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Data back up and sendhome

To transfer data from the /data/mcfuser directory, you can ssh into bl831:

ssh -l mcfuser bl831.als.lbl.gov "download holton semet_2_E1_035.img" | tar xvBf -

Here files are always transferred in chronological order (of collection), and any new files will be transferred as soon as they appear on the disk. The word "holton" means to download all files containing the string "holton", so use your data directory name here. The word "semet_2_E1_035.img" means to only send files that occur after semet_2_E1_035.img. This is useful if your first attempt at a download dies and you want to start the second transfer where the first one left off.

If "semet_2_E1_035.img" is omitted, then all files containing "holton" in their pathname are transmitted. If "holton" is omitted, then only newly-collected files are transmitted. Therefore, only use "download" with no arguments before you start collecting data.

NOTE THAT THIS MEANS YOU CAN BYPASS YOUR MAC's OR PC's HARD DISK. Simply mount the scratch disk using the normal samba method. Then in your terminal window cd /Volumes/xscratch1/yourdirectory and then type the above ssh command and the data should be transfered directly to the scratch disk.
On the computer on the way right, graphics2 (make sure the KVM switch is set so you are looking at the computer you think you're on, see the box with lights to your right), you can type burn.com and get directions on backing up various directories, file types, skipping certain directories, types and putting it all on DVD.  It makes 2 DVD's at a time and also prints labels.  Takes about 40 minutes to burn two fullish 2xDVD's.

Have you tried James' sendhome script?  Very convenient.  Type:

sendhome /data/mcfuser/myimages/oldest_image_to_send username@msg.ucsf.edu:my/image/directory

and after entering your password you should be good to go.  If you want to pick up where it left off, just enter a specific image to start from and it will send all images more recent than that one.  You can also bring a laptop with a big drive (internal or firewire) and plug into the DHCP network connection and copy files over that way.  There is an iMac there, so you could just bring the external firewire drive if you fancy.

Processing

You are in the very backyard of the Elves suite. So they'll do a lot for you, if you like, generally using mosflm to give you collection strategies.  Get thee to a working directory, type "Elves" and the path to your starting frame.  They should ask you stuff from there.

For you UCSF people, I'm our local Elf (contact) so it's available in /public/apps/bin on the SGI machines. Remember to set up any environment elves might be needing using the prepare scripts (i.e. ccp4, solve, etc.) or else Elves will try to download ccp4 for you.  You don't want it to do that.

You can use multiple processers on the crush cluster.  
ssh crush
and then launch your processer jobs there.  I don't think you can do the graphics stuff there, like the initial indexing with mosflm.


Some older frames may require an additional keyword for mosflm if you are running manually:

           PIXEL 0.1024

This is to get it to know how big the detector really is.

Denzo is working on 8.3.1 data, now.

The best way to make this work is go to any one of crush01 to crush06 and type:

source ~/denzo/denzo.setup

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