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Dear All,
Thanks everyone for the suggestions and clarifications. As Eleanor and Garib wrote, I cannot find real differences in map quality or statistics after refinement depending if I set or
not the resolution edges.
This is more a matter of how the remarks in the pdb are recorded for validation/deposition for which a big red exclamation mark is pointing to the mismatch values. This is happening
only when the ccp4i2 interface is used for refmab but not with ccp4i. Maybe a script problem for the pdb remark data extrapolation?
Also if I manually set the resolution I found that the pdb remark is still not correct exactly (in ccp4i2). But when I ran with the same files a refmac refinement using the ccp4i interface,
everything is running smoothly and perfectly with no “error” at all.
Just as an open question: As seems more a pdb file writing issue than a refinement problem, correcting the pdb file manually writing with a text editor in in the remark the exact low
resolution, could be also a fix or can be considered as faking the file? ( I didn’t test it yet, just mornings idea…)
All the best,
Roberto
-------------------------------
Dr. Roberto Orru, Ph.D.
Insitute of molecular biology (IMB) and
JGU - Institut für Molekulare Physiologie (AG Prof. Wolf)
Mainz, Germany
From: CCP4 bulletin board [mailto:[log in to unmask]]
On Behalf Of Garib Murshudov
Sent: Sunday, March 18, 2018 5:14 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] Resolution mismatch aimless/refmac
On 18 Mar 2018, at 16:02, Eleanor Dodson <[log in to unmask]> wrote:
Does it matter? The refinement will only use observed reflections.
It should not matter for refinement and map calculations (needs to be checked carefully). However it does matter for deposition when multiple entries are analysed and the PDB deposition software (rightly so) says that you have information
mismatch. And it confuses users and most of all it confuses deposition. It would confuse me.
Best wishes,
Garib