[ccp4bb] REFMAC5 and read-only file systems

Howdy Y'all, I have a lab where REFMAC jobs are blowing up trying to access the monomers database. The logfile looks like this: Open failed: Unit: 7, File: /programs/x86_64-linux/ccp4/6.3.0/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif (logical: /programs/x86_64-linux/ccp4/6.3.0/ccp4-6.3.

Re: [ccp4bb] CCP4 package and update managers: relocating installations

need modification, but the CCP4 packaging QA is generally quite good, and we haven't had many problems. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

[ccp4bb] areaimol bugs

tream regardless of whether that is the correct solution. So which binary should we be using? Thanks. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

Re: [ccp4bb] CCP4 update 6.3.0 006

administrator privileges to update. It would be nice if the application checked for write privileges before assuming it needs to be run with escalated privileges. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

Re: [ccp4bb] Various OSes and Crystallography

On Thu, Aug 09, 2012 at 10:29:10AM -0500, Jacob Keller wrote: > Question--do macs have multiple-button mice? Last I checked they had only > one button, which seemed almost criminal. You're about 7 years behind the times on that one: http://en.wikipedia.org/wiki/Apple_Mighty_Mouse -

Re: [ccp4bb] CNS installation

rrectly, so now you have to install gfortran and build a 32-bit CNS to use. You don't need ia32-libs on a 32-bit system. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

Re: [ccp4bb] Refmac executables - win vs linux in RHEL VM

e developer, we'll let you use them for free: http://www.sbgrid.org/wiki/developers/support -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

Re: [ccp4bb] HKL2000/3000 Error

_bind_size 0 lazy_bind_off 2310280 lazy_bind_size 1784 I have filed this exact bug report with HKL Software in the past. If you wait long enough, they will usually compile a version that runs on 10.5 machines. The support email for HKL Software is supp...@hkl-xray.com. No one here can help you.

Re: [ccp4bb] ARCIMBALDO Sample Script

an request a copy here: http://chango.ibmb.csic.es/ARCIMBOLDO/ -b -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

[ccp4bb] Desmond 3.0 Tutorial, Oct 5 in Boston, MA

options, preparing a membrane protein simulation, an example of FEP relative binding free energy calculation, and, if time permits, a metadynamics example. Each participant will have a dedicated remote server running Desmond on the Amazon CC2 cloud. -ben -- | Ben Eisenbraun | SBGrid Consortium

Re: [ccp4bb] help offline for cns 1.3?

On Thu, Sep 08, 2011 at 02:28:28PM -0500, Jacob Keller wrote: > Is there a CNS BB? Yes. http://tech.groups.yahoo.com/group/cnsbb/ -b -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | h

Re: [ccp4bb] off-topic: Synchrotron look alike

tured for > years ... The Zalman passive stereo solution works nicely on Macs. That's our recommendation these days. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

Re: [ccp4bb] unsubscription request

to:ccp4bb-requ...@jiscmail.ac.uk> List-Archive: <http://jiscmail.ac.uk/cgi-bin/webadmin?LIST=CCP4BB> -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

[ccp4bb] Postdoctoral Position in Structural Biology Computing, Boston, MA

candidates should email a cover letter, CV, publications list, and names and contact information for three references to Dr. Piotr Sliz. -ben [1] CCP4 being the obvious exception! -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org| | Harvard Medical School

Re: [ccp4bb] ccp4i fft O format

tput from ccp4i ? Make sure "mapman" from Gerard Kleywegt's USF software is installed and in the PATH. That will enable the O format output option. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

Re: [ccp4bb] Ubuntu 10.10 installation Issues

64-bit Ubuntu machine _without_ the 32-bit compatibility libraries installed. So are you running a 64-bit installation? (uname -m) Do you have the ia32-libs package installed? (dpkg -l ia32-libs) -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | |

Re: [ccp4bb] Coot "Bad magic number" errors

be hesitant to delete those. That said, in theory it really shouldn't matter. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

Re: [ccp4bb] Coot "Bad magic number" errors

the non-2.7 directories from the PYTHONPATH got about 5 more of the installations working. The remaining machines wouldn't run the package no matter what I tried. Good luck! -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

Re: [ccp4bb] PYMOL installation in openSUSE 11.3 (64 bit)

or directory You're missing the Python header files. There should be an OS package that provides this. You should really post your PyMOL questions to the PyMOL mailing list though. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harva

Re: [ccp4bb] linux flavors

primary support person knows best. If the person supporting the machines is you, then pick the distribution you know best (or want to learn). If you have access to institutional IT support with linux experience, then pick the distribution they support. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

Re: [ccp4bb] A script is needed to renumber image

ou might as well go down James' path and create a generalized script that can be used in many cases, but it's definitely more work to write the generalized script than to toss off one liners. -ben -- | Ben Eisenbraun | Software Sysadmin

Re: [ccp4bb] A script is needed to renumber image

he loop, but too much magic gives me the willies. -b -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

Re: [ccp4bb] Hardware question

rranty. The lower-end drives will have 3 year or shorter warranties, and the higher-end drives will have 5 year warranties. Buy a model with a 5 year warranty. -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://s

Re: [ccp4bb] update REFMAC

ses LINK rather than LINKR. Note that I'm just a keyboard puncher, so your mileage may vary. Thanks to all for the suggestions. -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

Re: [ccp4bb] stereo (again - sigh)

dels and additional info on set up are on our website: http://sbgrid.org/wiki/install/stereo I hope this helps. -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medica

[ccp4bb] refmac 5.6 and the ccp4i task interface

s the dictionary go? Is there some elegant way of letting users choose between the two? Thanks. -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical S

[ccp4bb]

