button) to get
informat
ion on, exit picking mode with the middle mouse button or with
Done picking

from the
popup menu
.



Distance
: measure the distance between two atoms: Select
Distance

(you enter picking mode;
annotated in the log area of the
main interface window
), pick the
atom pairs (left mouse button),
exit picking mode with the middle mouse button or with
Done picking

from the
popup menu
.



All distances
: measure all bond length in the active molecule.



Angle
: measure the angle between three atoms within the same molecul
e: Select
Angle

(you
enter picking mode; annotated in the log area of the
main interface window
), pick the atom
triples (left mouse button) exit picking mode with the middle mouse button or with
Done
picking

from the
popup menu
.



Dihedral
: measure the di
hedral angle between four atoms within the same molecule: Select
Dihedral

(you enter picking mode; annotated in the log area of the
main interface window
), pick
the atom quadruples (left mouse button) exit picking mode with the middle mouse button or with
Done picking

from the
popup menu

.



Remove values
: remove all distance, angle and dihedral angle annotations of the active molecule.



Add dummy
: add a dummy atom in the center of the selected atoms: Select
Add dummy

(you
enter picking mode; annotated i
n the log area of the
main interface window
), pick the atoms (left
mouse button) to define the position of the new dummy atom. Picking multiple atoms sets the
dummy atom to the geometrical center of all picked atoms. Confirm your selection and exit
picking

mode with the middle mouse button or with
Done picking

from the
popup menu
.



Remove dummies
: remove all dummy atoms of the active molecule.



Match
: superimpose two molecules: Select
Match

(you enter picking mode; annotated in the log
area of the
main
interface window
), pick the to be matched atoms in the order first atom first
molecule, first atom second molecule, second atom first molecule, second atom second
molecule... Confirm your selection and exit picking mode with the middle mouse button or with

Done picking

from the
popup menu
.

Dipole moment

Show dipole moment as an arrow.



show dipole moment
: toggle dipole moment arrow.



dipole scale
-
factor
: scale dipole moment arrow.







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Labels

Add labels to the atoms.



atom labels
: display element name.



atom charges
: display atom charges as read from the
log file.



atom spin
: display the spin density at the atom position
(if computed with
spin/atom

from the menu
Com
pute

).



labels on top
: draw labels on top of everything, labels
are not hidden behind any object.



hide measure labels
: do not draw the labels of
measures.



global label size
: set size of all labels. S, M, L and XL are bitmap fonts and are not scaled

with
the size of the molecule. "scalable" is rendered with as an object and scales with the size of the
molecule (useful for generating images to print).

Menu Compute



Orbitals
:
generate grid values of an orbital and display

it as an isosurface. Select an orbital from the list with
the left mouse button and click
Accept

or select the
orbital with the middle mouse button. The grid data will
be saved in a macu file (.macu), provide an appropriate
file name in the popup
file bro
wser window
. The
computation is started with a new process, therefore
you have to set the job priority in the popup
job priority
window

(not on Win32). This job will continue running
even if you quit MOLEKEL. To add more than one
isosurface to one molecule
, set
add surface

in the
popup
surface window
.



El. density
: generate grid values of the electron density
and display it as an isosurface. If MO
-
coefficients and
the density matrix are present in your logfile, you will
be asked what you would like to use
to generate the
grid values in the popup
coeff_or_matrix window
.
Provide a file name and the job priority as described
under
Orbitals
.



Spin density
: generate grid values of the spin density
and display it as an isosurface. See
El. Density

and
Orbitals
.



Spin / atom
: calculate the spin density at each atoms
position and display the number as an atom label (see
popup
labels window

atom spin
).



MEP
: generate grid values of the molecular
electrostatic potential based on the atom charges read
from the log fi
le. Choose in the popup
3D
-
grid or map
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to surface window

either to only map the potential to an existing isosurface (

map to surface
) or
to calculate the grid values and save them to a macu file (

3D
-
grid
) (see
El. Density

and
Orbitals
). If the active mole
cule has more the one isosurface you have to pick one (left mouse
button). In the popup
set vmin vmax window

you can set the minimum and maximum values to
map the color spectra to.



