Re: [ccp4bb] Macports and Fink - failed building open source pymol on MacOS Catalina
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 Version: Catalina 10.15.5; > > brew install brewsci/bio/pymol > > To verify, I just installed Pymol using brew 2 minutes ago. It works. > > On Sat, Jun 13, 2020 at 4:45 PM Javier Gonzalez wrote: > Hello, > I'm attempting to build pymol on a laptop running MacOS Catalina 10.15.5, > Processor 2.8GHz Quad-Core Intel i7, Graphics Intel Iris Pro 1536 MB > I downloaded the latest version of Xcode 11.1 > > I tried from Fink (fink install pymol-py27) and Macports (sudo port install > pymol), as indicated here: https://pymolwiki.org/index.php/MAC_Install > > Both scripts run to download all dependencies but at the end fail with > different messages (see below). Any ideas? Is it doable or am I just > following outdated instructions? > Thanks in advance! > Javier > > Fink: fails at compiling term-readkey-pm5184-2.37-1 > - > - > Failed: phase compiling: term-readkey-pm5184-2.37-1 failed > > Before reporting any errors, please run "fink selfupdate" and try again. > Also try using "fink configure" to set your maximum build jobs to 1 and > attempt to build the package again. > If you continue to have issues, please check to see if the FAQ on Fink's > website solves the problem. If not, ask on one (not both, please) of > these mailing lists: > > The Fink Users List > The Fink Beginners List , > > with a carbon copy to the maintainer: > > Christian Schaffner > > Note that this is preferable to emailing just the maintainer directly, > since most fink package maintainers do not have access to all possible > hardware and software configurations. > > Please try to include the complete error message in your report. This > generally consists of a compiler line starting with e.g. "gcc" or "g++" > followed by the actual error output from the compiler. > > Also include the following system information: > Package manager version: 0.45.1 > Distribution version: selfupdate-rsync Fri Jun 12 21:49:17 2020, 10.15, x86_64 > Trees: local/main stable/main > Xcode.app: 11.5 > Xcode command-line tools: 11.5.0.0.1.1588476445 > Max. Fink build jobs: 8 > - > - > Macports: apparently there is an issue with py38-pyqt5 > ---> Computing dependencies for pymol > The following dependencies will be installed: py38-pyqt5 > Continue? [Y/n]: > ---> Fetching archive for py38-pyqt5 > ---> Attempting to fetch py38-pyqt5-5.14.2_0.darwin_19.x86_64.tbz2 from > https://packages.macports.org/py38-pyqt5 > ---> Attempting to fetch py38-pyqt5-5.14.2_0.darwin_19.x86_64.tbz2 from > http://aus.us.packages.macports.org/macports/packages/py38-pyqt5 > ---> Attempting to fetch py38-pyqt5-5.14.2_0.darwin_19.x86_64.tbz2 from > https://ywg.ca.packages.macports.org/mirror/macports/packages/py38-pyqt5 > ---> Building py38-pyqt5 > Error: Failed to build py38-pyqt5: command execution failed > Error: See > /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_python_py-pyqt5/py38-pyqt5/main.log > for details. > Error: Follow https://guide.macports.org/#project.tickets to report a bug. > Error: Processing of port pymol failed > - > - > -- > Dr. Javier M. González > Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET) > Universidad Nacional de Santiago del Estero (UNSE) > RN9, Km 1125. Villa El Zanjón. (G4206XCP) > Santiago del Estero. Argentina > Tel: +54-(0385)-4238352 > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > -- > Kevin Jin > > Sharing knowledge each other is always very joyful.. > > Website: http://www.jinkai.org/ > > > > -- > Dr. Javier M. González > Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET) > Universidad Nacional de Santiago del Estero (UNSE) > RN9, Km 1125. Villa El Zanjón. (G4206XCP) > Santiago del Estero. Argentina > Tel: +54-(0385)-4238352 > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ###
[ccp4bb] PhD position (Denmark), Structural biology with a focus on sterol uptake mechanisms
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 position is available in membrane protein biochemistry and structural biology in the research group of Dr. Bjorn P Pedersen at the Department of Molecular Biology and Genetics, Aarhus University, Denmark. The group studies the structure-function relationship of membrane proteins involved in metabolite uptake, primarily sterol and sugar uptake, as well as their regulation from a structural perspective. The PhD project will involve expression, purification and structural/functional characterization of membrane proteins involved in sterol transport and homeostasis (Winkler et al. Cell 179 (2019)). Methods learned and used will be cryo-electron microscopy and X-ray crystallography, as well as various biochemical methods to elucidate function. The project is fully funded by the Danish Council for Independent Research, and will be based in the laboratory of Dr. Bjorn P. Pedersen (http://pedersenlab.dk). It would ideally suit an outstanding biochemistry graduate with a strong interest in structural biology. The candidate should have molecular biology, protein production and purification experience. Experience with membrane proteins or protein structure determination will be an advantage. Full training will be provided in all necessary areas of protein biochemistry and structural biology. Good English language skills are essential. Salary will be according to the collective agreement between the Danish Confederation of Professional Associations and the Danish State. The position will be filled as soon as a suitable candidate is identified. Applicant should send a CV, cover letter and names of two referees to Dr. Bjorn P Pedersen (b...@mbg.au.dk). The city In Aarhus you have easy access to beautiful nature and an exciting culture and city life that make Aarhus a wonderful place to live and work. See https://international.au.dk/life/locations/ for further details on the city and the university. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] web event | Cryo-EM for Drug Discovery | June 16, 2020
