[ccp4bb] Antechamber cannot determine atomic charge for Mn2+ to run PDB2PQR-APBS

Dear all, I am trying to generate the electrostatic surface for a protein that contains Mn in the 2+ state in its active site. I've tried to go about it in two ways but keep getting stuck. 1. If I use chimera or Pymol to use the PDB2PQR-APBS plug in, it cannot find GAFF type for Mn2+ so it canno

Re: [ccp4bb] Luzzati plots and estimates of coordinate errors in models

ucr.org/paper?buy=yes&cnor=vg5015&showscheme=yes&sing=yes> >> See also:- >> sciencedirect.com >> <https://www.sciencedirect.com/science/article/pii/S2665928X2300017X> >> <https://www.sciencedirect.com/science/article/pii/S2665928X2300017X> >>

[ccp4bb] Luzzati plots and estimates of coordinate errors in models

Hello, I am looking to estimate coordinate errors in my models before depositing them. Is there anything that automatically generates Luzzati plots for the pdb models and estimate coordinate errors? Thanks in advance! Medhanjali ##

Re: [ccp4bb] Way to resolve Ramachandra outliers in a structure

l 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 i

[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 Medh

Re: [ccp4bb] A challenging MR problem

nd 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 >&g

[ccp4bb] A challenging MR problem

, Medhanjali Dasgupta 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 mai

[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