Fast surface
: generate a simple isosurface wrapping the whole active mole
cule.



Connolly
:

generate a connolly surface using the external original
FORTRAN program of Connolly. Set the desired parameters and click
go

in the popup
connolly window
. The calculation will be started as a
new process (not on Win32 and LINUX). The gen
erated dots can be
triangulated (generate a solid surface) by clicking on
dot triangulate

(see
surface window
).



Adjust box
:

modify the size and position of the box to calculate the
grid values for the orbitals and densities.




show box
: display the box



cubesize
:

determines the grid: smaller number
-
>

finer grid

(数値が小さいほど細かくなる)



zoom box
:

scale box proportionally in all directions



update values
:

update the min max values after zooming, the
zoom boxes

s
pinner is not
synchronized with the
min max

spin
ners.



x
-
min
,
y
-
min
,
z
-
min

,
x
-
max
,
y
-
max
,
z
-
max
:

move one side of the box



reset box
:

set the box back to the default size

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Surface

gives you detailed control over grid data and surfaces.



load
: load grid data from a fi
le.



unload
: remove the grid data from memory.



add
: add grid data from a file to the currently loaded data.
Adding means add the value at each grid point in the file to
the already loaded value at each grid point. This requires
equivalent grids in both
data sets.



subtract
: subtract gird data from a file from the currently
loaded data. Subtracting means subtract the value at each grid
point in the file form the already loaded value at each grid
point. This requires equivalent grids in both data sets.



macu
: the file contains data in the macu format (MOLEKELs
own grid format, binary).



gaussian cube
: the file contains data in the gaussian cube file
format (only one data set per file).



adf tape41
: the file contains data in the formated adf tape41 for
mat (use dmpkf to dump the data
to an ascii file).



both signs
: create two isosurfaces, one for negative data and one for positive data (e.g. orbitals).



add surface
: add the new surface to the existing surfaces. Default is to remove any existing
surfac
e from the molecule, before creating a new one.



V
-
min
: set the minimum value for color coding. Has only an influence for
planes

(see below).



V
-
max
: set the maximum value for color coding: Has only an influence for
planes

(see below).



cutoff
: set the
cutoff value for the isosurface generation.



reset
: reset
V
-
min
,
V
-
max

to the extremes in the currently loaded data.



pick surface
: pick a surface to become active (left mouse button).



switch surface
: make the next surface in the surface list active (u
seful if a surface is not visible
anymore and can't be picked easily).



create surface
: create a new isosurface based on the currently loaded data, the
cutoff

and the
settings of
both signs

and
add surface
.



delete surface
: delete the currently active su
rface. The two phases of the orbitals are linked
surfaces and they are deleted both.



grid value
: map the values of the currently loaded data to an existing surface of the currently
active molecule. If multiple surfaces are present you have to pick one (
left mouse button).



planes
: display a plane representing a slice of the currently
loaded grid data. The actual texture is used for color coding
(see
texture
).



show plane
: show the plane.

x
-
axis
,
y
-
axis
,
z
-
axis
: choose between the three
possible orien
tations.



move plane
: move the plane along its normal axis.
Click on
move plane

(left
mouse

button) and move the mouse up and down.



reset position
: reset the plane to its initial position.

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project
: project the currently loa
ded grid data to a plane. The actual texture is
used for color coding (see
texture
).



x
-
axis
,
y
-
axis
,
z
-
axis
: choose a projection axis and click
go
.



del projection
: delete the projection plain.



surface option
: choose between different surface display
modes.



transparent
: render the active surface transparent using polygon
stippling (see
color window

on how to use alpha values).



chickenwire
: render the active surface as a wire model.



dots
: render the active surface as a dotted model.



flatshade
: r
ender the active surface flat shaded.



dot/sld
: save and load surfaces; do dot triangulations.



load ms
: load a surface described by dots as generated by the
external connolly program (see
connolly
).



save ms
: save a surface
in the connolly dot format. Only the edge
points of the triangles are saved. To generate a solid surface from
it, you have to triangulate it again, which is not always an easy
task (see
dot triangulation
).



load sld
: load a solid surface (binary file).



save sld
: save the active surface as a solid surface (binary file).



dot triangulation
: triangulate a dot surface. Default parameters
recommended. Click
go

to start triangulation.



surface clip
: add a clipplane to the active surface (cuts the active sur
face).



move rot clip
: enable rotation and translation of the clipplane. Rotation: press left mouse button
and move mouse; translation: press middle mouse button or <SHIFT
>

and left mouse button and
move mouse. To rotate the molecule in move rot clip mode
, press <CONTROL
>

and left mouse
button and move mouse.

