Re: [ccp4bb] Strange density in arginine

2011-07-04 Thread Shiva Bhowmik
Hi Ruheng, Curious to know what was in the crystallization cocktail, cryoprotectant? Did you collect the dataset at a synchrotron? Shiva 2011/7/4 ruheng > Dear all, > > Recently we are working on an archaebacteria protein which was expressed > and purified from *E.coli *by conventional proced

Re: [ccp4bb] Strange density in Arg

2011-07-04 Thread Miri Hirshberg
Mon. July 4th 2011 EBI Good evening, firstly, it could be something that came form the buffer/crystallisation soup etc. What about phosphate? Secondly, if you think it is a "natural" post-translation modification of your specific protein this is gene/source depended. Check the uniprot entry

Re: [ccp4bb] Strange density in Arg

2011-07-04 Thread Artem Evdokimov
Before ruling this a covalent modification, did you check if a sulfate or some other tetrahedral ion (or a disordered acetate) fit the bill with respect to distances to the neighboring atoms? Artem 2011/7/4 ruheng > Dear all, > > Recently we are working on an archaebacteria protein which was e

Re: [ccp4bb] Strange density in arginine

2011-07-04 Thread Roger Rowlett
Looks like an anion, possibly sulfate or phosphate. What's in the crystallization mix? Roger Rowlett On Jul 4, 2011 11:33 AM, "ruheng" wrote: > > Dear all, > > Recently we are working on an archaebacteria protein which was expressed and purified from E.coli by conventional procedures. After we so

Re: [ccp4bb] Strange density in arginine

2011-07-04 Thread Vellieux Frederic
The distance to your modelled water seems to be in agreement with an ionic interaction. What are the components of all buffers in the crystallisation components ? Fred. ruheng wrote: > Dear all, > > Recently we are working on an archaebacteria protein which was > expressed and purified from /E.co

[ccp4bb] 2 Postdoctoral Positions - Research Complex at Harwell

2011-07-04 Thread Arwen Pearson
*** Research Officers in Dynamic Structural Science at the Research Complex at Harwell and the University of Bath (2 posts, fixed term for 4 years) *** Applica

Re: [ccp4bb] Twinning and Free R set generation

2011-07-04 Thread Eleanor Dodson
This is a problem not properly addressed - if you generate your FreeRflags in the highest possible Laue group for a system - eg P6/mmm if you SG is trigonal, then add these to the lower symmetry reflection list you are safe. It really should be done at the pointless stage but it isnt.. Here i

[ccp4bb] Twinning and Free R set generation

2011-07-04 Thread Peter Vidani
Hi all, I am worried about mixing working and free reflexions during TWIN refinement. Is there any keyword in UNIQUEIFY to generate a R-free flag in the case of twinning? I mean in that way that the possible twinning operators are taken into account for a following refmac job using the TWIN k

[ccp4bb] Twinning and Free R set generation

2011-07-04 Thread Peter Vidani
Hi all, I am worried about mixing working and free reflexions during TWIN refinement. Is there any keyword in UNIQUEIFY to generate a R-free flag in the case of twinning? I mean in that way that the possible twinning operators are taken into account for a following refmac job using the TWIN k

Re: [ccp4bb] Error in scalepack(Denzo)

2011-07-04 Thread Eleanor Dodson
Can you send a bit of the input file and the command script generated by the GUI Eleanor On 07/02/2011 07:48 AM, Sudhir Kumar wrote: Dear all I am trying to convert a scaled file (scaled using Automar) to mtz butit is showing follwoing error : #CCP4I TERMINATION STATUS 0 Error from script /o

[ccp4bb] Notebook and stereo

2011-07-04 Thread Duangrudee Tanramluk
Hi All, I am looking for a laptop computer that works well with stereo viewing on Coot, Pymol, and Discovery Studio. Nvidia 3Dvision webpage offers quite a few models but almost all of them in market is 17" and thus too heavy to carry around. Please, if any of you could suggest any model of