To add to Tim's references, the algorithms that pdb-redo uses to deal with Rfree and possible bias are described here: https://journals.iucr.org/d/issues/2012/04/00/ba5174/index.htmlIf you happen to have a very small dataset (< 5000 reflections) pdb-redo does 10-fold cross validation and returns Rc
Dear Qixu Cai,
it is a misconception that Rfree was not free anymore. The gap does
not close when you swap the reflections in Rfree set. The 'free'
reflections are freed when you do proper refinement, i.e., when the
value of the target function becomes stationary.
See https://doi.org/10.1107/S090
Dear Robbie and Tim，
Thanks a lot for your reply. I just do not understand that if we can change
the R free set during different rounds of refinement, the gap between Rwork
and Rfree would be small, and Rfree would be meaningless, as R-free set is
not "free".
Best regards,
Qixu Cai
Email: caiq..
Hi Qixu,PDB-REDO tries to have a minimum number test set reflections to reduce the error margin in R-free. As Tim says this is not a problem but if you reach out privately we can change your calculation to use your current testset. That is not recommended though.Cheers,RobbieOn 28 Apr 2023 04:51, Q
Dear Qixu Cai,
the sets do not have to be identical, as long as refinement reaches a
steady state.
Best regards,
Tim
Am 28.04.2023 04:51, schrieb Qixu Cai:
Dear all,
I'm using the PDB-REDO server to refine my structure. I found that
PDB-REDO said that 5% R-free set is too small and it created
Dear all,
I'm using the PDB-REDO server to refine my structure. I found that PDB-REDO
said that 5% R-free set is too small and it created a new R-free set.
Is possible for the PDB-REDO server to keep the original R-free set to make
final Rfree value comparable?
Best regards,
Qixu Cai
Email: cai
Dear BB-ers,
Due to electrical maintenance at our host institute pdb-redo.eu will be
unavailable from 20:00h (Amsterdam) on October 15th to roughly 12:30h on
October 16th. Apologies for the inconvenience.
Best wishes,
Robbie Joosten
#
: CCP4 bulletin board On Behalf Of Joern
> Krausze
> Sent: Friday, May 28, 2021 10:26
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] PDB-REDO question
>
> Dear all,
>
>
> I want to do the following: I want to download several structures from
> PDB-REDO and pipe
Dear all,
I want to do the following: I want to download several structures from
PDB-REDO and pipe them into Refmac5 for re-refinement, replacing the
restraints dictionary of a certain ligand with a customized one. The
refinement settings I want to keep otherwise unchanged. We are talking
a
Dear CCP4bb-ers,
The server room that hosts the PDB-REDO infrastructure will be getting a new
air conditioner soon. This means that PDB-REDO will be unavailable from 20:00h
(CET) on April 18th until the same time on the 19th (give or take). After that
PDB-REDO will be available again, cooler th
Dear BB'ers,
Due to electrical maintenance and testing at the Netherlands Cancer Institute,
the PDB-REDO server and databank will be unavailable on Saturday October 17th
from approximately 6:00h to 16:00h CEST (Amsterdam local time).
Sorry for the inconvenience,
Robbie
###
Hi everyone,Due to major electrical work at our institute, PDB-REDO will be down from Sunday August 16th 20:00h CET to Tuesday August 18th 11:00h CET.Any calculations still running at the start of the downtime will be restarted once we are back online, but feel free to email me to remind me on Tues
gt; Ethan Merritt
> Sent: Tuesday, February 06, 2018 23:59
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] PDB redo and biased/unbiased R-free
>
> On Tuesday, 06 February 2018 17:25:13 Nadia Leloup wrote:
> > Dear all,
> >
> > I was looking at a 3 angstr
On Tuesday, 06 February 2018 17:25:13 Nadia Leloup wrote:
> Dear all,
>
> I was looking at a 3 angstrom structure from 2015 with relatively bad
> statistics, so I decided to look at the pdb-redo of said structure.
> Surprisingly, pdb-redo statistics are even worse.
You say "even worse", but the
Dear all,
I was looking at a 3 angstrom structure from 2015 with relatively bad
statistics, so I decided to look at the pdb-redo of said structure.
Surprisingly, pdb-redo statistics are even worse. As you can see on the
attached picture, the pdb-redo Rfree comes with a caveat:
R-free was consider
dag 20 oktober 2017 19:19
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] PDB-REDO
Hi,
for the past few weeks we have been trying to use the PDB-redo server to
improve our refinement of two different structures. We usually use PHENIX.
Consistently PDB-REDO gives
Hi,
for the past few weeks we have been trying to use the PDB-redo server to
improve our refinement of two different structures. We usually use PHENIX.
Consistently PDB-REDO gives much better stats (Rfree <025 vs 0.28 with PHENIX)
BUT the resulting electron density maps are clearly worse. It l
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