Frequency

controls animation and display of vibrational normal modes.



animate
: animate the chosen normal mode.



stop
: stop the animation.



show arrows
: represent the chosen normal mode using
arrows.



solid arrows
: use solid arrows instead of just lines.



arrow scale
-
factor
: scale the arrows.



choose
: Select a normal mode from the list with the left
mouse button and click
Accept

or select
the orbital with the
middle mouse button.




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Menu Animate

Frequency
: see above.

Series of coords
: Animate a series of coordinates from a geometry
optimization (not all output formats support this featu
re) or a multiple
structure coordinate file.



play
>
: play forward.



play<
: play backward.



first
: go to the first structure in the file.



last
: go to the last structure in the file.



next
>
|
: step forward to next structure.



next|<
: step backward to

next structure.



stop
: stop animation.



single
: go once through all structures



loop
: display structures continuously in one direction.



swing
: display structures continuously, forward than backward.



keep bonds
: do not regenerate bonds for ever
y structure.



show fixed
: has currently no effect.

Color

define the actual material and assign materials and colors to objects.
First define your actual material than assign it to an object.



mat
erials
: define a material

default materials
: a few materials are predefined.

diffuse color
: basic color of the material (r: red, g: green, b:
blue).

specular color
,
ambient color
,
emission color
: play with it,
than you best see what effect every color has.

shininess
: shape of the shiny spot.

alpha value
: sets transparency level for surfaces if enabled (see
enable alpha blending
).



assign material to
: assign the material to an object

atom type
: assign material to an atom type. Click an atom of the
type you
want to assign the material to.

bond
: assign the material to the bonds. This material is used if
own bond color

in the
bond attributes window

is active.

surface
: assign material to a surface. Click a surface to assign
the material to.

arrow
: assign materia
l to the arrows.

box
: assign material to the box (see
Adjust box

in the
compute menu

).



assign diffuse color to
: assign the diffuse color to an object not represented by a material.

background
: the background can have a top and a bottom color.

label
: ass
ign diffuse color to the labels.

distance
: assign diffuse color to the labels, lines and dots indicating distance measurements.

angel
: assign diffuse color to the labels, lines and dots indicating angel measurements.



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dihedral
: assign diffuse color to the

labels, lines and dots indicating dihedral angel
measurements.



enable alpha blending
: enable alpha blending for surfaces. Surfaces with materials with an alpha
value smaller than 1.0 appear transparent. If multiple surfaces are present, the order of
ge
neration (rendering them) plays a role. To achieve most realistic results they need to be drawn
in the order far to close (or back to front).



get material from
: make a material of an object the editable material.

atom type
,
bond
,
surface arrow
,
box
: ge
t the material from those objects (see
assign materials
to
).

Texture

define the actual texture and assign the texture to an object. First
define the actual texture then assign it to an object. If yo
u modify
the actual texture, you have to reassign it to the object, to become
active.



assign no texture
: select to assign no texture to an object.



texture properties
: play with them. The texture
implementation in different OpenGL versions differs quiet

a lot. Not all settings have an effect, some simply disable
texture completely with some implementations, but nothing
should cause a crash.



tex list up
,
tex list down
: move within the list of defined
textures. There are four contour textures predefined.



load rgb
: load an image file to be used as texture (SGI
RGB format).



duplex texture
: duplicate an existing texture (easy way to define a second texture with different
texture properties

but the same image).



add texture to
: add texture to an object
(GL_OBJECT_LINEAR).

surface
: assign texture to a surface. Click a surface to assign the texture to.

