Running PIXEL using Oscail is easy using Orca or Gaussian to calculate electron density
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 intermolecular contacts

Installing Pixel Gaussian and Orca for use with Oscail
Changing a values for specific atoms
Basis set problems with heavy elementand other cases where manual intervention is required

Published example of PIXEL use -
Pixel was used to answer the question "Why does CSD code VUKRAW grow as needles" (VUKRAW is in C:\ortex as HPS1)."
The answer has nothing to do with hydrogen bonding. Look at N. Walshe et al., Cryst. Growth Des.2015 15 (7), pp 32353248. DOI

General Points
1.  You should read the PIXEL documentation
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 to CSD
5.  A good way to quickly test the CIF file is to run CLPCRY as outlined below.


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 PIXEL.
The message

In Oscail click to run ORTEX.
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 PIXEL.

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
The message

appears. Open the job in the NXH folder and in Oscail click Run Job on the menu and select PIXEL.

Running CLPCRY or PIXELC
 
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
temperature,date,r-factor
# o--- 0.0 0. 0.00
Coulomb-London-Pauli coefficients
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
AA-CLP energies,Coul-pol-disp-rep-celldip-tot
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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Running PIXELC

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 to use.
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.

Click Run Job on the menu


Select Add / Activate Centroids and click  to start ORTEX. Click or press a/A to go to atom mode.