Re: [ccp4bb] Mac OSX 10.7 Lion
Hi, Overall, the transition from 10.6 is seemingless, crystallographically-wise. Of course you need to have the new XCode 4.1 installed, and you should also download new, 10.7-dedicated 64bits gcc/gfortran/g77 bundles from http://hpc.sourceforge.net/ And then, CNS, Phenix, CCP4, etc... will just run perfect. I had to reinstall Coot -- but that's minor. (Mac)Pymol also works fine, yet (for some reason) uses a lot of resources even when idle. As per the Upsalla Soft. Factory programs, you'll have to recompile then using the above mentioned bundles, or get already compiled binaries from Mark Harris. You'll also need to recompile Gromacs (and fftw3) if you're using it -- but it then works great. I agree with W. Scott on the fact that the new OS is really greedy in terms of resources. I surely wont upgrade my other, older mac computers that run just fine on 10.6. But if you have a new Mac, Lion is is really neat. Best Jacques Le Sep 10, 2011 à 2:09 AM, William Scott a écrit : Hi Phil: I've found few, if any advantages. I fear for the future. I've had problems getting coot to run stereo due to the X11 implementation in 10.7. Apart from that, no major problems with crystallographic software. Lion greedily uses memory, and any computer I have with less than 4 gig of memory has become extremely sluggish as a consequence of the upgrade. Ideally, you need 8 gig. Even with that, on my 2010 mini that I use for music playback, I regressed to 10.6.8, because of the audio interface. (It seems less robust, more prone to dropouts and now lacks integer mode output). Sara has been screaming at me for the last two weeks (nothing us usual in of itself) because Apple decided to get rid of Save As. Xcode and the compiler set is free again on 10.7. I've put some suggestions here for how to get rid of the most annoying new features: http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Lion_upgrade_notes All the best, Bill On Sep 9, 2011, at 1:28 AM, Phil Evans wrote: Is there any opinion or experience about whether Lion is ready for crystallographic use? Should I upgrade? Phil William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] phenix rigid body ref.
Hi Tommi You will find all the information you need on the following web page: http://www.phenix-online.org/documentation/refinement.htm as per your question, you could try : phenix.refine yourdataset.mtz yourmodel.pdb strategy=rigid_body rigid_body.number_of_zones=1 sites.rigid_body=chain A sites.rigid_body=chain B sites.rigid_body=chain C sites.rigid_body=chain D etc... (I suggest you take only one zone for the rigid body refinement because at 6A you only have so many reflections) Best Jacques Le Nov 26, 2009 à 8:32 PM, Tommi Kajander a écrit : Apologies, i know this is not phenix bb but since i am here (and not subscr. there), does anyone know how to control rigid body ref positions in phenix.refine, i am trying to do very low res check (6 Å) with quite many molecules, and they start landing on each other while the MR solution from molrep has perfect packing isnt there a packing constraint somwhere saying atoms cant be on top of each other... there was something about clashes but didnt seem to do anything.. the parameter definitions in .eff are bit cryptic to me in places... (would it be possible to step back a bit (sorry if i am wrong) to the ancient world of x-plor, still like that manual a lot..). thanks Tommi K.
Re: [ccp4bb] buster-tnt on OSX ?
Dear All Thank you all a lot for your answers, and sorry for the trouble that my question has generated. Gerard B. : Thanks a lot to you and your colleagues for releasing, in the forthcoming time, an OSX version of BUSTER-TNT. Best from LA Jacques 2008/10/28 Pete Meyer [EMAIL PROTECTED] Gerard, Thank you very much for clearing that up. It's always good to hear that there's one less things I need to worry about. Pete Gerard Bricogne wrote: Dear Pete, Thank you for your message. I can confirm that you need not worry about this clause: it is meant to prohibit the aggressive use of code decompilers with the intention of stealing the content of the source code. What you have described in your hypothetical example is nothing of the sort, but instead a very useful kind of comparative evaluation. With best wishes, Gerard. -- On Mon, Oct 27, 2008 at 09:53:19AM -0500, Pete Meyer wrote: Apologies for going slightly further off-topic... Last time I had a free half-day to look into sharp, I noticed that the academic license prohibits reverse-engineering. This seemed to put any comparative testing into a slightly grey area. For example, if I find that sharp does the best job refining sites, but bp3 outputs better phases for a dataset due to different representation of phase probabilities*, I've implicitly constructed a primitive model of how sharp is working. This seems close enough to a first step of reverse-engineering that I was concerned. Could someone confirm that I'm worrying about things I don't need to here? Pete * Purely hypothetical example.
[ccp4bb] buster-tnt on OSX ?
Hi everydoby, I`d like to know if there is a version of BUSTER-TNT available on MacOSX ? Anyone knows ? * Dr. Jacques-Philippe Colletier UCLA / DOE Institute for Genomics and Proteomics 90095 Los Angeles, CA, USA * [EMAIL PROTECTED] [EMAIL PROTECTED] *
Re: [ccp4bb] Measuring the volume and surface area of an active site
You can use CastP http://sts.bioengr.uic.edu/castp/calculation.php Best Jacques Le Dec 13, 2007 à 2:44 PM, Rajan Pillai a écrit : Hi All, Can anyone tell me if there is any program available that can measure the surface area and volume of the active site of a protein? Thanks, Rajan. * Dr. Jacques-Philippe Colletier Biological Structure Group MBI - UCLA / DOE 90095 Los Angeles, CA, USA * [EMAIL PROTECTED] [EMAIL PROTECTED] *
