[ccp4bb] Quantifying electron density inside of a given volume
Dear All, I would like to quantify electron density inside of positive Fo-Fc blobs in active sites of multiple protomers in the map and compare them. I am aware that I can interpolate maps and obtain density values at coordinate points using either MapMan, Chimera or Coot, but I would like to know if there is a tool that would let me designate a sphere of a certain volume and calculate total electron density inside it? Best Regards, Neno 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] PDB file secondary structure annotations
Dear All, I noticed that files available in the Protein Data Bank contain secondary structure information which allows for them to be imported in a program such as BioRender in order to make structural figures. However, the PDB files generated by PHENIX for structures that I haven't deposited yet do not contain such information so BioRender displays them as coils. Is there an easy way to add secondary structure information to a PDB file? Best Regards, Neno 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] Coot/Phenix.refine C-terminus issue
Dear All, Thank you so much for the suggestions. There was indeed a TER in my PDB file and removing it solved the problem. I was using Coot 0.8.9.2. Best Regards, Nen On Thu, Feb 18, 2021 at 11:07 AM Paul Emsley wrote: > On 18/02/2021 15:21, Neno Vuksanovic wrote: > > > > I've been having an issue when manually adding C-terminal residue in > Coot (I add a terminal residue, then > > add OXT atom, and perform real space refinement). The residue links the > previous one properly and the > > density matches it well, but after refining in Phenix.refine, the > residue is unconnected from the rest of > > the chain. The log file does not mention having any issues with it. Do I > need to change the linking settings > > in Phenix.refine and what could be causing the issue? > > > > Why don't you tell us which version of Coot that you're using? > > Old Coots used to not properly handle TER records on chain extension. > Maybe it's that. > > Paul. > > > > 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/
[ccp4bb] Coot/Phenix.refine C-terminus issue
Dear All, I've been having an issue when manually adding C-terminal residue in Coot (I add a terminal residue, then add OXT atom, and perform real space refinement). The residue links the previous one properly and the density matches it well, but after refining in Phenix.refine, the residue is unconnected from the rest of the chain. The log file does not mention having any issues with it. Do I need to change the linking settings in Phenix.refine and what could be causing the issue? Best regards, Neno 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/
