Hi all,
Huw was correct, there is potential to delete temp files that the script did
not create that I had not considered. I've changed "rm temp* "$cif_file" 2>
/dev/null" to "rm temp.mtz temp.pdb "$cif_file" 2> /dev/null"
Best,
Donald
On Jun 15, 2015, at 3:56 PM, Huw Jenkins wrote:
>
>> O
Hi Huw,
$cif_file is a variable that holds the sf-cif file downloaded from www.RCSB.org
see line 126 of the script
>> cif_file="$pdb_id-sf.cif"
After converting the cif to an MTZ, the cif is no longer necessary. That is why
the script deletes it (clean up).
Best,
Donald
On Jun 15, 2015,
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> On 15 Jun 2015, at 20:00, Donald Damian Raymond wrote:
>
> Hi,
>
> I've written a bash script that does just what you want.
and potentially deletes a lot of files it didn’t create...
#cleanup
rm temp* "$cif_file" 2> /dev/null
Huw
Hi,
I've written a bash script that does just what you want.
Find it here -->
https://github.com/donaldraymond/crystallography-scripts/blob/master/PDB_data.sh
Run the script with a PDB ID. Like this "PDB_data 1yks"
The script downloads the PDB and sf.mmCIF files from the PDB. It then converts
Thank you all.
I got several options, and I am using phenix pdb sf-cif to mtz protocol.
Thanks once again for your help.
On Mon, Jun 15, 2015 at 1:38 PM, Shibom Basu wrote:
> Well, you can also try sf-convert program from PDB to convert sf.cif file
> to any other format mtz, or cns whatever you
Well, you can also try sf-convert program from PDB to convert sf.cif file
to any other format mtz, or cns whatever you want.
On Mon, Jun 15, 2015 at 10:52 AM, StrBio wrote:
> Hi All,
>
> How one can convert pdb-sf.cif file downloaded from PDB to a workable
> format for further refinement (may
Why not just use CIF files directly? Note, most Phenix tools accept input
model and data in cif format (and can write them back in cif too).
Pavel
On Mon, Jun 15, 2015 at 10:52 AM, StrBio wrote:
> Hi All,
>
> How one can convert pdb-sf.cif file downloaded from PDB to a workable
> format for furt
Dear StrBio,
you can use the command line tool cif2mtz. If the file is rather recent,
and you are only interested in the first block, you can type
cif2mtz hklin yourciffile.sf hklout yourmtzfile.mtz << eof
end
eof
There are some subtleties that you may only convert correctly after
looking int
Or "Convert to/modify/extend MTZ" in "Reflection Data Utilities”. You can
“Import reflection file in mmCIF format and create MTZ file”.
// Johan
> On Jun 15, 2015, at 13:58, Schubert, Carsten [JRDUS]
> wrote:
>
> Phenix has a menu item for this: Reflection Tools -> Import CIF structure
> fa
Phenix has a menu item for this: Reflection Tools -> Import CIF structure
factors
HTH
Carsten
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of StrBio
Sent: Monday, June 15, 2015 1:53 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] workable data from PDB sf-ci
Hi All,
How one can convert pdb-sf.cif file downloaded from PDB to a workable
format for further refinement (may be by phenix or Refmac) of the deposited
structure?
I need help.
Hi Colin,
You may have tried this but just in case you haven't, perhaps you should try put a few water molecules in the blob and refine? After that the geometry of the water arrangement may give you a better idea what the blob represents. It worked for me in quite
a few cases.
Cheers,
Dear Colin,
I think the residual blob usually represents a combination of different
chemical entities.
I think the correct thing to do is to try to dock all the possible chemical
entities you have in your crystallisation buffer, purification buffers and
things that have carried through in an
Ursula,
After extensive testing, I have found out that in most cases pH changes
during flash freezing does
not pose a problem. In some cases it can be beneficial. I encourage you
to try +/- 2 pH units
from your crystallization pH.
Sometimes a sub-optimal pH is chosen just because the cryst
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Dear Ursula,
just a stupid question: did you try freezing a crystal? There are quite a few
crystal structures in the PDB with (a) bound Tris molecule(s), so quite some
crystals were not destroyed by a pH shock during freezing.
If you tried freezing and saw no/bad diffraction, you should try to
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