real space refinement of 3Fe4S cluster
Hello Phenix BB, I'm attempting to refine a model with a 3Fe4S cluster into a medium resolution cryoEM map. Every time I run a refinement job, the cluster comes out all wonky, as in the attached image. I found one previous thread on this topic and when I played with the "superpose_ideal_ligand" setting, I got an error stating that the F3S residue is missing atoms. Should I just generate a restraint file? Any advice on how others have handled this welcome. Best, Amy __________________________________________________ Amy Fernandez Berger Labhttps://berger.med.jhmi.edu/ - The Johns Hopkins University School of Medicine PhD Candidate - Program for Molecular Biophysicshttps://pmb.jhu.edu/
Hi Amy, first step, to help you we need to reproduce the problem on our end. For that, we need all input files, as well as the *.eff and *.log files. Also, please send us the refined model and describe what’s not right with it more precisely than just “comes out all wonky.” We will take it from there! All the best! Pavel On 12/30/25 18:21, Amy Fernandez via phenixbb wrote:
Hello Phenix BB,
I'm attempting to refine a model with a 3Fe4S cluster into a medium resolution cryoEM map. Every time I run a refinement job, the cluster comes out all wonky, as in the attached image. I found one previous thread on this topic and when I played with the "superpose_ideal_ligand" setting, I got an error stating that the F3S residue is missing atoms. Should I just generate a restraint file? Any advice on how others have handled this welcome.
Best, Amy
The atom names of F3S (and SF4) have been switched around at least once since it was introduced (or perhaps they weren't standardized before). Using the current library with a cluster from an old file, the restraints will pull it all out of shape- "wonky" as you say. Generate a cluster with modern param (coot get ligad?), superimpose on your input structure, and see if the atom names are the same, if not rename them. And if you explicitly define the links to amino acids, be sure they are revised where necessary to fit the new names. Here is what worked for me when I was refining an old structure in a new phenix about 2 years ago: SF4: FE2 -> FE3 FE3 -> FE2 S2 -> S3 S3 -> S2 F3S: FE1 -> FE4 FE3 -> FE1 FE4 -> FE3 S1 -> S2 S2 -> S4 (S3 -> S3) S4 -> S1 good luck, eab Amy Fernandez via phenixbb wrote on 12/30/2025 9:21 PM:
Hello Phenix BB,
I'm attempting to refine a model with a 3Fe4S cluster into a medium resolution cryoEM map. Every time I run a refinement job, the cluster comes out all wonky, as in the attached image. I found one previous thread on this topic and when I played with the "superpose_ideal_ligand" setting, I got an error stating that the F3S residue is missing atoms. Should I just generate a restraint file? Any advice on how others have handled this welcome.
Best, Amy __________________________________________________ Amy Fernandez Berger Labhttps://berger.med.jhmi.edu/ - The Johns Hopkins University School of Medicine PhD Candidate - Program for Molecular Biophysicshttps://pmb.jhu.edu/
_______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s
Good to know about these atom name discrepancies in older structures, thank you Edward! I wanted to add that, having ruled out a wrong naming convention, you might still get seemingly wrong inter-atomic distances in metal clusters likely due to radiation damage. This is discussed in this recent paper on a high-resolution cryoEM structure of photosystem II: https://doi.org/10.1126/science.adn6541 "the metal-metal, metal-oxo, and metal-ligand distances are elongated by up to 0.2, 0.4, and 0.2 Å, respectively (figs. S4 and S5 and table S2). This aligns with previous observations that high-valent metal centers are rapidly reduced by electron beam exposure during cryo-EM data collection (29, 30)." This could happen to iron-sulfur clusters too. Cheers, Guillaume On 12/31/25 6:19 AM, Edward Berry wrote:
The atom names of F3S (and SF4) have been switched around at least once since it was introduced (or perhaps they weren't standardized before). Using the current library with a cluster from an old file, the restraints will pull it all out of shape- "wonky" as you say. Generate a cluster with modern param (coot get ligad?), superimpose on your input structure, and see if the atom names are the same, if not rename them. And if you explicitly define the links to amino acids, be sure they are revised where necessary to fit the new names. Here is what worked for me when I was refining an old structure in a new phenix about 2 years ago: SF4: FE2 -> FE3 FE3 -> FE2 S2 -> S3 S3 -> S2 F3S: FE1 -> FE4 FE3 -> FE1 FE4 -> FE3 S1 -> S2 S2 -> S4 (S3 -> S3) S4 -> S1 good luck, eab
Amy Fernandez via phenixbb wrote on 12/30/2025 9:21 PM:
Hello Phenix BB,
I'm attempting to refine a model with a 3Fe4S cluster into a medium resolution cryoEM map. Every time I run a refinement job, the cluster comes out all wonky, as in the attached image. I found one previous thread on this topic and when I played with the "superpose_ideal_ligand" setting, I got an error stating that the F3S residue is missing atoms. Should I just generate a restraint file? Any advice on how others have handled this welcome.
Best, Amy __________________________________________________ Amy Fernandez Berger Labhttps://berger.med.jhmi.edu/ - The Johns Hopkins University School of Medicine PhD Candidate - Program for Molecular Biophysicshttps://pmb.jhu.edu/
_______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s
_______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s
VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
participants (4)
-
Amy Fernandez -
Edward Berry -
Guillaume Gaullier -
Pavel Afonine