Re: [ccp4bb] To Trim or Not to To Trim

;s the best we can do (at present). Hence why we need to educate users. And absolutely, none of the current solutions is ideal, that's also why we're having this discussion again and again. It seems no one has found a better solution yet. /Julia On 3/10/23, 17:15, "Phil Jeffrey&

Re: [ccp4bb] To Trim or Not to To Trim

3, at 18:25, Phil Jeffrey <mailto:pjeff...@princeton.edu>> wrote: > > On 3/10/23 4:05 AM, Julia Griese wrote: >> Hi all, >> My impression has been that the most common approach these days is to “let >> the B-factors take care of it”, but I might be wrong. Maybe it

Re: [ccp4bb] To Trim or Not to To Trim

was the most important thing you learned today?” is: “Don’t blindly trust anything.” Cheers /Julia -- Dr. Julia Griese Associate Professor (Docent) Principal Investigator Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri

Re: [ccp4bb] Fwd: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2

Oh, I hadn’t thought of trying that, that works! Obviously it would still be great if this issue was fixed (I guess it’s MacOS rather than PyMOL that’s to blame here), but this is a decent workaround. Thanks! /Julia -- Dr. Julia Griese Assistant Professor/Docent Department of Cell and

[ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2

knows how to fix it? Best, Julia -- Dr. Julia Griese Assistant Professor/Docent Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se phone: +46-(0)18-471 4982 http://www.icm.uu.se/structural-biology/griese-lab/ När

Re: [ccp4bb] PDBeMotif and like methods

Hi Andy, I’ve used PINTS, http://www.russelllab.org/cgi-bin/tools/pints.pl Hope that helps. Best, Julia -- Dr. Julia Griese Assistant Professor, Docent Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se phone: +46

[ccp4bb] Postdoctoral fellowship in experimental structural biology at Uppsala University

. Please note that suitable candidates must have obtained their PhD no earlier than 6 years ago and be able to start at the latest in March 2023. Please also note that this position is funded by a stipend. Informal inquiries and applications should be sent to Julia Griese, julia.gri...@icm.uu.se

Re: [ccp4bb] Quantifying electron density inside of a given volume

Dear Neno, Mapman can do exactly that too. Shameless plug: How to do it is described in this paper: http://scripts.iucr.org/cgi-bin/paper?S2059798319009926 Mapman appears to available on github now: https://github.com/martynwinn/Uppsala-Software-Factory Best, Julia -- Dr. Julia Griese

[ccp4bb] Open postdoc position in structural biology/biochemistry/biophysics at Uppsala University

.se>). Best, Julia (Any inquiries or applications directed to me will not be answered, I am only posting this on behalf of Cissi.) -- Dr. Julia Griese Assistant Professor, Docent Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: jul

Re: [ccp4bb] the complex structure of protein and DNA

-- Dr. Julia Griese Assistant Professor Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se phone: +46-(0)18-471 4982 http://www.icm.uu.se/structural-biology/griese-lab/ From: CCP4 bulletin board on behalf of Mark Roe

Re: [ccp4bb] Mean B factors and number of atoms (Refmac/baverage)

Answer to self: the number of non-H atoms per chain can be found in the PDB validation report! Duh! I guess I’ll trust the average B values reported by Refmac. /Julia -- Dr. Julia Griese Assistant Professor Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124

[ccp4bb] Mean B factors and number of atoms (Refmac/baverage)

there is another way to extract these numbers, I would much appreciate it! Best, Julia -- Dr. Julia Griese Assistant Professor Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se phone: +46-(0)18-471 4043 http

[ccp4bb] Postdoctoral Fellowship in Structural Biology at Uppsala University

://www.researchgate.net/job/944899_Postdoctoral_Fellowship_in_Structural_Biology You are welcome to contact me for more information, but please apply through ResearchGate. Best regards, Julia -- Dr. Julia Griese Assistant Professor Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE

[ccp4bb] Postdoctoral researcher position in Structural Biology at Uppsala University

/?positionId=199363 You are welcome to contact me for more information, but please note that you have to apply through the university system. Applications sent directly to me cannot be processed. Best regards, Julia -- Dr. Julia Griese Assistant Professor Department of Cell and Molecular

[ccp4bb] Postdoctoral Fellowship in Molecular Biology at Uppsala University

Dear all, *A two-year postdoctoral fellowship, funded by the Carl Tryggers Foundation, is available in the group of Julia Griese in the Department of Cell and Molecular Biology at Uppsala University, Sweden. * Research in the Griese lab is at the intersection of structural biology

[ccp4bb] Opening for a PhD student at Stockholm University

crystallography. Further information regarding the position and how to apply can be found here: http://www.su.se/english/about/vacancies/vacancies-new-list?rmpage=job&rmjob=2634&rmlang=UK Best regards, Julia -- Dr. Julia Griese Postdoctoral Researcher Department of Biochemistry and Bi

Re: [ccp4bb] Strange Ancient Diffraction Pattern...

iology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) -- Dr. Julia Griese Postdoctoral

Re: [ccp4bb] Off-topic - Crystallisation in anaerobic glove box

glas.co.uk <mailto:patr...@douglas.co.uk> Douglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994,

Re: [ccp4bb] which dimer?

Hi Karolina, I would suggest you do SAXS. You can compare the scattering profile you get from your protein in solution to the calculated profiles of the three possible dimers (or other oligomers) you have in the crystal structure. This should give you a definitive answer. See for example this p

Re: [ccp4bb] Stabilization of crystals and ligand exchange

sed xtals? Or any ideas how to stabilise them? I appreciate any ideas or comments! Sorry for the lengthy email! Best, Sabine -- Dr. Julia Griese Stockholm Center for Biomembrane Research Department of Biochemistry and Biophysics Stockholm University 106 91 Stockholm Sweden phone: +46-(0)8-162 746 email: gri...@dbb.su.se

[ccp4bb] nmr question

Dear members, I know that it is not possible to solve a structure by nmr of more than approx. 30 kda. But I have to admit that I dont know why. What exactly is overlapping? With best regards, Lena

[ccp4bb] Milestones in Crystallography

Dear CCP4ers, after 3 years without working in structural biology and crystallography, this summer I will have my PhD defence. As I am now working in a complete different field I would be happy to know what happened in structural biology the last years worth to mention. Is there finally the "solve