Re: [ccp4bb] Contouring Patterson map?
I use mapslicer -James Holton MAD Scientist On 10/8/2020 2:21 PM, Gloria Borgstahl wrote: What is the best way to display Harker sections... these days? To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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] [EXTERNAL] [ccp4bb] Contouring Patterson map?
Sorry - go back to CCP4i Under maps Calculate patterson ( diff - anom - native - whatever. Click polt harker sections Oh dear That is meant to produce a postscript file but on my new Mac - it doesnt work.. On Sat, 10 Oct 2020 at 16:24, Mooers, Blaine H.M. (HSC) < blaine-moo...@ouhsc.edu> wrote: > Hi Gloria, > > The lack of repsonse to your question sadly suggests that not many people > have made a Harker section recently. > > You could probably make a fancier plot with matplotlib in Pytbon or > Gnuplot, but > I use Map Slicer under the Visuallization pulldown in the ccp4i gui to > make old-fashion contour plots of Harker sections. > > You have to play around with the scale and and other settings to get what > you need, especially if you have a > unit cell angles that not equal to 90 degrees. In such a case, you may > have to spend an hour tweaking these parameters. > If you can live with a bitmap image of the map, you can always take a > snapshot of the image in the gui, which is > not always replicated completely in the exported postscript file. If > needed, you can also edit the postscript file in a text editor. > > Best regards, > > Blaine > > Blaine Mooers, Ph.D. > Associate Professor > Department of Biochemistry and Molecular Biology > College of Medicine > University of Oklahoma Health Sciences Center > S.L. Young Biomedical Research Center (BRC) Rm. 466 > 975 NE 10th Street, BRC 466 > Oklahoma City, OK 73104-5419 > > > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Gloria > Borgstahl [gborgst...@gmail.com] > Sent: Thursday, October 08, 2020 4:21 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [EXTERNAL] [ccp4bb] Contouring Patterson map? > > What is the best way to display Harker sections... these days? > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1< > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1=DwMBaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=qf1Jq5ykHF9fzngXaWeNGRkB1vNwHE1ok-J03SkgEVw=rwG7QDb4VqJ-bZvrEi5dYdDIjYVz8a1aRcm-dlhrKYw= > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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=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] [EXTERNAL] [ccp4bb] Contouring Patterson map?
Hi Gloria, The lack of repsonse to your question sadly suggests that not many people have made a Harker section recently. You could probably make a fancier plot with matplotlib in Pytbon or Gnuplot, but I use Map Slicer under the Visuallization pulldown in the ccp4i gui to make old-fashion contour plots of Harker sections. You have to play around with the scale and and other settings to get what you need, especially if you have a unit cell angles that not equal to 90 degrees. In such a case, you may have to spend an hour tweaking these parameters. If you can live with a bitmap image of the map, you can always take a snapshot of the image in the gui, which is not always replicated completely in the exported postscript file. If needed, you can also edit the postscript file in a text editor. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Gloria Borgstahl [gborgst...@gmail.com] Sent: Thursday, October 08, 2020 4:21 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [EXTERNAL] [ccp4bb] Contouring Patterson map? What is the best way to display Harker sections... these days? To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1=DwMBaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=qf1Jq5ykHF9fzngXaWeNGRkB1vNwHE1ok-J03SkgEVw=rwG7QDb4VqJ-bZvrEi5dYdDIjYVz8a1aRcm-dlhrKYw=> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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] Contouring Patterson map?
What is the best way to display Harker sections... these days? To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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] Contouring Patterson map?
What is the best way to display Harker sections these days? To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
