[ccp4bb] Crystallography methods development post at Diamond Light Source

Good morning all, We are looking for an enthusiastic methods developer to join the team here at Diamond developing integration methods for small molecule X-ray diffraction data: http://www.diamond.ac.uk/Careers/Vacancies/All/132_17_CH.html The focus of this work is the analysis of more

[ccp4bb] EMBL-GSK Postdoctoral Position in Cryo-EM of Chromatin Complexes

Dear colleagues, The Müller group at EMBL Heidelberg in collaboration with GlaxoSmithKline (GSK) seeks to recruit an outstanding postdoctoral fellow to explore the use of cryo-EM to study small-molecule ligand-bound structures of chromatin complexes. The successful candidate will apply

Re: [ccp4bb] coordinate transformation

I showed you pdbset .. Find the centre of mass for your assembly. Move it where you will pdbset xyzin mow.pdb end Find CoM 0.7 1.3 -0.2 Hmm - a little thought - centre at 1 -1 0 say pdbset yzin now.pdb xyzout changed.pdb symgen x , y-2, z end New CoM 0.7 -0.7 -0.2 Eleanor On 18

[ccp4bb] PostDoc positions in Membrane Protein Structural Biology

Dear all, We are looking for two highly motivated Post-Docs with a Ph.D. in Structural biology, Biophysics or related disciplines to work in the lab of David Drew at Stockholm University in Sweden. Our international team aims to dissect the molecular mechanisms of small molecule transport

[ccp4bb] EMBO Practical Course on Characterization of macromolecular complexes by integrative structural biology

Dear ccp4 community, I would like to remind you of the announcement below. You can now find the complete programme of the Course following the indicated link. Kind regards, Marco Marcia ** EMBO Practical Course on *Characterization of macromolecular complexes by

[ccp4bb] Higher Scientific Officer positions available at The Institute of Cancer Research

The Institute of Cancer Research, London, is one of the world’s most influential cancer research institutes, with an outstanding record of achievement dating back more than 100 years. We provided the first convincing evidence that DNA damage is the basic cause of cancer, laying the foundation

Re: [ccp4bb] coordinate transformation

On 12/18/2017 05:39 AM, Eleanor Dodson wrote: I showed you pdbset .. Find the centre of mass for your assembly. Move it where you will Thanks. What James was suggesting was somewhat different (if I understood correctly): move EVERY ATOM to 1,1,1. like: awk -v FIELDWIDTHS="30 24 26" \

Re: [ccp4bb] AW: Re: [ccp4bb] AW: Re: [ccp4bb] coordinate transformation

This is something you would normally not do in the course of refining a protein structure, because the structure would no longer correspond to the observed structure factors and no longer be consistent with the symops of the particular space group. There are applications for it in

Re: [ccp4bb] AW: Re: [ccp4bb] AW: Re: [ccp4bb] coordinate transformation

thanks. i may mean something other. for example, if i rotate the pdb by 30 degree (or 29.5 degree), or i shift the pdb along x-axis by something for example 0.123*a, then how i move the mtz map correspondingly for the fitting of mtz into the transformed map? | | Smith Liu | |

Re: [ccp4bb] AW: Re: [ccp4bb] AW: Re: [ccp4bb] coordinate transformation

Assuming you have a good reason for doing that, I'd suggest the best approach would be to first generate a real-space map covering your original coordinates, and then apply the transform to that. To transform a volumetric map, all you're actually transforming is the (x,y,z) coordinate of its

[ccp4bb] AW: Re: [ccp4bb] coordinate transformation

If you use coot with on the fly map calculation (e.g. you load an mtz and not a map file), you do not need to transform the map. Otherwise I would recommend to run one more round of refinement and produce a new map your usual way. This will also get rid of any rounding errors due to the

[ccp4bb] Scientist position in SM protein science - Biogen - #33174BR

Dear Colleagues, We have an immediate job opening in our protein sciences group for a molecular biologist/protein expression scientist (Application link and details provided below). I would greatly appreciate if you can forward to suitable candidates. 33174BR

