This even seems to have a”batch” mode (similar to the well-known homology modelling server Phyre2) that might accept a zip file containing multiple PDBs. If it does, and if it will take my ~700 PDBs, then that would save me a little bit of scripting.
Harry > On 27 May 2021, at 22:03, Jon Cooper > <[email protected]> wrote: > > 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. > [email protected] > > Sent with ProtonMail Secure Email. > > ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ > On Thursday, 27 May 2021 08:48, Harry Powell - CCP4BB > <[email protected]> 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 [email protected] > 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 < > [email protected]> 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 > [email protected] 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 < > [email protected]> 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 [email protected] > 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 > [email protected] 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 > > </[email protected]> > > ######################################################################## > > 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/<mobi3.png> ######################################################################## 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/
