Internet Workshop for AXAA99

Lachlan M. D. Cranswick]

CCP14 for Single Crystal and Powder Diffraction

CLRC, Daresbury Laboratory X-ray Synchrotron

Daresbury, Warrington, Cheshire, WA4 4AD, UK

E-mail: [email protected]

Web: http://www.ccp14.ac.uk

Overall Aim:

(By default, the internet can be a major time wasting engine so it can be a good idea to work out which uses are beneficial and the amount of resources (time, money) you wish to spend)

Only a brief subset of internet software is mentioned here as there is a major and growing software glut which makes it very difficult to keep up to date. (Stick with the software you trust)

Search Engines

Before Starting, it is good to note information about Internet Search Engines to find/refind information:

Inference Find (searches other search engines):

http://www.infind.com

Altavista

http://www.altavista.com/

http://www.altavista.yellowpages.com.au/

Hotbot

http://www.hotbot.com

Lycos

http://www.lycos.com

Yahoo

http://www.yahoo.com

Not so long ago, a connection of Academic Networks

http://www.aarnet.edu.au

http://www.internet2.edu/

http://www.ukerna.ac.uk/

Internet Society:

http://www.isoc.org/internet-history/

http://info.isoc.org/guest/zakon/Internet/History/HIT.html

Connecting to the Internet

Connecting to the internet has become so trivial that it does not need to be discussed in any depth but be wary of buggy software drivers for network cards, modems and network protocols.

If having difficulty, make sure you have the latest drivers. Unfortunately, obtaining the latest drivers is normally done via the internet. Thus you may have to use a colleague's internet connection to do this.

Network support should setup most laboratory PCs (or provide instructions). Most decent commercial ISPs now have a Wizard setup or generic setup that is friendly to most major operating systems.

Sending and Receiving text, messages, data and binaries

Some Software:

Eudora (Eudora Lite /Eudora Pro):

http://www.eudora.com

Pegasus E-mail (freeware):

http://www.pegasus.usa.com/

http://www.let.rug.nl/pegasus/

Pine for UNIX, DOS and Window

http://www.washington.edu/pine/

Elm for UNIX

comp.mail.elm

Netscape

http://www.netscape.com/

MicroSoft Based

MS-Mail, MS-Exchange, Internet Explorer(?)

(MS-Software is quite a nightmare)

http://www.microsoft.com/

Others. Refer the online software archives, indexes:

http://www.winfiles.com/

http://garbo.uwasa.fi/

http://www.tucows.com

http://wuarchive.wustl.edu/

http://www.simtel.net/simtel.net/

E-mail: Attaching Binary Files

Generally the most frustrating part of E-mail due to three differing methods of encoding files (some mail systems are quite limited to the size of files you can send via E-mail 50kB to 2Meg):

MIME,

UUENCODE

BINHEX

Advice, if possible, use an E-mail program that can handle all the main formats. Eudora is a personal favourite though any decent E-mail program should be able to attach and extract binary files in an easy and efficient manner:

In the following case, double clicking on the attached file line with the mouse will open the file with an appropriate program:

Different software allows different methods of manipulating attachments.

Is a very large bulletin-board system on the internet.

Very useful for solving computer problems (large amount of computer based newsgroups) and also useable for scientific discussion.

sci.techniques.xtallography

http://www.unige.ch/crystal/stxnews/stx/welcome.htm

sci.techniques.spectroscopy

http://lolita.colorado.edu/faq/DEFAULT.HTM

sci.techniques.microscopy

sci.techniques.testing.nondestructive

sci.engr.metallurgy

sci.engr.mining

sci.geo.mineralogy

sci.geo.geology

sci.chem.analytical

sci.materials.ceramics

Scientific newsgroups tend not to be overly used, but they can have their good moments:

Background links at:

http://www.bio.net/BIOSCI/docs.html

Your Network Support or ISP should be able to provide information on the news-server "address" you should use.

Forte Agent

Free Agent (freeware), Agent (commercial)

Also can be used as an off-line newsreader

http://www.forteinc.com/agent/

Trumpet Newsreader

http://www.trumpet.com.au

Netscape communicator has a newsreader

http://www.netscape.com

Pine for UNIX, DOS, Window has a Newsreader

http://www.washington.edu/pine/

Tin for UNIX

http://www.tin.org/

(Note, this is a highly specialist question)

On the 3rd of December, 1998, Bath, UK

Martin McLoughlin Queries:

Newsgroups: sci.techniques.xtallography

Subject: PBC analysis software

Sender: [email protected] (Verified by Kerberos)

Organization: School of Material Science, University of Bath, UK

Date: Thu, 3 Dec 1998 15:29:49 GMT

Hi,

Does anyone know of any public domain/shareware software for finding

periodic bond chains in crystal structures.

