Re: [ccp4bb] Crystallographic computing platform recommendations?
Axel: Um... it works fine for us. I just tested it about 10 seconds ago (names have been changed to protect the guilty): [EMAIL PROTECTED] ssh [EMAIL PROTECTED] Password: macclient:~ myaccount$ pwd /Network/Servers/osxserverbox.some.domain/afp/myaccount macclient:~ myaccount$ echo $HOME /Network/Servers/osxserverbox.some.domain/afp/myaccount This is OS X Server 10.5.5 and a 10.5.5 client, with an extremely vanilla configuration. After fighting the setup for two days to try to get it to mount somewhere *other* than /Network/Servers/blahblahblah, I left it alone and put in the following link on the client (we only have one, but could have more without any problems, as far as I can tell): /people - /Network/Servers/osxserverbox.some.domain/afp And: macclient:~ myaccount$ df -h FilesystemSize Used Avail Capacity Mounted on /dev/disk0s2 465Gi 24Gi 441Gi 6%/ devfs107Ki 107Ki0Bi 100%/dev fdesc1.0Ki 1.0Ki0Bi 100%/dev map -hosts 0Bi0Bi0Bi 100%/net map auto_home 0Bi0Bi0Bi 100%/home map -fstab 0Bi0Bi0Bi 100% /Network/Servers trigger0Bi0Bi0Bi 100% /Network/Servers/osxserverbox.some.domain/afp afp_05oXza0007GeoMVU-1.2d3a 298Gi 82Gi 216Gi28% /Network/Servers/osxserverbox.some.domain/afp I think this homedir mounting feature is a function of using OSX Server, rather than vanilla OS X, to do the AFP exporting, which is why we are using Server. Best, -- Steve Lane System, Network and Security Administrator Doudna Lab Biomolecular Structure and Mechanism Group UC Berkeley On Tue, Nov 18, 2008 at 10:51:44PM -0800, Axel Brunger wrote: Brian, There is one disadvantage with using AFP rather than wide open (potentially insecure) NFS mounts. Remote login via ssh into a client computer won't by default mount the user's AFP home directory. While it is possible to manually mount the AFP home directory it may preclude other users from using the client computer from the console. This feature of AFP is due to user-specific mounting of the remote disk on the client computer. I assume the same feature would apply to Kerberized NFS mounts, but I haven't tried it. This limitation of AFP requires some thought when using idle client computers as compute servers. We're using the Mac Server Xgrid service, along with the freely available GridStuffer.app application to make submission of batch jobs to all our Macs relatively easy. Axel On Nov 18, 2008, at 9:10 PM, Brian Mark wrote: Francis, From your response and others to my question about OS X server 10.5, AFP seems to be the preferred networking protocol over NFS. Yes, in our case the RAID is connected to a G5 (via firewire 800 - which provides surprisingly good transfer rates BTW) that is running OS X server 10.5 . I'll try AFP for the user home directories. Thanks, Brian Axel T. Brunger Investigator, Howard Hughes Medical Institute Professor of Molecular and Cellular Physiology Stanford University Web:http://atbweb.stanford.edu Email: [EMAIL PROTECTED] Phone: +1 650-736-1031 Fax:+1 650-745-1463
[ccp4bb] Pymol: Zoom without Mouse
How does one zoom into the molecule in Pymol without a mouse and with just the Mac trackpad and keyboard? Have tried to look it up in the manual and on the web. No success finding it yet; I did figure it out once before but can't redo it now for the life of me. Need to know how to do it without the mouse. Thanks, Raji
Re: [ccp4bb] Pymol: Zoom without Mouse
move z, [number] (where [number] is (of course) a number) will do it but you have to be careful about clipping. There may well also be a zoom command ... -Original Message- From: CCP4 bulletin board on behalf of Raji Edayathumangalam Sent: Wed 19/11/2008 9:29 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Pymol: Zoom without Mouse How does one zoom into the molecule in Pymol without a mouse and with just the Mac trackpad and keyboard? Have tried to look it up in the manual and on the web. No success finding it yet; I did figure it out once before but can't redo it now for the life of me. Need to know how to do it without the mouse. Thanks, Raji
Re: [ccp4bb] difficult MR in R32(H32)
Thanks Eleanor and everyone else that replied privately. Twinning was a common thought and the data was not by several tests. The MR was solved by getting better data, clean 2.8A vs. the 3.0A I had. With this data phaser was able to solve it easily in R32 with 3 molecules. There was not significant conformational change. I believe the difficulty with the earlier data was due to a translational NCS, but am not completely sure. The density is not great and the R factors very high. I did try refining in R3 and the density and statistics didn't improve. Shane -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Eleanor Dodson Sent: Monday, November 17, 2008 2:03 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] difficult MR in R32(H32) Answer is NO to difficulty; H32 is no easier or harder in principal than any other SG.. However do you have a NCS translation? or twinning? Is your model likely to be an oligomer? Eleanor
Re: [ccp4bb] NMR resolution (delete if you believe that ccp4bb is limited to CCP4 and maybe few other crystallography-related topics)
Thanks to all who answered (so quickly). To summarize, the premise fails because NMR/FRET and crystallography are based on different phenomena, and the energy-distance relationship is only valid for the latter. One has to wonder why they need to build bigger and bigger accelerators instead of inventing some clever radiationless transfer method :)
[ccp4bb] Order of scale/merge and reindexing
Hi, I have been working on the 2A data. Though almost done, R/Rfree was around 0.20/0.27. Then I noticed that structural factors were reindexed from P222 to P212121 after scaling/merging in the early process (I am finishing up a little bit old data). To escape any problems from wrong merging of structural factors, I reindexed the raw mtz first and scaled/merged again. As new scale/merge assigned new test set of structural factors, R/ Rfree after 10 new cycles of refmac5 refinement was quite low around 0.20/0.23. With a hope to make the new test set truly free, I ran almost 300 cycles of refmac5 refinement. Then R/Rfree converged to 0.20/0.25. However, I am not sure whether this improvement was really from correcting order of scale/merge and reindex, or still from including previous test data in the new refinement. Thanks, Young-Tae Young-Tae Lee, Ph. D. Research Associate The Scripps Research Institute Dept. of Molecular Biology