Re: [ccp4bb] AW: Re: [ccp4bb] AW: Re: [ccp4bb] coordinate transformation

sorry, how i move the mtz into the transformed pdb for the question in my previous email? | | Smith Liu | | 邮箱：smith_liu...@163.com | 签名由 网易邮箱大师 定制 在2017年12月18日 23:37，Smith Liu 写道： thanks. i may mean something other. for example, if i rotate the pdb by 30 degree (or 29.5 degree), or i

[ccp4bb] Electron density map for publications

Hi Which electron density map (fo-fc or 2fo-fc) should I use for representing the density of the bound ligand? Thanks Raj

Re: [ccp4bb] coordinate transformation

Dear All, If I have a set of PDB with the corresponding density map, after I transform the PDB based on the suggestion of everybody, is any way to transform the map so that the map will be fit with the transformed PDB? Smith At 2017-12-18 18:39:34, "Eleanor Dodson"

Re: [ccp4bb] Electron density map for publications

Thanks sir On Tue, Dec 19, 2017 at 11:05 AM, Bernhard Rupp wrote: > *Unbiased positive omit* difference density, not just any fo-fc. > > Br > > On Dec 18, 2017 9:22 PM, "chenzhonghao...@163.com" < > chenzhonghao...@163.com> wrote: > > Dear Raj, > > Usually, fo-fc

Re: [ccp4bb] Eiger 16M detector in HKL2000

Dear Aidong, as I don't have access to HKL2000 myself, I can't tell you what might need to be done to have the software display EIGER X 16M images. Wladek showed me that it was possible. It might just be a question of getting the latest version. There are alternatives to HKL-2000. DIALS can

Re: [ccp4bb] 3D stereo and pymol

Dear all, in case anybody is interested in a used 3D setup for crystallography one is still available: See here for more details: https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg41144.html Kind regards, Matic. On 12. 12. 2017 08:39, Jim Fairman wrote: Reporting in a setup that we just

Re: [ccp4bb] Eiger 16M detector in HKL2000

Dear Aidong, As Dr. Förster has rightly pointed out you need to have the latest version of HKL2000 to work with the HDF5 files from the Eiger detectors and as you must be aware the HKL2000 license should include use of Eiger detectors. We have recently used HKL2000 to process data from

Re: [ccp4bb] coordinate transformation

Well, yes, a one-liner to move every atom to 1,1,1 would be: awk '! /^ATOM|^HETAT/{print;next} {print substr($0,1,30) " 1.000   1.000   1.000" substr($0,55)}' whatever.pdb > ref.pdb Which I suppose is a bit of a long one-liner, but still only one line.  The next line would be a call to

Re: [ccp4bb] Crystal structure of an unknown protein

HI Jiyong, If you still have protein left, you may try to sequence it. In some cases, even N-terminal digestion is very helpful. In my previous, I always got a 90KDa protein, which was very close to my target kinase. Based on the protein sequencing, we identified it was one of those chaperones.

Re: [ccp4bb] Electron density map for publications

http://journals.iucr.org/d/issues/2013/02/00/index.html Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of raj kumar Sent: Monday, December 18, 2017 8:37 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Electron density map for publications Hi Which electron

Re: [ccp4bb] Electron density map for publications

Dear Raj, Usually, fo-fc is the best way to show. best, chenzhonghao...@163.com From: raj kumar Date: 2017-12-19 13:07 To: CCP4BB Subject: [ccp4bb] Electron density map for publications Hi Which electron density map (fo-fc or 2fo-fc) should I use for representing the density of the

Re: [ccp4bb] Electron density map for publications

*Unbiased positive omit* difference density, not just any fo-fc. Br On Dec 18, 2017 9:22 PM, "chenzhonghao...@163.com" wrote: Dear Raj, Usually, fo-fc is the best way to show. best, -- chenzhonghao...@163.com *From:* raj kumar

[ccp4bb] Eiger 16M detector in HKL2000

Hi All, We have recently collected several data sets in the Shanghai synchrotron facility with a newly installed Eiger 16M. However, we are not able to process these data using our home HKL2000 package. Even though we can easily add this detector in, we can not display images. I believe ours

[ccp4bb] Map transformation [was Re: [ccp4bb] coordinate transformation]

On 18/12/2017 13:15, Smith Liu wrote: Dear All, If I have a set of PDB with the corresponding density map, after I transform the PDB based on the suggestion of everybody, is any way to transform the map so that the map will be fit with the transformed PDB? Seeing as no-one else has