Running PIXEL using Oscail
is easy using Orca or Gaussian to calculate electron density
Published example of PIXEL use -
Video showing PIXEL run on CSD code VUKRAW
(VUKRAW is in c:\ortex as the ShelxL CIF file hps1.cif)
CLPCRY and PixelC
Calculate the energy between any two molecules in any lattice using
PIXELS (a version of PIXELC)
Getting pictures of the important
Installing Pixel Gaussian
and Orca for use with Oscail
values for specific atoms
Basis set problems with heavy elementand other
cases where manual intervention is required
Pixel was used to answer
the question "Why does CSD code VUKRAW grow as needles" (VUKRAW is in C:\ortex as
The answer has nothing to do with hydrogen
bonding. Look at N. Walshe et al., Cryst. Growth Des.2015 15 (7), pp 3235–3248.
1. You should read the PIXEL
2. Run the Oscail file
checker (? on the toolbar) on the INS file and if there is an SFAC
element name case error fix it in INS and CIF files.
3. The CIF file used as input to PIXEL
must contain full molecules. As an example you could have the
following - a structure in Space Group P-1 (No.2) with an asymmetric
unit that is a half molecule and with Z =1. This would need to be changed to a
full molecule in Space Group P1 (No.1).
4. PIXEL requires a CIF
file in CSD reduced format. When you run
PIXEL within Oscail there is an option to convert ShelxL CIF files
A good way to quickly test the CIF file is to run CLPCRY as outlined
Running CLPCRY or
PIXELC and using X-H neutron diffraction distances
CSD code VUKRAW is in C:\ortex as
a ShelxL cif with the jobname HPS1. Set the Oscail file EXT to CIF
and open HPS1 in c:\ortex
Use save as on the Oscail file options to save a copy
of the file in a sub folder called pixel and open that job.
In Oscail click Run Job on the menu and select PIXEL
When you attempt to use a CIF with PIXEL in which the Jobname has
more or less than 8 characters a copy of the file is written which
has 8 characters. In the case of HPS1 the message
appears. Open the
hps1xxxx job and click Run Job on the menu and select
In Oscail click
In ORTEX click Setup/Main Setup.
Check X-H calc. in the red box and OK. You can click OK to
accept the default suggestions for the X-H distances. When finished
exit ORTEX and and click Run Job on the Oscail menu and select
This CIF was written by ShelxL and it first
needs to be converted to CSD format to do
this check Reformat CIF from SHELX etc. to CSD and click Run.
To add the new X-H distances Check Add X-H Neu. from Ortex to CIF
and click Run. Find the file XH_neu.lst it should be
in the Pixel folder click Open
appears. Open the job in the NXH folder and in Oscail click Run Job on the menu and select PIXEL.
Running CLPCRY or
Select Run CLPCRY and click OK.
