Re: [ccp4bb] Mosflm Error Msg

No--but thanks to you I just found it hanging in the process manager and killed it, which seems to have done the trick. Guess I should have thought of that sooner... Thanks for the help, Jacob -Original Message- From: Edward A. Berry [mailto:ber...@upstate.edu] Sent: Tuesday,

Re: [ccp4bb] Mosflm Error Msg

Is the old mosflm.lp open in an editor? Some editors will put a lock on the file which would prevent mosflm from overwriting or renaming it. On 02/03/2015 11:38 PM, Keller, Jacob wrote: Dear Crystallographers, Has anyone come across this message before with imosflm in Win7? I think

Re: [ccp4bb] Mosflm Error Msg

It would be nice though if imosflm did the killing for you - it happens to me a large fraction of the time on windows. (I imagine windows doesn't make mosflm's life easy, mind you.) phx On 04/02/2015 05:11, Keller, Jacob wrote: No--but thanks to you I just found it hanging in the process

[ccp4bb] Mosflm Error Msg

Dear Crystallographers, Has anyone come across this message before with imosflm in Win7? I think restarting cures it, but I've got other jobs going... JPK *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA

[ccp4bb] INSTRUCT course on Computational Tools Combining Atomic and Volume Data

Instruct with CCP-EM is proud to announce the following workshop: 'INSTRUCT course on Computational Tools Combining Atomic and Volume Data' * Event Details There is increasing overlap between structural biology disciplines, a common example being the interpretation of volume data from electron

Re: [ccp4bb] Bulk solvent correction in Phaser MR LF

Hi Bernhard, You're right, it's a Babinet-style correction to the SigmaA curve for the effect of neglecting bulk solvent in the model. We gave a formula in equation 19 of the main Phaser reference (McCoy et al., 2007), but actually we've changed the form of this since then. It looks like the

[ccp4bb] Postdoc position in Structural Characterization of the Sec Translocon machinery - Stockholm University

Postdoc position in Structural Characterization of the Sec Translocon machinery. Daniel Daley and Arne Elofsson, DBB and SciLifeLab Stockholm University A post-doc position is immediately available in membrane biochemistry and structural biology at Stockholm University. The position aims to

[ccp4bb] proton scattering by X-rays

Hi, Colin, ... I've been carrying a (very beaten up) 5'' x 3'' (April 1986) edition of the LBL ‘X-ray Data Booklet’ around in my briefcase for the past ¼ century or more. (An invaluable reference work.) So, I’m most pleased to follow the link that you refer to now, to the online

Re: [ccp4bb] proton scattering by X-rays

Hi Tim Although my SHELX comment was in jest, your point illustrates the programs versatility. You are also right about the flat(ish) form factor for the proton. To get to a resolution where there is a cross over would require a very short wavelength. Other processes would then dominate. A nice

Re: [ccp4bb] serial MR / refinement

Dear Eike, we have a simple automation exactly for this problem: a pipeline called DIMPLE. In Diamond it's run automatically after data collection, if the user provided pdb file. If you have CCP4 installed try: dimple file.mtz file.pdb output_dir The last arg is a directory where you want

[ccp4bb] Bulk solvent correction in Phaser MR LF

Hi Fellows, I cannot find the proper reference for the implementation of bulk solvent corrections in the Phaser Molecular replacement likelihood functions. For the unplaced model, it can only be a Babinet model to improve the scaling, and I believe that is implemented via a Babinet

[ccp4bb] [Job Posting] Software developer position at DNASTAR (Madison, WI USA)

Greetings, My company is hiring software developers for our structural biology group in Madison, WI USA. If interested, please submit applications to res...@dnastar.com. Best regards, Steve Darnell -- DNASTAR is a leading developer of desktop computer software for molecular biologists.

[ccp4bb] MrBump Behaves Strangely

Dear Crystallographers, I am trying to get MrBump to complete a partial solution, but on my windows7 machine, the CCP4i interface essentially freezes (cannot see logfiles therein, nothing responds, although it does not completely die), and those log files which I think are the correct ones

Re: [ccp4bb] proton scattering by X-rays

Hi Colin, I understood the jest, of course. Now I got curious: At 2theta=0, the scattering from H is 1e, so I assume the the scattering length for its nucleus is 1e/1860 = 0.00054. According to the data from Phil Coppens web site, the atomic scattering factor for H reaches this value at sin

[ccp4bb] serial MR / refinement

Dear all, I am looking for a way to automate molecular replacement and refinement runs. From ligand / fragment screening trials we have many datasets of the same protein with various resolutions (2.8 – 1.2Å). The apo-structure is known and well refined. The cell constants are fairly similar

[ccp4bb] OFF TOPIC: Cooling system for columns

Hello, we have an AKTA Avant that we keep at room temperature. We would like to be able to use it for preps at 4 degrees, so we would like to keep the FPLC columns (type 10/30 from GE) in the cold. We were thinking of buying a circulating water bath and connect it somehow to the columns

Re: [ccp4bb] OFF TOPIC: Cooling system for columns

Hi Chiara, We also have an Avant at room temperature. My recommendation would be to forgo using a water bath. Instead you can achieve a prep near enough to 4C by doing 2 things: Firstly, keep your columns stored in the cold room or a fridge to pre-chill them before use. Secondly, make your

Re: [ccp4bb] Bulk solvent correction in Phaser MR LF

Dear Bernhard, For the unplaced model, it can only be a Babinet model to improve the scaling, This is not fully true, and the flat mask correction can be used as well. Please look : Fokine, A. Urzhumtsev, A.G. (2002) On the use of low resolution data for translation search in molecular