Hi, As far as I recall (and I could well be wrong/not uptodate) Chimera reads the SS description on the input PDB and implements them. So you could perhaps edit the pdb to have the correct descriptions, as you wish. My 2p contribution. Boaz
Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On 17 Aug 2021 15:30, Firdous Tarique <kahkashantari...@gmail.com> wrote: Hi The representation of secondary structures have changed in my model. Helices and sheets are no longer appearing in the form it should be but appearing in the coiled conformation. It all started when I splitted the 40S ribosome into two parts: head and body (In order to make head and body from the 40S subunit, I had deleted a few nucleotides and amino acids in the connecting region.), then I did rigid body fitting in chimera, then saved them separately with respect to map, then opened these coordinates in coot and joined them together (merged) and finally ran real space refinement in Phenix. Now when I am opening the refined pdb in Chimera, while the secondary structures are in their proper shape and form in the body, all have changed into coil-coil conformation in the head of 40S. Is this a problem of Chimera or ChimeraX or something changed in the output of the refinement job due to which this is happening?. Is there any option in Chimera or ChimeraX to fix it ? I remember in Pymol one can assign secondary structures if there is misrepresentation from the original structure. Your suggestions and advice are appreciated. Attached is the model in case someone wants to have a look. Best Firdous ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 On 17 Aug 2021 15:30, Firdous Tarique <kahkashantari...@gmail.com> wrote: Hi The representation of secondary structures have changed in my model. Helices and sheets are no longer appearing in the form it should be but appearing in the coiled conformation. It all started when I splitted the 40S ribosome into two parts: head and body (In order to make head and body from the 40S subunit, I had deleted a few nucleotides and amino acids in the connecting region.), then I did rigid body fitting in chimera, then saved them separately with respect to map, then opened these coordinates in coot and joined them together (merged) and finally ran real space refinement in Phenix. Now when I am opening the refined pdb in Chimera, while the secondary structures are in their proper shape and form in the body, all have changed into coil-coil conformation in the head of 40S. Is this a problem of Chimera or ChimeraX or something changed in the output of the refinement job due to which this is happening?. Is there any option in Chimera or ChimeraX to fix it ? I remember in Pymol one can assign secondary structures if there is misrepresentation from the original structure. Your suggestions and advice are appreciated. Attached is the model in case someone wants to have a look. Best Firdous ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## 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/