Thanks in advance

Martin McLoughlin

Dept. of Materials Science

On the 6th of December, 1998, Bulgarian Acad. Sci.

Thomas Kerestedjian Replies:

From: [email protected]

Newsgroups: sci.techniques.xtallography

Subject: Re: PBC analysis software

Date: Sun, 06 Dec 1998 09:32:32 GMT

Hi Martin,

To the best of my knowledge, there is only one piece of software for this

purpose. You can contact the author: Dr. Christina Strom; [email protected]

This is a very proffesional tool for finding literaly ALL possible PBCs. The

only bad news is that it is not user friendly at all and you definitely need

authors assistance to get introduced to its operation.

Good luck,

--

Dr. Thomas Kerestedjian,

Geol. Inst., Bulgarian Acad. Sci.‰

-------== Posted via Deja News, The Discussion Network ==----------

On the 7th of December, 1998, Bradford, UK

John Osborn Follows On:

From: John Osborn <[email protected]>

Newsgroups: sci.techniques.xtallography

Subject: Re: PBC analysis software

Date: Mon, 07 Dec 1998 10:40:11 +0000

Organization: University of Bradford

A more user-friendly version of the Hartman-Perdok morphology

calculation with periodic bond chain analysis is implemented in the

latest version of the Cerius2 molecular modelling package (Molecular

Simulations Inc.). However this package is commercial, not public

domain as requested by the original poster.

--

John Osborn

University of Bradford, UK.

These are discussion groups/bulletin boards that are distributed via E-mail. Like newsgroups, there are a large variety of mailing lists (especially for computer software):

Rietveld Users Mailing List:

http://www.unige.ch/crystal/stxnews/riet/welcome.htm

CCP14 Software Hints Mailing List:

http://www.ccp14.ac.uk/maillist/

Clay Minerals Mailing

http://shadow.agry.purdue.edu/clay/claymin/listserv.html

Very-low-grade metamorphism mailing list

http://www.geol.uni-erlangen.de/vlgm/mail/mailing.html

(Possibly relevant for "collaboratories")

Normally done to UNIX, VAX or Mainframe computers.

You log in to the remote computer and can use any of the programs on the remote computer remotely. This can be databases, number crunching software, scientific equipment, etc.

If you are doing this, basic telnet is unencrypted and information including passwords is passed over the network in plain text. A common way around this is to use Secure Shell (SSH). The requires the installation of a "sshd" daemon on the remote computer which the system manager normally does.

There are many client programs for non-UNIX systems (client "slogin" programs.

Free - Teraterm and TTSSH for Teraterm for Win95/NT

http://hp.vector.co.jp/authors/VA002416/teraterm.html

http://www.zip.com.au/~roca/ttssh.html

As mentioned later, Security over the internet has become a major issue and also money spinner is selling security software and solutions. This is also relevant when using "remote" systems over the internet or "collaboratories".

Stands for File Transfer Protocol

Overshadowed by the World Wide Web but still a used protocol for transferring files.

Has advantages over attaching files to E-mail in that much larger amounts of data can be transferred (Megs to Gigs).

"Anonymous FTP" is support by any decent Web Browser such as Netscape, Internet Explorer, Opera, etc.

Windows and UNIX provides a command line FTP program (in a shell prompt, type ftp).

Point and Click GUI Freeware/shareware/commercial FTP programs are available. An example is WS_FTP:

http://www.ipswitch.com

NS: After "getting" a file via FTP, you find out it is corrupted, try "getting" the file in binary mode.

Presently the common method of presenting information on the internet for either general or "restricted" access:

It is also becoming a common method to control equipment via the internet:

Collaboratories

Configuring computers and equipment

Common Software:

Netscape http://www.netscape.com/

Internet Explorer http://www.microsoft.com/ie/

Opera http://www.operasoftware.com/

Lynx http://www.fdisk.com/doslynx/lynxport.htm

(many other web browsers are available)

Keyboard based real time meetings

Only use this myself for Australasian Web Publishers Association committee meetings (http://www.awpa.asn.au) - no longer even that as Daresbury Lab blocks IRC from the network as an anti-hacker measure.