On Tue, Jul 13, 2010 at 09:39:12PM +, KUMARASWAMI MUTHIAH wrote: > http://bit.ly/98W5FY Spam, spam, spam, spam, spam. But he got 1088 of us so far. http://bit.ly/98W5FY+ Bah. -b -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology G

Re: [ccp4bb] Compilation of CNS 1.21 on Mac OSX 10.6.3

ted at: 14:44:03 on 09-Jun-2010 It was 5 minutes of work for someone with the right background. Some days I hate computers. :-/ -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid

Re: [ccp4bb] Zalman LCD availability

Anyway, a few of those listed retailers have them. I think we bought our last one from Provantage and another lab around the corner got one from xPCgear. -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | ht

[ccp4bb] refmac5/ccp4i GUI error

ocedure "tk::ButtonUp" line 22) invoked from within "tk::ButtonUp .module.menu.action.canvas.frame.t.f_5" (command bound to event) == And the shell prints out: ERROR no type for TWINREF_TYPE ERROR no type for F+ ERROR no type for F- ERROR

Re: [ccp4bb] bltwish and RHEL5

# but note the SGI distributed version of Tcl/Tk is not # appropriate version -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

Re: [ccp4bb] Minimum hardware requirement of Mac OSX for CCP4

(and > stereo glasses & emitter) for that. He could buy a Zalman 3d LCD and hook it up to the external video port on the iMac. It works fine with Coot, PyMOL, Chimera, etc. -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid

[ccp4bb] refmac 5.5.0092 not writing pdb/mtz files

if the new versions address this problem. The new Refmac binaries for OS X Intel only run on 10.5. It would be nice if the build scripts set the environment for: MACOSX_DEPLOYMENT_TARGET=10.4 So the binaries would run on Tiger. (Maybe need a -mmacosx-version-min=10.4 in the CFLAGS/LDFLAGS as we

Re: [ccp4bb] XDS Viewer

It's usually best to start your own thread instead of replying to a very old one. It helps to keep your message from getting lost. In any case, the version of XDS-Viewer on Source Forge does not appear to be compatible with OS X 10.4. I had to recompile it for our 10.4 machines. -ben

Re: [ccp4bb] CCP4i problem on RHEL5

on RHEL 5 systems before: http://www.ccp4.ac.uk/ccp4i/install_tcltkblt.html#scim -ben -- | Ben Eisenbraun | Software Maintainer| | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

[ccp4bb] CCP4 updates and the problem pages

things by hand? Thanks. -ben -- | Ben Eisenbraun | Software Maintainer| | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

Re: [ccp4bb] Problem sourcing

ome light on this? I'm using C shell. It can't be the > syntax since I could source as root. root might well have a different PATH. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu

Re: [ccp4bb] CCP4i can NOT run

act as miniature servers and bind to localhost to communicate between the GUI and the process. If this is actually the problem, you should see output in the shell that started ccp4i similar to this: ERROR running script can not connect to server port (RunNotification) SERVER_HOST localhost SERVE

Re: [ccp4bb] Reminder - still no 3D stereo under OS X 10.5

ou follow the x11-users mailing list at Apple, you can get all the gory details of how broken X11 was when Leopard shipped and how much work has gone into fixing it. http://xquartz.macosforge.org/trac/ticket/45 That's the ticket that tracks broken stereo 3d. -ben -- Ben Eisenb

Re: [ccp4bb] Reminder - still no 3D stereo under OS X 10.5

s in a timely manner. http://lists.apple.com/archives/x11-users/2008/Apr/msg00130.html Even if/when Apple fixes stereo on Leopard, I don't think I'll be recommending OS X for stereo applications. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Me

Re: [ccp4bb] Reminder - still no 3D stereo under OS X 10.5

ed: "as soon as any other window overlaps the stereo 3D OpenGL context (e.g. a File Open Dialog...), Mac OS starts randomly dropping screen updates, causing PyMOL's UI to become unusable." I have second hand reports that O works with stereo 3d under 10.5, but I haven't seen

[ccp4bb] Early registration deadline extended for Quo Vadis Structural Biology?

Pardon the interruption: We have extended the early registration deadline for the SBGrid user summit 'Quo Vadis Structural Biology?' Information from the initial mailing is below. Come on by and see us now, ya hear? -ben -- Ben Eisenbraun Structural Biology Grid http://sbgrid.org

Re: [ccp4bb] sgi dials on intel mac

ow. You can get the latest driver from his personal page: http://gohara.wustl.edu/software/crystallography_and_em_bina/ I don't know if he's on this list, but his email address is in the PDF of dials set up instructions linked off that page. -ben -- Ben Eisenbraun Structural Biology Grid http://sbgrid.org/

[ccp4bb] Conference Announcement: Quo Vadis Structural Biology?

conference website: http://www.sbgrid.org/quovadis The full list of speakers is also available via PDF: http://sbgrid.org/downloads/QuoVadis_poster2.pdf I hope we'll see you there. -ben -- Ben Eisenbraun Structural Biology Grid - http://sbgrid.org/ Center for Molecular and Cellular D

Re: [ccp4bb] Help Superposition programmes!

rds MOL1 and MOL2, even though the files exist. This can be fixed by applying the patch topp.f-r1.16.2.5-r1.16.2.6.diff (also available from ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches) to $CCP4/src/topp_/topp.f and remaking topp." -ben -- Ben Eisenbraun Structural Biology Grid http://sbgrid.org/

Re: [ccp4bb] Suggestion: Wiki -- was:Re: [ccp4bb] need help--Rfree is not decreasing

ttp://en.wikipedia.org/wiki/WP:NOT#GUIDE But the wiki idea is interesting nonetheless. -ben -- Ben Eisenbraun Structural Biology Grid http://sbgrid.org/