Re: [ccp4bb] Recommendations for crystallization screens

2024-12-18 Thread Ben Bax
ltration assay that ran on 6uls of protein (automatically injected from a 96 well plate). This assay was used to optimize the length of the DNA, the DNA sequence, and the metal ions used - it is described in the supplementary material to the Nature article. Best regards, Ben Bax On Tue, Dec 17, 2

[ccp4bb] Jeffamine dictionary

2024-11-12 Thread Ben Bax
Dear CCP4BB, I am refining a structure crystallised in the presence of Jeffamine 600. The CCP4 dictionary for Jeffamine says all nine chiral atoms have a defined chirality. Is this correct or not? Thanks, Ben Bax loop_ _chem_comp_chir.comp_id _chem_comp_chir.id

Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

2024-06-06 Thread Ben Bax
). Thanks, Ben On Fri, May 31, 2024 at 4:36 PM Ezra Peisach <d150cd71a251-dmarc-requ...@jiscmail.ac.uk> wrote: > > In fall of 2024, electron density map coefficients will be available in > the public PDB archive for all X-ray structures. These map coefficients > will be the sam

Re: [ccp4bb] RES: [ccp4bb] Rwork and Rfree the same?

2024-03-03 Thread Ben Bax
Fcalc maps look fantastic. Are you sure they were not using an Fcalc for the missing 35% of the data? Ben On 29 Feb 2024, at 21:33, Rafael Marques wrote: Sorry for jumping into the post, but I would like the community’s opinion about completeness, once this topic was raised here

[ccp4bb] Postdoc and Research Technical Assistant Position at Queen Mary University of London

2023-10-15 Thread Ben Stieglitz
Dear colleagues, A Postdoc position and Research Technical Assistant position are available in the lab of Ben Stieglitz at Queen Mary University of London. Both positions will focus on molecular mechanisms of ubiquitin conjugation in the context of immunity and inflammation. The post holders

Re: [ccp4bb] Regarding the diffraction image

2023-02-06 Thread Ben Bax
Hi Kavya, More than one crystal? Epitaxial growth (protein crystal growing on salt crystal or vice versa) Did you try IZIT? (https://hamptonresearch.com/product-Izit-Crystal-Dye-33.html). I have seen salt and protein crystals in the same drop before now - but not growing together. Ben On

Re: [ccp4bb] symmetry possibilities

2022-07-23 Thread Ben Bax
images to help. Kind regards, Ben On Wed, Jul 20, 2022 at 10:12 PM Kay Diederichs < kay.diederi...@uni-konstanz.de> wrote: > Dear Jorge, > > what you write makes sense to me, and I cannot answer your questions. This > is just to say that the situation you encounter is not com

Re: [ccp4bb] Refmac automatically handles twinning?

2022-03-30 Thread Ben Bax
The twin fraction can vary during data collection - if the beam is smaller than the crystal For example you could have crystals which are like two very short ends of pencils - with flat ends together (in your case these might pencils could be in P3) In some orientations you could have the beam g

[ccp4bb] Postdoctoral position in structural bioinformatics at RCSB @ UCSF

2022-02-14 Thread Ben Webb
Dear colleagues, The research group of Andrej Sali at UCSF (https://salilab.org) is seeking a highly motivated postdoctoral researcher in bioinformatics, with domain experience in structural biology. The candidate should be interested in structural biological data and enjoy engaging with other

Re: [ccp4bb] teaching question: graphics for chromebook?

2018-05-23 Thread Barad, Ben
http://molstack.bioreproducibility.org/ (based on UglyMol) is the best tool I have found for my chromebook. You could definitely spin up something simpler using UglyMol yourself but that's probably outside of scope! molstack molstack.bioreproducibility.or

Re: [ccp4bb] [Fwd: Re: [ccp4bb] FW: New ligand 3-letter code (help-7071)]

2015-06-24 Thread Ben Bax
(and protonated) forms of AMPPNP the same. When I tried to deposit a specific AMPPNP tautomer in 2013, they would not accept it. The PDB also seems to believe, as I understand it, that the overall charge on AMPPNP is zero and that the phosphates do not carry negative charge. Ben Bax Senior

Re: [ccp4bb] Residual density feature

2015-06-15 Thread Ben Bax
pdb header. Regards, Ben Ben Bax Senior Scientific Investigator BioMolecular Sciences UK RD Platform Technology & Science GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK Email benjamin.d@gsk.com<mailto:benjamin.d@gsk.com> Mobile +44 (0) 7912

[ccp4bb] REFMAC5 and read-only file systems

2013-06-27 Thread Ben Eisenbraun
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

2013-01-16 Thread Ben Eisenbraun
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

2012-11-20 Thread Ben Eisenbraun
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] imosflm, bad predictions

2012-10-18 Thread Ben
I had a very similar problem with data collected on a particular beamline. The issue was that I had to reverse the spindle direction in imosflm settings. Also, when I load data from this beamline into imosflm the program rotates the images by 90 degrees for some reason (this does not happen in