Software:

mIRC http://www.mirc.com/

ICQ http://www.icq.com/

Other software - check out via various software archives:

Coast to Coast Windows Software Archive

http://www.coast.net/

Tucows: http://www.tucows.com/

Wuarchive: http://wuarchive.wustl.edu/

simtel.net: http://www.simtel.net/simtel.net/

Garbo: http://garbo.uwasa.fi/

WinFiles.com: http://www.winfiles.com/

32bit.com: http://www.32bit.com/

download.com: http://www.download.com/

Despite requests, personally don't use this as prefer to use a conventional phone. Mainly (given E-mail takes enough of the day) adding IRC and ICQ type facilities has the potential to further erode "productive time" especially when people enjoy using this just to check out the technology.

There are a number of competing programs; normally supplied with hardware that enables this for video conferencing.

e.g:

Freetel: http://www.freetel.inter.net/

Iphone: http://www.vocaltec.com/

TeleVox/Cyberphone: http://www.voxware.com

(protect your data; confidential information; stop hackers and other illegal entry into your network and computer)

Implement at the "required" level consistent with your setup and computer systems. Is really a network support/ISP issue. But if they are under-resourced, you may end up having to implement this yourself.

Decent passwords can help.

Latest security patches for your operating system.

Avoiding dodgy areas of the internet - pirate software, pornography (many software viruses and Trojan horses are attached to pirate software or viewers available from pornography sites)

Firewalls

Help limit people's ability to hack into your network.

Various types of security software and links to information relevant to the above:

http://www.ccp14.ac.uk/ccp14admin/security/

NB:

It is normally safe to assume private E-mail messages may eventually reach the pubic domain. Especially if sent on a mailing list.

Finding Software/Software Upgrades

Transfer of Data and Results

Convenient information about the latest hardware.

Assistance in Solving Technical Problems

Databases

On-line ICSD Inorganic Structure Database

Demo: http://icsd.ccp14.ac.uk/icsd/

American Mineralogist Crystal Structure Database

http://www.geo.arizona.edu/xtal-cgi/test

http://www.geo.arizona.edu/xtal/personal.html

Remote Control of Equipment

Barns at ILL:

http://barns.ill.fr

Web Controllable Diffractometer:

Computers & Geoscience Vol 24, No 7,

pp 633-640, 1998

http://www.geosci.ipfw.indiana.edu/

Source Code Available via:

http://www.iamg.org/CGEditor/index.htm

Rather than bombard with a large range of links (that may or may not die in the near future) following are starting links into XRD, X-ray related resources

Australian X-ray Analytical Association

http://www.latrobe.edu.au/www/axaa/

Society of Crystallographers In Australia

http://www.sca.asn.au

International Union of Crystallographers

http://www.iucr.org/iucr-top/

IUCr - Crystallography World Wide:

(database of software links)

http://www.iucr.org/sincris-top//

IUCr - Crystallography World Wide:

(links to vendors, resources, educational material, databases, jobs, news)

http://www.iucr.org/cww-top/

http://www.us.iucr.org/cww-top/ (USA)

http://www.za.iucr.org/cww-top/ (South Africa)

http://www.se.iucr.org/cww-top/ (Sweden)

http://www.il.iucr.org/cww-top/ (Israel)

http://www.ch.iucr.org/cww-top/ (Switzerland)

CCP14 - Collaborative Computation Project for Single Crystal and Powder Diffraction (archive of software/web resources, Q&A, tutorials, developer resources)

http://www.ccp14.ac.uk

International Centre for Diffraction Data

http://www.icdd.com

Interacting with Machine Operator Remotely as though you were there in the lab.

Using/controlling equipment via the internet

Telemicroscopy SEMs/Microprobes

References - http://www.minerals.csiro.au/em-unit/microres.htm

Though in practise, the most successful applications are those where the user interacts remotely with the actual machine operator.

Can be started with relatively cheap off the shelf equipment such as the Logitech "QuickCam" (http://www.quickcam.com/)

The National Center for Microscopy and Imaging Research (NCMIR) http://www-ncmir.ucsd.edu/

ANL Microscopy and Microanalysis WWW Server - http://www.amc.anl.gov

http://tpm.amc.anl.gov

Options for Authorised Users

Controlling the Position of a Camera in the USA at CSIRO Australia

Telepresence Microscopy at the University of Queensland Centre for Microcopy and Microanalysis, Brisbane, Australia at

http://www.uq.edu.au/nanoworld/nanohome.html

Based around the CU-SeeMe software

(http://www.cu-seeme.com)

The internet can be a major asset when used appropriately. However, don't end up wasting too much time!