Re: [ccp4bb] Question about Refmac

2020-06-15 Thread Jonathan Cooper
I remember we discussed this a lot about a year ago when Ed Berry revived a thread from 2003! https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind1905=CCP4BB=D=72099 I think the upshot of it all was that you do not need to use shells even with quite high NCS since Ian Tickle rightly persuaded

Re: [ccp4bb] Coot labels

2020-06-15 Thread Paul Emsley
On 15/06/2020 22:06, Cygler, Miroslaw wrote: Hi Hi. I just started using coot 0.9 and see some differences in behaviour from version 0.8. When I move to the next residue using space bar the residue name of the residue does not appear. How can I make appear automatically? Wow, 0.8 and

[ccp4bb] Coot labels

2020-06-15 Thread Cygler, Miroslaw
Hi, I just started using coot 0.9 and see some differences in behaviour from version 0.8. When I move to the next residue using space bar the residue name of the residue does not appear. How can I make appear automatically? Best, Mirek

Re: [ccp4bb] Questions regarding MTZFIX and EDSTATS

2020-06-15 Thread Ian Tickle
Hi Joao The top of the page was cut off in your screenshot so I can't see the command line you typed. It would be better to copy/paste the entire text, including the input command line and the output, into the email rather than taking a screenshot. 'Cannot open file' most likely means that the

Re: [ccp4bb] Question about Refmac

2020-06-15 Thread Eleanor Dodson
Hmm - this finally was rather deprecated - there are some less happy consequences to have all reflections in a particular resolution shell excluded. If your NCS means there is pseudo- symmetry in the diffraction and it would be possible to have a cell with higher point symmetry (an example might

[ccp4bb] Question about Refmac

2020-06-15 Thread
Hello, I'm refining protein structure in Refmac and I have NCS greater than 4 ( I've 8 identical subunits in the asymmetric unit). In the "Refinement parameters" section in Refmac, how can I pick Rfree set based on thin resolution shells rather than in the normal random method? I've read

Re: [ccp4bb] Questions regarding MTZFIX and EDSTATS

2020-06-15 Thread Ian Tickle
Hi Joao For all CCP4 programs you need to source your CCP4 setup script. Cheers -- Ian On Mon, 15 Jun 2020 at 15:29, Joao Ramos wrote: > Dear CCP4bb, > > I'm trying to obtain RSC metrics using the CCP4 program EDSTATS for a > Phenix refinement job, in order to have a more reliable analysis

[ccp4bb] Questions regarding MTZFIX and EDSTATS

2020-06-15 Thread Joao Ramos
Dear CCP4bb, I'm trying to obtain RSC metrics using the CCP4 program EDSTATS for a Phenix refinement job, in order to have a more reliable analysis of model quality. From what I read, one should go through the program MTZFIX and then create the FFT maps (density and difference maps). However,

[ccp4bb] web event | Cryo-EM for Drug Discovery | June 16, 2020

2020-06-15 Thread H. Raaijmakers
Last chance to register: Cryo-EM for Drug Discovery | June 16, 2020 What if you could get structural insights at near-atomic resolution of your most challenging drug targets at a pace that meets that of your drug discovery projects? >From around the world you are invited to join Thermo

[ccp4bb] PhD position (Denmark), Structural biology with a focus on sterol uptake mechanisms

2020-06-15 Thread Bjørn Panyella Pedersen
Dear colleagues, Please pass this along any one who might be interested. Thanks! /Bjørn STRUCTURAL AND FUNCTIONAL STUDIES of eukaryotic membrane proteins involved in sterol transport (http://pedersenlab.dk/source/phd_position_2020.pdf) A PhD

Re: [ccp4bb] Macports and Fink - failed building open source pymol on MacOS Catalina

2020-06-15 Thread Harry Powell - CCP4BB
Why not just use QTMG rather than Pymol? This is, after all, the _CCP4_ bulletin board… H > On 14 Jun 2020, at 23:56, Javier Gonzalez wrote: > > Thank you so much Vijaykumar and Kevin, it worked smoothly! > Best wishes, > Javier > > On Sun, Jun 14, 2020 at 5:04 PM Kevin Jin wrote: > My OS