and the output in the jobnameclp.pri file and should look like
AA-CLP program version 3.0 nov 2015
# o--- 0.0 0. 0.00
Coulombic,polarization,dispersion and repulsion
0.410 235.000 650.000 77000.0
cell parameters 5.2290 8.6307 25.7760 90.00 90.00 90.00
symmetry operator matrices 4
1 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 0.0000 0.0000 0.0000 TR
2 -1.0 0.0 0.0 0.0 -1.0 0.0 0.0 0.0 1.0 0.5000 0.0000 0.5000 SC
3 -1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 -1.0 0.0000 0.5000 0.5000 SC
4 1.0 0.0 0.0 0.0 -1.0 0.0 0.0 0.0 -1.0 0.5000 0.5000 0.0000 SC
fragm.,n.at,weight,charge+,- 1 28 249.30 3.0020 -3.0021
# density check warning,calc 1.424 input 0.000
fragm.,volume 1 204.4
cell volume,density,packing coeff.,T/K,press/MPa
# o--- 1163.27 1.424 0.703 0.0 0.000
max c.o.m. dist vector, cells on a,b,c 40.00 9 6 3
1 1 5.229 1 -1.00 0.00 0.00 -5.0 -9.0 -33.0 10.5 -36.5
1 1 7.164 4 -0.50 0.50 0.00 0.2 -4.0 -23.7 5.9 -21.6
1 1 8.575 4 -0.50 1.50 0.00 -1.3 -3.8 -18.2 6.7 -16.7
1 3 1 4 O29 O31 2.744 3.160 109.8
1 1 8.631 1 0.00 -1.00 0.00 -6.8 -5.8 -15.0 20.1 -7.6
1 1 8.216 3 0.00 -0.50 0.50 -0.5 -5.9 -14.8 4.5 -16.6
1 1 8.216 3 0.00 0.50 0.50 -0.5 -5.9 -14.8 4.5 -16.6
1 1 7.164 4 0.50 0.50 0.00 0.2 -4.0 -23.7 5.9 -21.6
1 4 1 18 O31 H 5 1.962 2.680 -83.1 HB
1 1 8.631 1 0.00 1.00 0.00 -6.8 -5.8 -15.0 20.1 -7.6
1 1 8.575 4 0.50 1.50 0.00 -1.3 -3.8 -18.2 6.7 -16.7
1 1 9.298 3 1.00 -0.50 0.50 -4.3 -3.4 -10.0 5.6 -12.1
1 1 5.229 1 1.00 0.00 0.00 -5.0 -9.0 -33.0 10.5 -36.5
1 1 9.298 3 1.00 0.50 0.50 -4.3 -3.4 -10.0 5.6 -12.1
924 fragment pairs 924 within cutoff 40.00
per entire molecule in asymmetric unit
# o--- -16.9 -49.5 -124.0 53.3 -0.0 -137.1
Cell dip module and E/molecule 0.0000 -0.0
end of data stream, structures read,ok,wrong 1 1 0
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PIXELC can be used for structures with one or
two molecules in the asymmetric unit.
Open the hps1xxxx CIF file in the NXH folder and click Run Job on the menu and select
PIXEL.Select Run Gaussian / Orca and click Run
Select the theory level The values for density step,
condensation and Rad ext are usually OK. N.B. Check Edit Orca
Input if you need to change the basis set.
If there is more than one molecule in the asymmetric unit charges
should have been set using
on the ORTEX
line mode toolbar and they should appear in this dialog
automatically. Click OK
If you have Gaussian (G09 or G16) or Orca installed on your PC in the
locations given below then you will be asked if you want to run Orca and Gaussian.
On the first occasion the program will ask how many threads you want
Answer with a suitable number > 1 if you have the a multicore PC
and a parallel version
of Gaussian. Orca works in parallel mode
If you answer No to Orca the Gaussian question will appear and if
the answer to either was Yes an Orca or Gaussian window will open..
The default is to have PIXELC run automatically when Gaussian/Orca
has finished. If + PIXELC was unchecked on the dialog above then you
will need to run PIXELC
The results from PIXELC will be in the .mlp file.
Auto add symmops to the MLP file and Visualize Molecules in
PIXEL output using ORTEX
First do a centroid contacts scan to 20
Open the hps1xxxx job using Oscail.
Run Job on the menu
Select Add / Activate Centroids and click
or press a/A to go
to atom mode.
to bring up the Contacts / Packing dialog. Select Calculate Contacts
Calculate Lattice Contacts the Max. Contact Distance should be
automatically set to 20.0,
and Verbose should be checked Click OK.
Click OK until the ORTEX screen returns.
A copy of the GEO file containing the Centroid scan is saved as
jobname_CEN.geo and LSYMOP.LST is written.
When you exit ORTEX select Deactivate centroids on the Oscail.Run Job list.
