Hi,
I'm attempting to run ResolveCryoEM, and I have a few questions
about setting the job up correctly. My half-maps were reconstructed with C4
symmetry to ~2 Å (CryoSPARC), and my model was refined into the density
with the "Ncs constraints" box checked (Phenix RSR). My sample is a
protein-DNA complex (4 copies of a protein protomer, 4 copies of a
ssDNA protomer). I'm running Phenix 1.21.1-5286-000 (the latest
installation provided by SBGrid).
In the first version of the run, I only supplied the two half-map files and
a seq file.
Question 1:
My current seq.dat file looks like this (as mentioned previously in the
forum, I was getting errors when I tried the version where my seq.dat file
has only 1 protomer and I set the number of copies to 4 in the GUI field
"Copies of sequence file in map"):
>protein_protomer1
MGSRSG...
>protein_protomer2
MGSRSG...
>protein_protomer3
MGSRSG...
>protein_protomer4
MGSRSG...
>DNA_protomer1
AAAAAA
>DNA_protomer2
AAAAAA
>DNA_protomer3
AAAAAA
>DNA_protomer4
AAAAAA
Currently, Phenix is reading in the "AAAAAA" as a protein chain ("Chain
types considered: PROTEIN"). How do I tell Phenix that those are
deoxyadenosines, not alanines?
Question 2:
Is Phenix automatically detecting the C4 symmetry and density-modifying
with that constraint? The resulting map looks symmetric in the noise, but I
don't see anything in the log suggesting that it knows the symmetry. Here
are some settings from the log that seem relevant (all left to default
values):
refine_symmetry_in_denmod = True
use_symmetry_in_denmod = False
symmetry_in_denmod_last_cycle_only = True
fraction_ncs = None
I attempted to supply a symmetry file (the output of a MapSymmetry job on
the full map = "symmetry_from_map.ncs_spec"), but the file fails to load
into the input ("Phenix error: Phenix did not recognize the file type for
****/symmetry_from_map.ncs_spec").
Question 3:
A part of my protein is disordered and does not appear in the cryo-EM
density (and was thus left unmodeled). Is it correct to leave that piece
out of the seq.dat file?
Question 4:
If I include a model in the input, Phenix demands a symmetry file, but I
couldn't get my symmetry file to load as explained above. What is the
symmetry file supposed to look like?
Thank you!
-Josh