Re: [ccp4bb] CCP4 update 6.3.0 006

2012-10-12 Thread Ben Eisenbraun
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] wilson B and ARP/wARP

2012-08-26 Thread Ben
Problem has been resolved. There was a space in one of the directory names where my files were stored. This prevented ccp4 from displaying log graphs in the summary window of jobs, and prevented ARP/wARP from calculating the wilson B. Removing the space in the directory name took care of both

[ccp4bb] wilson B and ARP/wARP

2012-08-25 Thread Ben
B: no such variable exists" ARP/wARP does not display a Wilson B or solvent content under crystal parameters. All other crystal parameters are displayed. Has anyone else encountered this issue, or have a resolution to the problem? Thanks, Ben

Re: [ccp4bb] Various OSes and Crystallography

2012-08-09 Thread Ben Eisenbraun
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

2012-07-28 Thread Ben Eisenbraun
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

2012-04-08 Thread Ben Eisenbraun
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

2012-02-17 Thread Ben Eisenbraun
_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

2012-01-06 Thread Ben Eisenbraun
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

2011-09-22 Thread Ben Eisenbraun
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?

2011-09-08 Thread Ben Eisenbraun
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

2011-06-09 Thread Ben Eisenbraun
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

2011-06-08 Thread Ben Eisenbraun
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

2011-05-26 Thread Ben Eisenbraun
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

2011-05-09 Thread Ben Eisenbraun
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

2011-03-11 Thread Ben Eisenbraun
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

2011-03-10 Thread Ben Eisenbraun
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

2011-03-10 Thread Ben Eisenbraun
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)

2011-03-07 Thread Ben Eisenbraun
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

2011-02-24 Thread Ben Eisenbraun
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

2010-12-10 Thread Ben Eisenbraun
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

2010-12-09 Thread Ben Eisenbraun
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

2010-10-26 Thread Ben Eisenbraun
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

2010-10-15 Thread Ben Eisenbraun
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)

2010-10-05 Thread Ben Eisenbraun
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

2010-09-29 Thread Ben Eisenbraun
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

Re: [ccp4bb] Force UC size in HKL2000

2010-08-06 Thread Ben Flath
Hi Thanks to everyone who responded so quickly. I have found the answer I am looking for. Ben On 8/6/10 2:37 PM, Ethan Merritt wrote: > On Friday 06 August 2010 01:32:47 pm Ben Flath wrote: > > Hi all > > I believe I have near perfect pseudo translation; alternating stron

[ccp4bb] Force UC size in HKL2000

2010-08-06 Thread Ben Flath
Hi allI believe I have near perfect pseudo translation; alternating strong and weak reflections however the weak reflections are barely visible at low res and invisible to higher res. HKL2000 will only index using strong reflections (half cell). How can I force it to use the full cell???  I fugure

[ccp4bb]

2010-07-13 Thread Ben Eisenbraun
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

2010-06-09 Thread Ben Eisenbraun
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

[ccp4bb] CLS school

2010-02-11 Thread Ben Flath
Registration now open!! The Canadian Light Source (CLS) is pleased to introduce the fifth annual Saskatoon Synchrotron Summer School (S4V) scheduled for June 13 - 18th, 2010 in Saskatoon, Saskatchewan. This year's school is for students and researchers interested in learning synchrotron techniq

Re: [ccp4bb] Zalman LCD availability

2010-01-15 Thread Ben Ammar Youssef
Hi Francois, Zalman LCD (21") is available in Japan. We already bought 2 sets one month ago and both are working perfectly with mac pro, windows and Linux. For William: I think the best way to get extra glasses is to go, in the weekend (or late night show if you like), to the nearest movie th

Re: [ccp4bb] Zalman LCD availability

2010-01-14 Thread Ben Eisenbraun
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

2009-11-19 Thread Ben Eisenbraun
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

2009-11-13 Thread Ben Eisenbraun
# 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

2009-10-27 Thread Ben Eisenbraun
(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

Re: [ccp4bb] anisotropic data

2009-10-05 Thread Ben Spiller
cases. It¹s unclear where Katja is stuck. For the refinement case, do others think that Fcalcs become anisotropic? Or that the liklihood method developed by Read and others is superior even at late stages? Thanks, Ben On 10/5/09 11:21 AM, "Pavel Afonine" wrote: > Hi Katja, > &g

Re: [ccp4bb] perfect twin test

2009-09-24 Thread Ben Flath
and P 32 1 2 solutions are the same. in fact I could not find a solution in P 32 searching with a single component it was not until I used two copies of the dimer found in P32 1 2 to make a tetramer which was subsequently used for MR in P32 thank you kindly for your input Ben On 9/24/09 2:43 AM

[ccp4bb] perfect twin test

2009-09-23 Thread Ben Flath
Hi Firstly thanks to all who replied to my original post. The clear consensus was to look for pseudo-symmetry. I must admit there is more to the story. Here goes the long version. Crystals are Hexagonal bi-pyramids (under ideal conditions they are very beautiful nice crisp edges etc.  non idea

