Re: [ccp4bb] a problem when using NOMACHINE Player from OSX 10.7.4

2013-09-18 Thread Scott Classen
The keyboard combo to get the settings is control+option+0 Sincerely, Scott > On Sep 18, 2013, at 19:14, Scott Classen wrote: > > I think if you press option + command + 0 a menu will pop up in the middle of > the screen. There should be a display settings icon there. You can choose > full s

Re: [ccp4bb] a problem when using NOMACHINE Player from OSX 10.7.4

2013-09-18 Thread Scott Classen
I think if you press option + command + 0 a menu will pop up in the middle of the screen. There should be a display settings icon there. You can choose full screen or 1:1 pixel ratio etc. Just explore the various options and something should work for you hopefully. Sincerely, Scott > On S

Re: [ccp4bb] a problem when using NOMACHINE Player from OSX 10.7.4

2013-09-18 Thread Bosch, Juergen
check out the hidden .nx folder in your home directory. You should have a folder named config. You may have a .nxs file or .cfg file there just edit the file with a text editor. You probably need to change this value: If you have a retina MacBook I guess you need to double that value perhaps. J

[ccp4bb] a problem when using NOMACHINE Player from OSX 10.7.4

2013-09-18 Thread Alexander Aleshin
I've got a question to people using a remote access to synchrotron computers. I've got Macbook pro with Mac OSX 10.7.4, which requires the use of nxplayer instead of commonly used nxclient. It works, but the size of emulated screen gets twice bigger than the size of my computer's screen. As a r

[ccp4bb] Docking models into low-res SAD map

2013-09-18 Thread Oliver Clarke
Hi all, Can anyone recommend software to dock previously solved domains into a (very) low-resolution experimentally phased map? I am working on a rather marginal case where this would be useful - very large assembly (500kDA per ASU), native goes to 6.9A, and the best derivative goes to 8A with

Re: [ccp4bb] Code to handle the syntax of (mm)CIF data correctly.

2013-09-18 Thread Marcin Wojdyr
On Wed, Sep 18, 2013 at 03:41:34PM +0100, Peter Keller wrote: > I hope that this isn't quite what you meant There are already > mutually-incompatible CIF dialects out there that have been created > by developers coding to their own understanding and interpretations > of the CIF/STAR format. I

Re: [ccp4bb] Code to handle the syntax of (mm)CIF data correctly.

2013-09-18 Thread yayahjb
Dear Colleagues, There are two major issues that tend to trip up CIF programmers: 1. Dealing with the order independence of CIF. Unlike PDB format, tags in CIF can validly be presented in any order. This means you cannot simply scan a CIF for a tag you want and start processing from th

Re: [ccp4bb] Code to handle the syntax of (mm)CIF data correctly.

2013-09-18 Thread Phil Evans
I didn't mean that, though reflection loop data shouldn't be problematic I think (and may be very long). As you say tokenization is necessary but not sufficient I'm sure you have faced lots of corner cases, and naive approaches (that I would have gone for) like "divide at spaces, then strip quo

Re: [ccp4bb] Code to handle the syntax of (mm)CIF data correctly.

2013-09-18 Thread Peter Keller
Hi Phil, I agree that the issue that you raise (about the need to define the data items and categories propery) is an important one that needs proper consideration. However, your mail could be read to suggest that correct parsing of CIF-format data is a secondary issue that doesn't deserve the

Re: [ccp4bb] from sca to CC1/2

2013-09-18 Thread Jim Pflugrath
The current version of scalepack already calculates CC1/2 and reports it in the log file. From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Francesco Angelucci [francesco.angelu...@uniroma1.it] Sent: Wednesday, September 18, 2013 5:21 AM To: CCP4BB@

Re: [ccp4bb] Code to handle the syntax of (mm)CIF data correctly.

2013-09-18 Thread Robbie Joosten
Hi Phil, When I wrote cif2cif to deal with reflection files from the PDB I opted for good-enough parsing to provide input for cif2mtz. This was a while ago, reflection files were still a mess at the time and my programming skills never tested in practice. I just added support for anything that cou

Re: [ccp4bb] Code to handle the syntax of (mm)CIF data correctly.

2013-09-18 Thread Phil Evans
As a novice looking at mmCIF from a developers point of view, for reflection data, the complication is not so much tokenising (parsing), but what items to write or to expect to read. For example as far as I can see an observed intensity may be encoded in a reflection loop (merged or unmerged) as

Re: [ccp4bb] from sca to CC1/2

2013-09-18 Thread Phil Evans
As long as the .sca file is scaled but unmerged, then one way is pointless -copy scain denzo.sca hklout denzo.mtz aimless hklin denzo.mtz << EOF scales constant onlymerge EOF Phil On 18 Sep 2013, at 11:21, Francesco Angelucci wrote: > Dear All, > > I am wondering if is possible to calculate

[ccp4bb] from sca to CC1/2

2013-09-18 Thread Francesco Angelucci
Dear All, I am wondering if is possible to calculate the CC1/2 factor from the denzo .sca file. Thank you in advance Francesco Angelucci

Re: [ccp4bb] off topic: Fluorescence labeled protein, neutral at pH=7

2013-09-18 Thread rajakumara eerappa
Hi Xiang. If you are doing in vitro experiments like binding studies then try BODIPY Fluorophores. It conjugates the protein. Advantage is molecular weight of these BODIPY Fluorophores is few hundreds Da. Also, these dyes have well separable absorption and emission spectrums. Good luck Raj On M

[ccp4bb] Old Oryx

2013-09-18 Thread mizuta
Dear All, My name is Ryo Mizuta, I am a placement student working at the Institut Laue-Langevin in Grenoble, France in the Life Sciences department. I am currently designing/developing a prototype crystallization module for proteins (based on batch crystallization) which enables automated temper

[ccp4bb] Postdoc position in Structural Biology at University of Bayreuth

2013-09-18 Thread Michael Weyand
*Postdoc position in Structural Biology at University of Bayreuth* We are currently looking for a highly motivated postdoc for our laboratory at the Dept. of Biochemistry at University Bayreuth, Germany. Our work involves biochemical and structural studies on cellular signalling systems with relev