Adding SYMMOPS to and MLP file from PixelC
Open the hps1xxxx CIF file and in Oscail click Run Job / Pixel
select Add symmops to MLP and click Run. Select the MLP
file when requested. MLP files from PixelS have _s added to the jobname (jobname_s.mlp)
The Output is in the file hps1xxxx_sym.mlp and this is comma delimited
for use with Excel. It looks like the example below.
The data has been sorted on the Pixel energy. The lattice energy is shown as "toto".
Note that the calculation method is included, Gaussian MP2..
SYMMOP and resid can be used with Ortex
to bring these units on screen. In Ortex when there is just one residue
in the asymmetric unit resid. is not required
This example, ambnac07, has two molecules in the asymmetric unit The first column indicates the
Getting pictures of the important
contacts for HPS1
The first 2 unique contacts in the hps1xxxx Excel list have Pixel energies of -40.1 and
-37 kJ/mol mainly composed of Coulombic (H-bonding) and dispersion energy
Put the codes 56501 and 65501 into the ORTEX symmop list
using Edit symmop_lst in ORTEX atom mode or Edit / symmop.txt in
Then in ORTEX do a search for contacts using defaults to identify H-bonds. When the H-bonds are
displayed clear the display back to the asymmetric unit.
Contacts/Units and OK.
Select Add Units from symmop_lst and OK.
The needle growth here is in the a
direction. The Pixel analysis shows that this corresponds to the direction with the large dispersion energy not along
b in the direction of the 1D H-bond chain.
Molecules A and B are stacked in vdW contact and molecules A and C are hydrogen
bonded. (This picture was made using Pogl OpenGL just clock the Pogl button on
the Oscail toolbar when you exit ORTEX).
N.B. vdW contact stacking is easily detected using centroid distance
matrix analysis See Tutorial 7.
Converting the Ortep
style SYMMOPS used by ORTEX into standard format
ORTEX will write any SYMMOPS in the jobsymmop.txt file into standard format in
the GEO file when you exit ORTEX.
If the hps1xxxxsymmop.txt file contains
Then when you exit ORTEX the GEO file will contain
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Calculate the energy between
any two molecules in any lattice using PIXELS
If there are one or two molecules in the asymmetric unit
of a crystal structure then you should use PIXELC as described above.
If there are more than two molecules in the asymmetric unit then PIXELS can be
used in two ways to calculate intermolecular interactions.
1. ORTEX can generate PIXELS input for a series
of molecular pairs selected on screen in Ortex and PIXELS can be
used to calculate intermolecular energies.
2. ORTEX can generate PIXELS input using an Indicative Lattice Analysis and
PixelS can be run to get an estimate of the most important interactions and an
estimate of the lattice energy. The lattice energy estimate is the total (at the
end of the MLP file) divided by the number of formula units in the asymmetric
Applying method 1 to CCDC code QIBCOW which has four molecules in its asymmetric unit.
N.B. do not use any other functions within Ortex before you write files for
The energy between one of the H-bonded pairs in the
asymmetric unit can be calculated as follows. In ORTEX line mode
click Symm.LAB on the menu. This will show the molecules with their
residue numbers. Click to
add residue charges. In this case all charges are 0 but you still need to add
them. Press e to go to edit mode, select (left click) an atom in the
first molecule, click SEL.Res. on the Oscail menu, File for PixelS on the
dialog and OK.
Select an atom in the second molecule, click SEL.Res. ,File for PixelS and OK.
(N.B. You must select the molecule with the lowest residue number first) You
will then be asked for a Jobname for the PIXELS run . The Default jobname is PIXELS01. If
you want to do more than one calculation then increase the number to 02 for the second pair
etc. to make the jobs unique. ORTEX will then ask for the parent CIF file.
If Gaussian and Orca have been installed you will be informed that files have
been created for the programs installed.
On the PixelS dialog select the theory level (charges
should be added automatically) and give a SymmOp
for the second molecule.
This message will appear after each set of files have been written. When
finished writing PixelS files close Ortex and run Pixel /PixelS. It is best to
use Orca for this calculation.