[ccp4bb] perfect twin test

2009-09-23 Thread Ben Flath
  Hi Firstly thanks to all who replied to my original post. The clear consensus was to look for pseudo symmetry. I must admit there is more to the story. Here goes the long version. Crystals are Hexagonal bi-pyramids (under ideal conditions they are very beautiful nice crisp edges etc.  non

Re: [ccp4bb] perfect twin test

2009-09-22 Thread Ben Flath
I have used phenix.xtriage. It finds three twin laws with alpha ~0.48 for all of them and the results of the perfect twin test are well over 2. Ben On 9/22/09 1:50 PM, Tanner, John J. wrote: > I suggest you analyze your data with phenix.xtriage. It does several tests > and

[ccp4bb] perfect twin test

2009-09-22 Thread Ben Flath
Hi allwhen subjecting my data to the perfect twin test /*2 I get values very close to 3 which is far off the theoretical values of 1.5 and 2 for twinned and untwinned data.can anyone shed some light on what might be going on with my data. Could tetartohedral twinning have anything to do with it?Tha

Re: [ccp4bb] Rfactor got stuck with a data having alternate strong and weak reflections.

2009-09-04 Thread Ben Ammar Youssef
/0.434) to (0.235/0.311). Youssef Anastassis Perrakis wrote: On Sep 4, 2009, at 11:04, Ben Ammar Youssef wrote: Hi all, I just want to ask another question related to this topic: Based on the example given by Jerry McCully and if the data has alternate strong and weak reflections, how can we

Re: [ccp4bb] Rfactor got stuck with a data having alternate strong and weak reflections.

2009-09-04 Thread Ben Ammar Youssef
Hi all, I just want to ask another question related to this topic: Based on the example given by Jerry McCully and if the data has alternate strong and weak reflections, how can we split it into two different files; one containing the weak reflections and the other containing the strong reflect

Re: [ccp4bb] Histogram matching in DM - question

2009-08-19 Thread Adam Ben-Shem
Hi Peter, You can specify in DM the mean density of the protein region in the SOLC keyword. However I am not sure this will affect the density distribution used for histogram matching. All the best, Adam.

[ccp4bb] refmac 5.5.0092 not writing pdb/mtz files

2009-06-15 Thread Ben Eisenbraun
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

2009-06-11 Thread Ben Eisenbraun
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

2009-06-04 Thread Ben Eisenbraun
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

2009-05-11 Thread Ben Eisenbraun
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

2009-03-27 Thread Ben Eisenbraun
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

[ccp4bb] RNA Torsion Angle Measurement Error

2008-11-28 Thread Ben Akiyama
Hi Everyone, I am measuring and comparing torsion angles in several solved crystal structures of RNA helices using AMIGOS. I was wondering if anyone knows of a program that can give me an idea of the error in these measurements based on coordinate error, b-factors, etc. Thanks, Ben Akiyama

Re: [ccp4bb] CCP4i can NOT run

2008-09-30 Thread Ben Eisenbraun
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

[ccp4bb] map and model do not fit when using Turbo-Frodo

2008-09-29 Thread Ben Ammar Youssef
Dear All, I am refining a structure of Se-protein solved with MAD using phenix. The unit cell is P 21 21 21 with a=36.898, b=59.450, c=393.909 and alpha=beta=gamma=90. There are two molecules in A.U. The problem is that when I use Turbo-Frodo for molecular modeling, the map does not fit to the

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

2008-06-27 Thread Ben Eisenbraun
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

2008-06-26 Thread Ben Eisenbraun
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

2008-06-26 Thread Ben Eisenbraun
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?

2008-03-18 Thread Ben Eisenbraun
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

2008-02-12 Thread Ben Eisenbraun
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?

2008-02-07 Thread Ben Eisenbraun
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!

2008-01-21 Thread Ben Eisenbraun
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] Fwd: [ccp4bb] CCP4i and modeller integration

2007-11-02 Thread Ben Webb
ut. For example, TOP scripts are deprecated in Modeller 9 in favor of Python scripts, and it would not be especially hard to change the script template to Python (although of course this would then break backwards compatibility with Modeller 4 and 6). Ben -- [EMAIL PROTECTED] http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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

2007-07-21 Thread Ben Eisenbraun
ttp://en.wikipedia.org/wiki/WP:NOT#GUIDE But the wiki idea is interesting nonetheless. -ben -- Ben Eisenbraun Structural Biology Grid http://sbgrid.org/

[ccp4bb] fit-protein in coot

2007-05-29 Thread Youssef BEN AMMAR
Dear all, I have installed the latest version of Coot on my Ubuntu computer, but surprisingly I couldn't run the script (fit-protein /imol/). Coot didn't execute that script. I returned back to the previous version installed on my iMac, but I had also the same problem, although this was working

[ccp4bb] Please take me off the list

2007-02-26 Thread Iris Ben-Efraim
Hi there, Could you please either take me off thelistof CCP4BB or instruct me how to do it myself? Thanks, Iris Iris Ben-Efraim, PhD Department of Biological Sciences Purdue University West Lafayette, IN 47906 e-mail: [EMAIL PROTECTED] Phone: 765-4946465 Fax: 765-4961189