[ccp4bb] Download link for CCp4i v7 for Windows
Hi! Does somebody have a download link for specifically v7 of CCp4i for Windows? Thanks Medhanjali Dasgupta 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] A challenging MR problem
The data resolution is 2A. I have 16 chains in my model out of which only one of the chains has the "missing" domain modeled. Is there a way to do MR to predict where the missing domains will go in the rest of the chains, based on my solved structure? Thanks for all the helpful suggestions!! M On Wed, Nov 9, 2022 at 3:11 PM Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > Well you could just try the buccaneer pipeline. It would use the phases > from your solved domain and try to fit the missing sequence. What are your > twin fractions? And what is the resolution? > Eleanor > > On Wed, 9 Nov 2022 at 21:06, Tim Gruene wrote: > >> Dear Medhanjali DasGupta, >> unless the resolution is really poor, the quickest try would be shelxe, >> starting from what you already have. It might work at, say, 2.8A >> resolution or better... >> >> Best, >> Tim >> >> On Wed, 9 Nov 2022 14:34:28 -0600 Medhanjali >> DasGupta wrote: >> >> > Hello! >> > My protein structure has a missing domain and I am trying to figure >> > out the best way to model this missing domain using the solved >> > (modeled) fixed core domain? My data is also imperfectly twinned, >> > with 4 twin fractions according to refmac5. >> > >> > Any help/ idea is appreciated! >> > >> > >> > >> >> >> >> -- >> -- >> Tim Gruene >> Head of the Centre for X-ray Structure Analysis >> Faculty of Chemistry >> University of Vienna >> >> Phone: +43-1-4277-70202 >> >> GPG Key ID = A46BEE1A >> >> >> >> 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 > -- Thanks, Medhanjali Dasgupta Postdoctoral Research Scientist Lawrence Berkeley National Laboratory 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] A challenging MR problem
Hello! My protein structure has a missing domain and I am trying to figure out the best way to model this missing domain using the solved (modeled) fixed core domain? My data is also imperfectly twinned, with 4 twin fractions according to refmac5. Any help/ idea is appreciated! -- Thanks, Medhanjali Dasgupta 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] Way to resolve Ramachandra outliers in a structure
Hello all! Is there an easy way to fix the backbone angles in a protein structure to fix the Ramachandran outliers in said structure? Coot has the "Edit backbone torsions" option but wondering if there's any other tools available in coot or elsewhere? Thanks Medhanjali Dasgupta 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] Way to resolve Ramachandra outliers in a structure
Very helpful, thank you so much! Medhanjali On Fri, Mar 3, 2023, 10:48 AM Nicholas Clark wrote: > Hi Medhanjali, > > In Coot, there are two additional options for "automated" correction of > Ramachandran outliers. You can find them under "Calculate". > > For the entire structure in the "Calculate->all molecule" tab, select > Refine/Improve Ramachandran Plot. For a specific region, you can use the > "Calculate->fit loop->fit loop by rama search". These will attempt to fit > to the Ramachandran plot but may still revert during subsequent refinement. > Hope this helps. > > Best, > > Nick Clark > > On Fri, Mar 3, 2023 at 11:24 AM Medhanjali DasGupta < > medhanjalidasgu...@gmail.com> wrote: > >> Hello all! >> >> Is there an easy way to fix the backbone angles in a protein structure to >> fix the Ramachandran outliers in said structure? >> >> Coot has the "Edit backbone torsions" option but wondering if there's any >> other tools available in coot or elsewhere? >> >> Thanks >> Medhanjali Dasgupta >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7C0c5dd5d3f0a54e2f586708db1c03c1f0%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638134574691699402%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=%2F7YAE6U9TmISVU0wejfzs0au9jHB56b8WNRQQxvjP%2BQ%3D=0> >> > > > -- > Nicholas D. Clark (He/Him) > PhD Candidate > Malkowski Lab > University at Buffalo > Department of Structural Biology > Jacob's School of Medicine & Biomedical Sciences > 955 Main Street, RM 5130 > Buffalo, NY 14203 > > Cell: 716-830-1908 > 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/
