If you have PyMOL installed, you can paste the bash function below into your
.bashrc file, enter 'source .bashrc', and then enter 'bu PDB-ID'.
All that you have to remember a month from now is 'bu'.
Otherwise, you can replace the pymol command with one of the other commands
that have been suggested and replace the filename stem with $1.
bu()
{
echo "Write out the biological unit for a PDB file from PyMOL."
if [ $# -lt 1 ]; then
echo 1>&2 "$0: not enough arguments"
echo "Supply the PDB-ID."
echo "Example: bu 3nd4"
return 2
elif [ $# -gt 1 ]; then
echo 1>&2 "$0: too many arguments"
echo "Supply the PDB-ID."
echo "Example: bu 3nd4"
fi
pymol -c -d "fetch $1,type=pdb1;set all_states,on;save $1bu.pdb,state=0"
}
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
University of Oklahoma Health Sciences Center
________________________________________
From: CCP4 bulletin board [[email protected]] on behalf of Marcin Wojdyr
[[email protected]]
Sent: Wednesday, May 26, 2021 2:10 AM
To: [email protected]
Subject: [EXTERNAL] Re: [ccp4bb] writing coordinates of full biomol into one
(PDB) file
another one:
gemmi convert --assembly=N input.pdb output.pdb
On Wed, 26 May 2021 at 07:30, Frank von Delft
<[email protected]> wrote:
>
> Thanks for the quick responses! I was looking for a command-line tool
> (should have said). Here's the list:
>
> 1. phenix.pdb.biomt_reconstruction
> 2.
> https://urldefense.proofpoint.com/v2/url?u=http-3A__Makemultimer.py&d=DwIBaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8&s=wMMX-ub8O19NLtJDQdelGfFOni2RMO7EVgZG1XZ1Uu4&e=
> :
> https://urldefense.proofpoint.com/v2/url?u=http-3A__watcut.uwaterloo.ca_tools_makemultimer_docs&d=DwIBaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8&s=XQ41GNcbJlsckrDR76D9n7YD0eKVop24nJpUYi5pTPA&e=
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__watcut.uwaterloo.ca_tools_makemultimer_docs&d=DwIBaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8&s=XQ41GNcbJlsckrDR76D9n7YD0eKVop24nJpUYi5pTPA&e=
> >
> 3. Quat in pymol:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_BiologicalUnit_Quat&d=DwIBaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8&s=K4dJU4Mq8Mi4SgQB6UFnQcTzfnkCfius8_QsRmWs_ZQ&e=
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_BiologicalUnit_Quat&d=DwIBaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8&s=K4dJU4Mq8Mi4SgQB6UFnQcTzfnkCfius8_QsRmWs_ZQ&e=
> >
> 4. BiologicalUnit in pymol:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_BiologicalUnit&d=DwIBaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8&s=yOPGY2fznON_wKdKHEXsGbfEj9dij-0NHHTuqHdH6tM&e=
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_BiologicalUnit&d=DwIBaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8&s=yOPGY2fznON_wKdKHEXsGbfEj9dij-0NHHTuqHdH6tM&e=
> >
>
> (CCP4bb is amazing....)
>
> Frank
>
> On 25/05/2021 20:44, Frank von Delft wrote:
> > Hello all - this presumably has a really simple solution:
> >
> > For a PDB file with a (correct) biomolecular assembly record (REMARK
> > 350), what program do I use to generate and write out the coordinates
> > of the biomolecular assembly (or one of them).
> >
> > Thanks
> > Frank
> >
> > ########################################################################
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