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 Fisher Scientific for Cryo-EM for Drug Discovery- a free, one-day virtual event featuring the latest solution to address current challenges with SBDD. Session Title: How to solve structures at a perfected pace for drug discovery Times: 11:00 CEST/05:00 a.m. EDT and 17:00 CEST/11:00 a.m. EDT You will discover: * An innovative cryo-EM solution optimized for drug discovery * How this solution can increase your chances in finding hits, lead compounds and beyond * Testimonials from your peers on this innovative solution and how this improves their outcomes and results This event also includes a virtual networking environment and exhibit hall. Register here [1] Cheers, Hans If you can't join us live, be sure to still register. All registrants will receive on-demand access to the material. Links: -- [1] https://www.thermofisher.com/us/en/home/about-us/events/industrial/structures-pace-drug-discovery.html?cid=3so-ccp4-ls To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Questions regarding MTZFIX and EDSTATS
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, while attempting to run the Phenix output mtz file in MTZFIX, I receive an error message saying: "Cannot open environ.def". My questions are: 1) Is the way to go from the Phenix refinement output files to EDSTATS described earlier correct? Are there alternative programs included in Phenix? 2) How to fix the error and run MTZFIX? I'm currently using the new ccp4 v7.1, in macOS v10.14.5. Best regards, Joao Ramos To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/wa.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Questions regarding MTZFIX and EDSTATS
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 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, while > attempting to run the Phenix output mtz file in MTZFIX, I receive an error > message saying: "Cannot open environ.def". > > My questions are: > 1) Is the way to go from the Phenix refinement output files to EDSTATS > described earlier correct? Are there alternative programs included in > Phenix? > 2) How to fix the error and run MTZFIX? > > I'm currently using the new ccp4 v7.1, in macOS v10.14.5. > > Best regards, > Joao Ramos > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/wa.exe?SUBED1=CCP4BB&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Question about Refmac
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 about the program "dataman" from the usf suite which could help with this but found it very complicated. Do you have any advice to solve this? or would you recommend any other program? Thank you in advance To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Question about Refmac
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 be be Pmmm or P4mm if a(Pmmm) ~ b(P). ) then you could assign freer flags in the higher symmetry group and extend then to the lower... What is your cell, and do you know the NCS operators? Eleanor On Mon, 15 Jun 2020 at 16:54, wrote: > 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 about the program "dataman" from the usf suite which could help > with this but found it very complicated. > > Do you have any advice to solve this? or would you recommend any other > program? > > > Thank you in advance > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Questions regarding MTZFIX and EDSTATS
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 input filename was not typed correctly or the path was not specified correctly if it's in another directory. Anyway you really shouldn't be calling the MTZFIX or EDSTATS programs directly. Using the Perl script 'edstats.pl' http://www.ccp4.ac.uk/dist/checkout/edstats/edstats.pl is much easier. It should be in your path after running the CCP4 setup script. Cheers -- Ian On Mon, 15 Jun 2020 at 18:41, Joao Ramos wrote: > Dear Ian, > > Thanks for the reply! > > I've sourced the setup script, but now I get a 'cannot open file' error > message (screenshot attached) when trying to run MTZFIX. > > Best regards, > Joao Ramos > > Ian Tickle escreveu no dia segunda, 15/06/2020 à(s) > 16:57: > >> >> 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 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, while >>> attempting to run the Phenix output mtz file in MTZFIX, I receive an error >>> message saying: "Cannot open environ.def". >>> >>> My questions are: >>> 1) Is the way to go from the Phenix refinement output files to EDSTATS >>> described earlier correct? Are there alternative programs included in >>> Phenix? >>> 2) How to fix the error and run MTZFIX? >>> >>> I'm currently using the new ccp4 v7.1, in macOS v10.14.5. >>> >>> Best regards, >>> Joao Ramos >>> >>> -- >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/wa.exe?SUBED1=CCP4BB&A=1 >>> >> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Coot labels
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 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Coot labels
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 0.9 are quite different (the patch for that is 526k lines). For a fresh install, atoms *are* labelled by default as you move from one residue to the next. It seems that you have some how turned that off. set_label_on_recentre_flag(1) Use Calculate -> Scripting -> Python or put it in a preferences startup script, say xenops.py Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Question about Refmac
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&L=CCP4BB&O=D&P=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 us that over-fitting is due to measurement errors and there is no reason to expect these to be correlated for NCS-related reflections. However, as you have probably found out by now, you can make an R-free set in shells using the reflection file editor in phenix. From memory you may also need to make sure that you use a CCP4-style R-free flag (i.e. the free-set reflections should be flagged zero) if you are going to use Refmac. There's a screenshot here: http://u.cubeupload.com/jbcooper/202006160114071280x8.png Hope this helps!On Monday, 15 June 2020, 17:42:15 BST, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: 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 be be Pmmm or P4mm if a(Pmmm) ~ b(P). ) then you could assign freer flags in the higher symmetry group and extend then to the lower... What is your cell, and do you know the NCS operators?Eleanor On Mon, 15 Jun 2020 at 16:54, wrote: 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 about the program "dataman" from the usf suite which could help with this but found it very complicated. Do you have any advice to solve this? or would you recommend any other program? Thank you in advance To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
