ect: [ccp4bb] R free flag
Hello,
I am trying to refine a structure that is deposited in PDB. I have downloaded
the _sigmaa.mtz file from the electron density server.
Trying to run refmac using this mtz file gives me the popup free R label has
not been set.
How can I set free R label in an
Hello,
I am trying to refine a structure that is deposited in PDB. I have
downloaded the _sigmaa.mtz file from the electron density server.
Trying to run refmac using this mtz file gives me the popup free R label
has not been set.
How can I set free R label in an existing mtz file so that af
Dear Lu,
The MTZ file produced at the end of the ARP/wARP protein model
building is created by Refmac and contains the following:
1. New columns created for the built model: (FC, PHIC, FC_ALL,
PHIC_ALL, FWT, PHWT, DELFWT, PHDELWT, FOM, FC_ALL_
Dear Lu Zuokun,
The option you mention "do not use the Free R flag", tells ARP/wARP to do
refinement without using the R-free flags, so it does not seem strange to
me that it would output a file without those labels.
I don't know why this would be a good idea, though, if you want to continue
buil
When you chose the option “Do not use the Free R flag”, then you were telling
Refmac not to use cross-validation and therefore to use all reflections as the
working set.
My experience (doubtless very limited compared to the ARP/wARP developers) is
that it’s significantly better to use the Rfree
Dear Colin and Tim,
But ARPwARP uses REFMAC5 for refinement, does this means that REFMAC5 uses
all reflections as working set?
How to validate that the refinement is not over fit?
Best wishes!
Lu Zuokun
--
卢作焜
南开大学新生物站A202
At 2014-10-20 17:38:58, "Tim Gruene" wrote:
>Dear L
Dear Lu Zuokun,
since you can use the output mtz-file from ArpWarp for model building,
but not for refinement, there is no need to include the Rfree flag in
its output file. Maybe the omission is a deliberate caveat to the users
to pay attention to this.
Best regards,
Tim
On 10/20/2014 04:41 AM,
Dear all,
I was using ARP/wARP in ccp4i, the input mtz file certainly has free R
flag, but the output mzt file doesn't have the free R flag label?
I chose " do not use the Free R flag" in the ARP/wARP GUI. Can anyone tell me
what's wrong with this?
best reagrds!
Lu Zuokun
--
卢作焜
南开大学新生
96.0 46167 N/A 0.1475 0.1741
N/A
Thank you all for your suggestions,
Best wishes,
Vinson
发件人： Ed Pozharski
收件人： CCP4BB@JISCMAIL.AC.UK
发送日期： 2010/10/23 (周六) 12:07:48 上午
主 题： Re: [ccp4bb] R-free flag problem
I must note that it is also
I must note that it is also interesting to know why the sfcheck produced
the R-factor that is twice as high. Of course, the R/Rfree are not
supposed to match precisely (as I recall, sfcheck uses Babinet bulk
solvent correction which is presumably inferior to the mask-based
approach), but 28.6 vers
Dear Vinson,
I would still be interested about what was the cause of the missing R-free flags
and how you resolved it (I hope I did not miss an email).
Kind regards, Tim
On Fri, Oct 22, 2010 at 02:33:03PM +0800, Vinson LIANG wrote:
>
>
> Dear all,
>
>
>
>
> Thank you very much for your su
Dear all,
Thank you very much for your suggestions.
I try Pavel's easy method. Hopefully, the result from phenix.model_vs_data
would be enough for PDB.
Best wishes,
Vinson
发件人： Pavel Afonine
收件人： PHENIX user mailing list
抄 送： Vinson LIANG
发送日期： 2010/10/22 (周五) 12:44:58 上
Dear Vinson, Liang
have a look at the penultimate table from
mtzdmp your_mtz_file.mtz
where your_mtz_file.mtz is the mtz-file you are using to deposit/ for
refinement.
That second last table lists the columns which are present in your mtz-file,
their types and names and should give a clue what
Dear all,
Recently I deposited a structure to PDB. However, I was told
>> The R value of SF check are different from your reported value.
>>
>> R work in SF check = 0.2859
>> your reported R work = 0.1474
>> Also there are no R free flags in your sending files, but you reported R
>> fre
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