Abihilasha,
Suggesting the files are in your local folder, you could read R values from PDB
file itself. I have made small python script (in attachment) that will read
files in a folder and output R/Rfree values to the terminal.
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import glob
import re
for pdb_filename in glob.glob('*pdb'):
R_w = ''
R_free = ''
with open(pdb_filename) as f:
for line in f:
if line.startswith('REMARK 3'):
res = re.search('3 R VALUE\s+\(WORKING SET\) : (\S+)',line)
if res and res.group(1):
R_w = res.group(1)
res = re.search('3 FREE R VALUE\s+: (\S+)',line)
if res and res.group(1):
R_free = res.group(1)
print('{}\tRw {} Rfree {}'.format(pdb_filename,R_w,R_free)) # format as you wish
--
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
KU Leuven O&N2
mobile: +32 484 38 26 01
> On 1 Jun 2022, at 08:17, Robbie Joosten <[email protected]> wrote:
>
> Depending on how you process the model, the reported R-value becomes invalid.
> So you need to get it from the PDB entry before processing or recalculate it
> with respect to the experimental data.
>
> Cheers,
> Robbie
>
>> -----Original Message-----
>> From: CCP4 bulletin board <[email protected]> On Behalf Of
>> Abhilasha Thakur
>> Sent: Wednesday, June 1, 2022 07:52
>> To: [email protected]
>> Subject: [ccp4bb] Regarding R factor value
>>
>> Hello!!
>>
>> I have 1500 processed PDB files and I need the R factor value for each pdb
>> files. How I get this R factor value, because it's there initially but, after
>> processing, some data from PDB is deleted. Manually to get R factor is not
>> possible.
>>
>> Please suggest me, how to get this R factor value for the entire PDB ids.
>>
>> ________________________________
>>
>>
>> To unsubscribe from the CCP4BB list, click the following link:
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>
>
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