Re: [ccp4bb] intrasubunit rotation axis

Hi, not certain to understand the question. In chimera, you can create axis (for example in alpha helix) or directly draw one and do the angle measurement between differents axis. I imagine that you can create the "same axis" in both of your monomer and measure the angle between these axis.

Re: [ccp4bb] intrasubunit rotation axis

On 18/11/2016 03:57, chemocev marker wrote: Hi All I am interested to measure the symmetry axis of individual sub-unit (chain A & chain B) along with the symmetry axis of the heterdimer (AB). Each chain is also 2 fold axis, and I can measure by removing 1 chain and measure for the other and

[ccp4bb] New version of Adxv (1.9.11) available

A new version of Adxv (1.9.11) is available: http://www.scripps.edu/~arvai/adxv.html#Download The manual is here: http://www.scripps.edu/~arvai/adxv/AdxvUserManual.pdf Adxv is a program to display diffraction images from many detector formats. It is free and does not require any registration.

Re: [ccp4bb] XDS questions

Thanks everyone for answering the question! Best, Wei On Thu, Nov 17, 2016 at 4:20 PM, Michael Martynowycz < michael.martynow...@gmail.com> wrote: > Wei, > > You can use the integrated integrated intensities only if you want to go > the ccp4 route. Sort the integrated reflections, then scale

Re: [ccp4bb] XDS questions

Wei, You can use the integrated integrated intensities only if you want to go the ccp4 route. Sort the integrated reflections, then scale and truncate them using: Pointless xdsin INTEGRATE.HKL hklout sorted.mtz Aimless hklin sorted.mtz hklout scaled.mtz Hope that helps. -Mike Sent from my

Re: [ccp4bb] XDS questions

Dear Wei, if you process your data with XDS, the best is probably to do the scaling in XDS (CORRECT) and be done with it. If you want to use Aimless for merging, you can turn off scaling with the ONLYMERGE keyword or use SCALES CONSTANT. All best. Andreas On Thu, Nov 17, 2016 at 9:40 PM,

Re: [ccp4bb] XDS questions

Wei, The flag MAXIMUM_NUMBER_OF_PROCESSORS= in XDS.INP should allow you to choose the number of processors you wish to use. Cheers, Jim

[ccp4bb] XDS questions

Hi, Is there a way to let xds_par use less than all processors/threads on the machine? Sometimes I would like to process something else while XDS is running. Another question is related to the scaling procedure. My understanding is that the XDS already does the scaling during correction. So if I

Re: [ccp4bb] intrasubunit rotation axis

Wont PISA do it? It sorts out the most likely biological unit for you after applying symmetry operators. Either submit your coordinates to the EBI PDB server or use the version in CCP4 Eleanor On 17 November 2016 at 19:57, chemocev marker wrote: > Hi All > > I am

[ccp4bb] intrasubunit rotation axis

Hi All I am interested to measure the symmetry axis of individual sub-unit (chain A & chain B) along with the symmetry axis of the heterdimer (AB). Each chain is also 2 fold axis, and I can measure by removing 1 chain and measure for the other and then combine all the symmetry axis in the 1 PDB

Re: [ccp4bb] AW: AW: AW: [ccp4bb] confusing crystal diffraction

On 11/17/2016 08:36 AM, herman.schreu...@sanofi.com wrote: Dear Shijun, The reject.hkl file is the file with all rejected reflections. The first three numbers are h, k and l. For the other items you have to consult the HKL manual. As I said, I am not familiar with HKL2000. However, in your

[ccp4bb] Industrial Postdoctoral Fellow Position: Structural Biologist at Pfizer

All, Pfizer Structural Biology group (Groton, CT) has a Postdoctoral Fellow opening for structural biologist who has a strong desire to learn cryo-EM and the candidate can apply the job in the link below. Thanks in advance for your interest! Seungil Han www.pfizercareers.com Postdoctoral

[ccp4bb] PhD in electron crystallography at PSI

Dear all, I would appreciate if you could bring the following PhD position to the attention of appropriate candidates. Please apply online at https://www.psi.ch/pa/stellenangebote/1426 The Laboratory of Biomolecular Research at the PSI offers a PhD Project in Electron Crystallography:

Re: [ccp4bb] Skin on the drop

Microbatch under oil in Terasaki plates or perhaps microdialysis might be an option. Then you don’t have a liquid/air interface. It is harder to do very small volumes then, especially with microdialysis. Or free interface diffusion in thin tubes (or with specialised equipment). Mark J van Raaij

[ccp4bb] Skin on the drop

Dear All, How to avoid the skin on the drop? These skins are believed to be a layer of denatured protein or caused by the polyethylene glycol. They will certainly slow down the rate of vapor diffusion. If you have any good suggestions to avoid skin forming? Best wishes, Xiaorong Li

[ccp4bb] Post-Doctoral position at SOLEIL

Dear Colleagues, A two year post doctoral position on Radiation Damage is immediately available on the PROXIMA 2A beamline at Synchrotron SOLEIL. Please forward the announcement to any interested candidates. PROXIMA 2A is a micro-focus beamline dedicated to macromolecular crystallography (MX)

[ccp4bb] AW: AW: AW: [ccp4bb] confusing crystal diffraction

Dear Shijun, The reject.hkl file is the file with all rejected reflections. The first three numbers are h, k and l. For the other items you have to consult the HKL manual. As I said, I am not familiar with HKL2000. However, in your case, I would look in the log files instead of the .hkl files

[ccp4bb] I don't want to Bragg, but...

Hi folks Students of crystallographic history may be interested in this archive made available recently by the Royal Institution - http://www.rigb.org/our-history/bragg-film-archive Harry -- Dr Harry Powell Chairman of International Union of Crystallography Commission on

Re: [ccp4bb] Problem with lattice disorder / tNCS / whatever ?!

Hi Tim, Thanks a lot for pointing that out! Here is the IDXREF-output from XDS, without input of unit cell constants. Sabine * DETERMINATION OF THE RECIPROCAL LATTICE BASIS ** NUMBER OF DIFFERENCE VECTOR CLUSTERS USED 200 MAXIMUM RADIUS OF DIFFERENCE VECTOR

[ccp4bb] AW: [ccp4bb] confusing crystal diffraction

Dear Could you send us some images of badly smearing spots? The images you sent us are absolutely fine and should not pose any problems processing. Also, what is the reason the reflections get rejected? I have no experience with HKL2000 but I am sure it will produce in the output a table with