I've done that at 6 Å with a large X-ray structure a long while ago and I think the trick was to define your own groups, by way of example snipped from the .eff file:

adp {
  individual {
    isotropic = None
    anisotropic = None
  }
  group_adp_refinement_mode = one_adp_group_per_residue \
                              two_adp_groups_per_residue \
                              *group_selection
      group = chain A
      group = chain B
      group = chain C
      group = chain D
      tls = None
  }
}

I wonder if you could define equivalent TLS groups ?

Phil Jeffrey
Princeton


On 12/16/24 9:39 AM, Derek Logan wrote:
Hi everyone,

I would like to do a quick rigid-body refinement of a model against a low resolution (6 Å) cryo-EM map. The model consists of four tetramers and I want to refine each tetramer as a rigid body, either with one (anisotropic?) ADP per tetramer or at the most one per chain. I haven't yet found a good way to do this. With phenix.refine the default is one ADP per residue and I can't see how to change that behaviour (at least through the Phenix GUI). I tried Servalcat but I can't see a way to restrict it to rigid body only. Given more time, I hope to reach a fuller understanding of each program, but I need to solve the immediate problem in the next couple of days (what with Christmas coming up...) Any suggestions?

I have also understood that the best practice is to refine against the unsharpened map, correct?

Thanks
Derek
_____________________________________________________
*Derek Logan*
Professor | Biochemistry and Structural Biology
Centre for Molecular Protein Science
Lund University, Box 124, 221 00 Lund, Sweden
www.cmps.lu.se













------------------------------------------------------------------------

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cpjeffrey%40PRINCETON.EDU%7C37784ce6049d4d47149208dd1ddf7d36%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C638699568070017907%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=pfsZH9B9TorhIglIP4cqlYKntYwCUex0hVQfy7YZVl4%3D&reserved=0>


########################################################################

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/

Reply via email to