When the calculation is finished the results should be in
Method 2 requires an Indicative Lattice Analysis. Add
residue charges by clicking
in Ortex line mode and
then click to generate
the PixelS input. Then run Pixel / PixelS. It is best to use Orca for this
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Installing Pixel Gaussian and
Orca for use
When Oscail is installed the Pixel files will be in
c:\clp and Pixel documentation is in c:\clp\doc.
Either Gaussian 09 / 16 or Orca is required and if using
Orca then MultiWFN is also required
Gaussian must be installed in the default location C:\G16W\
Orca must be in C:\orca\ and MultiWFN must be in C:\multiwfn.
Orca version 5.0 can be obtained from
https://orcaforum.kofo.mpg.de/app.php/portal and MultiWFN version 3.8 from
Microsoft MPI is required for parallel operation of Orca. Version 10 is
required for Orca5 download from
https://www.microsoft.com/en-us/download/details.aspx?id=57467 ensure that
the location of mpiexec.exe (usually c:\program files\microsoft MPI\bin\)
is in the Path after installation. If the mpiexec.exe folder is not in the PATH
after MPI installation then it must be added manually.
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CIF file Problems
The best method for obtaining CIF files is from
the CSD using Conquest.
In Conquest use file export and ensure that Additional CIF
data items is selected
If you have a CIF file from ShelxL or another
source it is unlikely to work with PIXEL. If the CIF is from ShelxL
it can be converted to CSD format as described
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Setting X-H distances to
This is part of the normal procedure when running Pixel
under Oscail and is described above. If the structure you
have was determined using neutron diffraction you should ignore the X-H distance
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a values for
values used by PixelC, PixelS and PixelCF are read from a file
polat.lst which is in c:\clp\source
This file can be edited with notepad it looks like
C 10 1.05
C 11 1.35
C 12 1.35
C 13 1.05
C 14 1.90
N 16 1.00
N 17 1.00
N 18 1.05
N 19 1.00
N 20 1.00
N.B. change only the last number and do not change
the number of lines in the file or the number of characters in a line.
There is a copy of this file in c:\clp\source called back_polat.lst
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Basis set problems and other
problems where manual intervention is required.
If atoms beyond Zn are present for example Pt or Br then you
will need to change the basis set for that atom.
Generate the files for Orca / Gaussian and check Edit
Gaussian/Orca input on dialog 30.
Then the Orca input files will open in if you select
Run Orca Notepad++ add
the lines below for Pt or Br
NewGTO Pt "SARC-DKH-TZVP" end
NewGTO Br "6-311G**" end
Gaussian Notepad++ will open the GJF input files. The changes in
red below are required. Notice the change to
GEN on the third line
#MP2/GEN guess=core nosym density=MP2 pop=esp
#TODBIAxx 'P -1' fragm 1
Br -0.005359 -0.090422 -2.238282
C -0.013907 0.517035 2.388654
C 0.006023 -0.791164 1.876813
C 0.022852 -0.957141 0.483370
C 0.020685 0.142444 -0.353523
C 0.010981 1.428340 0.161092
C -0.001786 1.605598 1.531408
C -0.004592 -1.971209 2.813075
N 0.029954 0.698935 3.779854
H 0.037170 -1.968096 0.056006
H 0.013886 2.295607 -0.511914
H -0.003245 2.622184 1.947500
H 0.792619 -1.853709 3.558900
H 0.160848 -2.894150 2.241629
H -0.976212 -2.024771 3.321758
H -0.366059 0.031806 4.235692
H -0.129930 1.557325 3.996030
C H N 0
The Spin multiplicity can also be easily
adjusted in the INO and GJF files.
To change the cutoff radius used by PixelC
edit the .INP file and change the value of cutma
before you run PixelC
To identify cutma in the .inp file read section
4.7.2 ofthe CLPmanual.doc which is in c:\clp\doc
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