[ccp4bb] Research technician position at EMBL Grenoble

A Research Technician position is available in the High Throughput Crystallization Laboratory at EMBL Grenoble The HTX lab is one of the largest platforms for automated macromolecular crystallization screening in Europe and is offering services through Instruct and the EC-funded project iNEX

[ccp4bb] PyMol: Which 3D setup for a new installation? (Since 3D Vision is discontinued)

Dear List, I've posted this question to the PyMol mailing list already, but i was told that the CCP4 list is a little bit more active. One of our research groups needs a new 3D PyMol setup. Looking through the wiki (https://pymolwiki.org/index.php/Stereo_3D_Display_Options) the most prominent

[ccp4bb] Reminder: Call open for BAG beamtime at DESY beamline P11, PETRA III

Dear all, Please note the approaching deadline for submission of Block Allocation Group (BAG) proposals for DESY beamline P11 at the PETRA III synchrotron in Hamburg. Proposals are to be submitted via https://door.desy.de The deadline for submission is ---

[ccp4bb] CryoEM senior scientist position in Sanofi

Dear All, We are looking to add to our Bio Structure and Biophysics department at Integrated Drug Discovery scientific platform in Sanofi – a CryoEM expert. Principal scientist CryoEM position is announced in our team near Paris. Please apply using the flowing link - CryoEM expert, senior scienti

[ccp4bb] Accessing full list of programs in CCP4I2

Hello, I am looking for a way to find the list of programs accessible using the new 7.1 CCP4I2 interface? Is this still possible or do I have to revert back to version 7.0? Best regards, Kelvin -- Kelvin Lau https://people.epfl.ch/kelvin.lau Protein production and structure core facility - P

[ccp4bb] Postdoctoral positions in structural biology of fertilization at Karolinska Institutet and Umeå University

Thanks to a long-term grant from the Knut and Alice Wallenberg foundation, our team (http://jovinelab.org) has openings for two postdoctoral fellows to study the molecular basis of gamete recognition by cryo-electron microscopy and cryo-electron tomo

Re: [ccp4bb] Accessing full list of programs in CCP4I2

Hi Kelvin, not quite sure if I understand you correctly, but if you press the Task Manager button you get on the right sight a list of topics (import data, Molecular Replacemnt etc.) each point can be open up like a file tree to see all programs or pipelines available. You can search with the sear

[ccp4bb] cavities volume calculations

Hi everybody, I am aware of programs which compute the volume of cavities and pockets. However, I am looking for a program which can compute the volume around a given point (given by its coordinates), and return also the information about if it is an open surface pocket or an internal cavity.

Re: [ccp4bb] cavities volume calculations

Hi Nathalie, I think Caver tools can do that: https://caver.cz/index.php?sid=133 Best wishes Joana > On 6. Jul 2020, at 15:39, Nathalie Colloc'h wrote: > > Hi everybody, > > I am aware of programs which compute the volume of cavities and pockets. > > How

Re: [ccp4bb] Protein-DNA covalent bond refinement

Hi Cristina, in Phenix it is: Refinement settings -> Select Atoms -> Custom Geometry Restraints : you can define bonds, angles, torsions, planes, etc... Pavel On Thu, Jul 2, 2020 at 8:11 AM Cristina Machon wrote: > Dear all, > > I am writing regarding a problem we are facing with the refineme

[ccp4bb] Scientific Software Developer position at RCSB PDB, UCSD

The RCSB PDB is seeking a Scientific Software Developer with skills as a seasoned, experienced bioinformatics programming professional and a broad understanding of computational algorithms. The incumbent will develop, implement, and maintain complex scientific and web-based software systems for th

[ccp4bb] Twin law definition in REFMAC5

Dear colleagues, I have a crystal with space group P21212 and merohedral twinning according to "-h, l, k" twin law. If I click "twin" in the interface, REFMAC5 recognizes a different twin law and does not refine the structure properly. Is there a way to tell REFMAC5 the proper twin law? I tried

Re: [ccp4bb] Twin law definition in REFMAC5

Is that twin law possible? Presumably the cell lengths for b and c are close but you are swapping a 2fold axis along c for a 21 axis along b? Eleanor On Tue, 7 Jul 2020 at 05:36, Petr Kolenko wrote: > Dear colleagues, > I have a crystal with space group P21212 and merohedral twinning according >

Re: [ccp4bb] Twin law definition in REFMAC5

Dear Eleanor, The unit cell parameters are 117.385 155.506 155.611 90.00 90.00 90.00, as you expected. The twin law was recognized using phenix.xtriage. If I refine the structure using phenix.refine with no twin law and the Rwork/free values were 28/33. With the twin law "-h,l,k" the R valu

Re: [ccp4bb] Twin law definition in REFMAC5

On Mon, Jul 6, 2020 at 10:33 PM Petr Kolenko wrote: > Dear Eleanor, > The unit cell parameters are 117.385 155.506 155.611 90.00 90.00 > 90.00, as you expected. The twin law was recognized using phenix.xtriage. > If I refine the structure using phenix.refine with no twin law and the > Rwork/f