bond
: assign texture to the bonds.

atom type
: assign texture to an atom type. Click an atom of the type you want to assign the
texture to.



reflect tex
ture from
: reflect texture from an object (GL_SPHERE_MAP).

surface
,
bond
,
atom type
: see
add texture to
.

surface phong
: emulate phong on a surface using the actual texture.



start texture
,
end texture
: the texture covers a range from 0.0 to 1.0 (left t
o right). On surfaces,
parts of the texture not included in the range become completely transparent (surface disappears).
To make a central part of a texture transparent, set the
start texture

value larger than the
end
texture

value. You have to reassign t
he texture to the object after modifying the two values.

Menu Write

export coordinates and surfaces.



xyz (orig. orient.)
: save coordinates of the active molecule in the original orientation in the xyz
format (babel xyz,
http://www.eyesopen.com/babel.html
).



xyz (current orient.)
: save coordinates of the active molecule in the current orientation in the xyz

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format.



pdb (orig. orient.)
: save coordinates of the active molecu
le in the original orientation in a
rudimentary PDB format (ATOM only).



pdb (current orient.)
: save coordinates of the active molecule in the current orientation in a
rudimentary PDB format (ATOM only).



Surface (sld)
, Surface dot (ms): see
surface win
dow

dot/sld
.

Menu Snapshot

save content of the
graphics window

to a file.



RGB
: SGI RGB format (RLE compression not available on all systems).



TIFF
: standard TIFF format.



TIFF LZW compressed
: LZW compressed TIFF format (d
epending on what libtiff you are using,
this does not work for license reasons, see terminal output).



Packbits
: Packbits compressed TIFF format.



JPEG
: standard JPEG format (quality as set in the
render window

).

Render

Re
nder an image at any size. Renders images in tiles and assemble them in memory. Makes use of the
tr library by Brian Paul (
http://www.mesa3d.org/brianp/TR.html

)



image width
,

image height
: set image width and
height (multiples of 4 only).



keep ratio
: keep ratio of image width and height



reset
: reset image size to current
main window

size.



file format
: see
Menu Snapshot

.

ppm
: assemble image parts directly in the file,
th
erefore needs only memory for one image tile
(512 x 512 pixels).

jpeg quality
: set quality of jpeg image (10
-
100%).



action
: what kind of image should be created.

current image
: generate image with content of
current
main window
.

freq animation
: genera
te a series of images (frames) containing the frequency animation. The
images can then be used to produce a movie or an animated GIF with an external program. Loop
through the images for a continuous animation.

structure animation
: generate a series of ima
ges (frames) containing a series of structures (geom.
optimization, multiple structure pdb, xyz) starting with the first structure read from the file (see
also
Menu Animate
). The images can then be used to produce a movie or an animated GIF with
an externa
l program.

start frame numbering at
: file names for series of images are set as follows: base name
"base.rgb" plus start frame numbering at "1"
--

base.001.rgb, base.002.rgb,...

Warning

: existing files in a series of images are overwritten without warni
ng!

Various



Pop maininterface
: Pop up maininterface to top of the window stack.


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Done Picking
: see picking mode.



Warranty, License
: Warranty and license info, see terminal output.



Quit
: quit MOLEKEL.

Picking mode

To select any object you enter picking mode. Within picking mode you still have the possibility to
rotate the objects. Press <SHIFT
>

and the left mouse button and move the mouse. If the command
does not automatically exit from picki
ng mode, click the middle mouse button or
Done Picking

from
the
popup menu

to cancel the command or exit picking mode.

File browser

gives you access to the file system.

Directory: path of the actual
ly listed directory.

Up
: go one directory up.

Original
: go to directory from which MOLEKEL was started.

Filter
: enable/disable filter for the extensions listed.

List
: Select file or directory with the left mouse button and press
Accept

or select file or
directory with the middle mouse button to
select and accept at the same time (equal to the common double
click).

Open File/Path
: type file or directory explicitly to be opened.

Cancel

Close the actual window! Do NOT close any wi
ndow by
double clicking on the appropriate frame area or using an
option from the window manager, this closes the application not just one window.