A bit late, I know, but a bit more googling gave me this site which I don't think has been mentioned so far:
http://old.protein.bio.unipd.it/mobi/ Given the pdb code, it is a one click job to get a pdb file with the "B-factors changed to averaged Scaled Distance x 100" and the resulting picture (attached) looks about right, I think/hope. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent with ProtonMail Secure Email. ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Thursday, 27 May 2021 08:48, Harry Powell - CCP4BB <hrp-ccp...@virginmedia.com> wrote: > Hi Jon > > The RMSD data (also NOEs, chemical shifts, etc) are not in the original PDB so I would have to calculate them - which takes me to my original question! > > Harry > > > On 26 May 2021, at 17:22, Jon Cooper jon.b.coo...@protonmail.com wrote: > > Hello Harry, > > Looking at: > > http://www.mcgnmr.mcgill.ca/ProtSkin/ > > It says: "If your input is a plain file containing your scalar data to map, such as heteronuclear NOE or chemical shift differences, ensure the first column in your file contains residue numbers and the second column contains the values to map, then click the Browse button to retrieve this file and select "Plain list of scores" > > If you can get the residue number and rmsd data into columns in a file, it should map them onto a pdb file for one monomer as pseudo-B-factors. > > HTH, Jon.C. > > Sent from ProtonMail mobile > > -------- Original Message -------- > > On 26 May 2021, 16:51, Harry Powell - CCP4BB < hrp-ccp...@virginmedia.com> wrote: > > Yes, Jon, but I was hoping I wasn’t the first person to ever want this… > > Harry > > > > > On 26 May 2021, at 16:34, Jon Cooper 0000488a26d62010-dmarc-requ...@jiscmail.ac.uk wrote: > > > The hard bit is to get the rmsd's into the B-factor column, but it shouldn't stretch you too much, Harry ;- > > > There is ProtSkin on the web which does something similar with sequence alignments. > > > Sent from ProtonMail mobile > > > -------- Original Message -------- > > > On 26 May 2021, 16:28, Harry Powell - CCP4BB < 0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > > Hi Jurgen > > > NMR structures don’t appear to have B_factors, or at least not meaningful ones (e.g. in 2kv5 they’re all 0.00…). > > > thanks for the response, though > > > Harry > > > > > > > On 26 May 2021, at 16:21, Jurgen Bosch jxb...@case.edu wrote: > > > > How about color by B-factor and look for the cold areas and hot areas? > > > > Jürgen > > > > > > > > > On May 26, 2021, at 11:04 AM, Harry Powell - CCP4BB 0000193323b1e616-dmarc-requ...@jiscmail.ac.uk wrote: > > > > > Hi > > > > > Given that there are plenty of people on this BB who are structural biologists rather than “just” crystallographers, I thought someone here might be able to help. > > > > > If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of structures that fit the NOEs, is there a tool available that will give me some idea about the bits of the structure that do not vary much (“rigid”) and the bits that are all over the place (“flexible”)? > > > > > Would superpose or gesamt be a good tool for this? Ideally I’d like something that could add a figure to the B columns in a PDB file so I could see something in QTMG (or PyMol if forced…) or do other useful things with the information. > > > > > Harry > > > > > ######################################################################## > > > > > 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/ > > > > > > ######################################################################## > > > 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 </hrp-ccp...@virginmedia.com> ######################################################################## 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/
