Most software used for cryo-em analysis (e.g. EMAN2,  Relion, Spider, Frealign 
etc)  runs better or only in Linux.



From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robbie 
Sent: Friday, October 14, 2016 11:55 AM
Subject: Re: [ccp4bb] Structural biology software that does not run on Windows 
or gives important Windows-specific problems

Windows 10 now allows a full Ubuntu within Windows. It actually works quite 

There is a good rsync for windows. I use it to make back-ups of the pdb_redo 
databank. Windows has it own system of incremental backups which works well in 
my hands. There are two scripting systems in Windows batch and PowerShell. 
Batchs is fun for simple things, PowerShell is extremely powerful and scarily 
object oriented for maintenance and administration, not for scientific work.

That said, I would totally use linux for scientific work, except writing and 
spreadsheet work.


Sent from my Windows 10 phone

Van: Tim Gruene<>
Verzonden: vrijdag 14 oktober 2016 17:23
Onderwerp: Re: [ccp4bb] Structural biology software that does not run on 
Windows or gives important Windows-specific problems

Dear Mark,

XDS does not run on Windows, and even if you take your mtz-file home from the
synchrotron nowadays, you sometimes may want to re-refine some data set.

Windows also costs a lot of money, and if you do a lot of scripting, Windows
may be cumbersome. WinCoot is also often mentioned with difficulties that
don't occur with Coot. If you like incremental backups to save disk space and
time, I am not sure rsnapshot/rsync works with a Windows file system.

A windows machine may also impede data exchange with other institutions. Eg.
downloading data from is based on rsync, and if I
gave you my usb-stick, Windows would only attempt to format it (well, same
would most likely happen with Mac OS X).

One caveat though: the MS Office version for Mac does not read OpenOffice
Format, so I was told.


On Friday, October 14, 2016 05:14:46 PM Mark J van Raaij wrote:
> Dear All,
> our institution requires me to provide a reasoning not to buy a Windows
> computer (I want to buy a new MacOSX system), so I am looking for software
> that does not run or is limited on Windows.
> Not available:
> (Auto)SHARP
> Available on Windows but with significant limitations
> Phenix (no MR-Rosetta, no parallelization)
> CCP4 (limitations on file-names)
> Please correct me if pertinent and provide additional examples if possible.
> Gratefully yours,
> Mark
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Principal Investigator
Biology and Chemistry
CH-5232 Villigen PSI

Phone: +41 (0)56 310 5297


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