[ccp4bb] postdoc 3

Los últimos 2 (numero 2 y 3 en el asunto, tienen una oferta de estudio de flagelos = flagella) Saludos De: CCP4 bulletin board en nombre de CCP4BB automatic digest system Enviado: martes, 19 de abril de 2016

Re: [ccp4bb] Refmac5 update water option

Got it. Thank you very much Christian! On Fri, Dec 16, 2016 at 12:14 PM, Christian Roth wrote: > Hi, > > the adding water option is basically a COOT script to find waters, which > get subsequently refined. There is no automatic evaluation and deletion of > waters

Re: [ccp4bb] does Refmac5 do density modification in the refinement of a structure?

Dear All, I really appreciate your nice explanations! On Fri, Dec 16, 2016 at 12:08 PM, Eleanor Dodson wrote: > > This isnt the sort of thing a refinement program does. > Refinement starts from the model you provide - uses that to generate > phases and the

Re: [ccp4bb] Refmac5 update water option

Hi, the adding water option is basically a COOT script to find waters, which get subsequently refined. There is no automatic evaluation and deletion of waters based on certain criteria. That you have to do manually. You can always try to automatically add new waters, which is done by this

Re: [ccp4bb] does Refmac5 do density modification in the refinement of a structure?

DM will be most helpful to you if you are as unbiased as possible to begin with. I *think* that DM right after MR is about as biased as DM after MR after a round of Refmac post-MR (given that MR these days includes rigid body refinement anyway) but I would be very curious to hear what the resident

Re: [ccp4bb] does Refmac5 do density modification in the refinement of a structure?

Dear Alex, Refmac doesn't do density modification. If you want take advantage of better starting phases you have to do DM prior Refmac or model building with Buccaneer for example. I recommend PARROT for that. I would use i2 Parrot and this as input in the Buccaneer pipeline with precomputed

Re: [ccp4bb] does Refmac5 do density modification in the refinement of a structure?

This isnt the sort of thing a refinement program does. Refinement starts from the model you provide - uses that to generate phases and the appropriately weighted difference map to alter the input coordinates. So that map is used in the close environment of a the model, so solvent flattening is not

[ccp4bb] Refmac5 update water option

Dear CCP4bb members, Does Refmac5 in CCP4i have an option of adding waters to the refined structure (the input coordinate does not have any water)? I see in Phenix refine there is an option of "update water", I tried to look for this option in Refmac5 but I could not find it. I am using CCP4i

[ccp4bb] does Refmac5 do density modification in the refinement of a structure?

Hi All, I am using CCP4i 7.0.0.025 linux version. I am wondering if Refmac5 automatically does density modification (e.g. solvent flattening, NCS, etc..) in the refinement after I put a solution coordinate from Phaser MR molecular replacement and the experiment data (MTZ file)? If Refmac5 does

Re: [ccp4bb] jligand help

Hi Nicholas, CCP4 6.5 is end-of-life and no longer supported. Please upgrade to version 7.0. Apart from the obvious benefit of having up-to-date softeare, JLigand should also work. Cheers, Robbie Sent from my Windows 10 phone Van: Nicholas Larsen

[ccp4bb] jligand help

Dear All, I have CCP4 6.5.0 installed on my laptop PC. Everything runs fine, to my knowledge, except JLigand. When I click this program from the program list, absolutely nothing happens. No error message, nothing. It doesn't launch. Do I need to reinstall cpp4 or is JLigand a separate

Re: [ccp4bb] Averaging of different proteins in heteromeric complex

"The proteins are stoichiometric" Huh? What is the stoichiometry? I'm expecting a ratio here, like 1:1 or some such. I see two possibilities: 1) The two proteins are completely interchangeable in the structure. 2) The two proteins are not interchangeable, but are being

Re: [ccp4bb] Averaging of different proteins in heteromeric complex

This seems like a case of what is called either static or statistical disorder. Axel Brunger has a JMB paper about this with DNA crystals: http://atbweb.stanford.edu/scripts/papers.php?sendfile=30 JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Graham Robinson Sent:

[ccp4bb] Averaging of different proteins in heteromeric complex

Dear Crystallographers, I have solved the structure of a complex, which is the average of its component proteins. The problem is as follows: The complex is composed of two proteins, which share 67%/84% sequence identity/similarity in the resolvable region. The proteins are stoichiometric

[ccp4bb] NIH-funded postdoc position

Dear colleagues, Please see below an ad for an NIH-funded postdoc position in my laboratory. Thank you, Alexandra *POSTDOCTORAL POSITION* *at Brown University, Providence, Rhode Island, USA* The Deaconescu Lab at Brown University is seeking a motivated and energetic postdoctoral research to

[ccp4bb] PhD opportunity in membrane protein structural biology (Leeds, UK)

Dear all, on behalf of a colleague I am posting a very interesting PhD position. For further information please see https://www.findaphd.com/search/ProjectDetails.aspx?PJID=81598=735 or email s.harbo...@leeds.ac.uk. Application deadline is the 31.01.2017. *Structural characterisation of the

[ccp4bb] CCP4 update 026

Dear All contains updates to coot for linux 32/64-bit and OS X. This re-corrects the auto-mutate problem on OS X, and various segv such as when using coot-mini-rsr. Hopefully we now have a functional coot. Thank you for bearing with us Charles on behalf of the CCP4 core team.

[ccp4bb] Call for access to Synchrotron Beamline Facilities, 2017 - EMBL Hamburg, Germany

CALL FOR ACCESS TO SYNCHROTRON BEAMLINE FACILITIES, 2017 - EMBL HAMBURG, GERMANY We announce a call for synchrotron beam time applications in biological small-angle X-ray scattering (SAXS) and macromolecular crystallography (MX) for the period April - December 2017. The following EMBL

Re: [ccp4bb] AW: Could this be a complex crystal? or only RNA crystal? or micromolecular？

dear Rachel, to me this seems more like a salt diffraction pattern... I agree with Kevin, run a SDS on your crystal and see if you have crystallized something "interesting" Good luck On Fri, Dec 16, 2016 at 9:26 AM, Camillo Rosano wrote: > dear

[ccp4bb] AW: Could this be a complex crystal? or only RNA crystal? or micromolecular？

Dear Rachel, You don’t have any spots with a resolution lower than ca. 15Å, which means that none of the cell axes can be longer than 15Å. This must be a crystal of some small molecule and not of a protein and/or RNA molecule. One question: you mention that the data could not be processed by