Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

2021-05-26 Thread Mooers, Blaine H.M. (HSC) 
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 [CCP4BB@JISCMAIL.AC.UK] on behalf of Marcin Wojdyr 
[woj...@gmail.com]
Sent: Wednesday, May 26, 2021 2:10 AM
To: CCP4BB@JISCMAIL.AC.UK
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
 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
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIBaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8&s=Zc5y9vtC54wj1EQkTlPSy1gDJXFDHGKDWtpCUt0pGWs&e=
> >
> > This message was issued to

Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

2021-05-26 Thread Marcin Wojdyr 
another one:

gemmi convert --assembly=N input.pdb output.pdb


On Wed, 26 May 2021 at 07:30, Frank von Delft
 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. Makemultimer.py: http://watcut.uwaterloo.ca/tools/makemultimer/docs
> 
> 3. Quat in pymol: https://pymolwiki.org/index.php/BiologicalUnit/Quat
> 
> 4. BiologicalUnit in pymol:
> https://pymolwiki.org/index.php/BiologicalUnit
> 
>
> (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
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> >
> > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> > available at https://www.jiscmail.ac.uk/policyandsecurity/
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

2021-05-25 Thread Frank von Delft 
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. Makemultimer.py: http://watcut.uwaterloo.ca/tools/makemultimer/docs 

3. Quat in pymol: https://pymolwiki.org/index.php/BiologicalUnit/Quat 

4. BiologicalUnit in pymol: 
https://pymolwiki.org/index.php/BiologicalUnit 



(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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Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

2021-05-25 Thread Pavel Afonine 
Hi Frank,

phenix.pdb.biomt_reconstruction command should do it.

Pavel

On Tue, May 25, 2021 at 12:44 PM Frank von Delft <
frank.vonde...@cmd.ox.ac.uk> 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
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>



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Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

2021-05-25 Thread Paul Emsley 
On Tue, 2021-05-25 at 20:04 +, Frank Von Delft wrote:
> Yes I thought so too, but discovered I am too stupid to decode the highly 
> parsimonious manual on the ccp4 pages. 
> 

The first thing that I'd try (using Coot) is Calculate -> PISA -> Assemblies...



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Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

2021-05-25 Thread Debanu Das 
And to run it as a single command line option:
http://legacy.ccp4.ac.uk/html/pisa.html

On Tue, May 25, 2021 at 1:07 PM Debanu Das  wrote:

> Easy way to do it online: https://www.ebi.ac.uk/pdbe/pisa/
> or here: http://www.ccp4.ac.uk/pisa/
>
> Best,
> Debanu
>
> On Tue, May 25, 2021 at 1:04 PM Frank Von Delft <
> frank.vonde...@cmd.ox.ac.uk> wrote:
>
>> Yes I thought so too, but discovered I am too stupid to decode the highly
>> parsimonious manual on the ccp4 pages.
>>
>> What I need is a command line that always works. Presumably that's a well
>> defined problem...?
>>
>>
>>
>> Sent from tiny silly touch screen <http://www.9folders.com/>
>> --
>> *From:* Debanu Das 
>> *Sent:* Tuesday, 25 May 2021 20:55
>> *To:* Frank Von Delft
>> *Cc:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* Re: [ccp4bb] writing coordinates of full biomol into one
>> (PDB) file
>>
>> Hi Frank,
>> PISA is your friend here.
>> Thanks,
>> Debanu
>>
>> On Tue, May 25, 2021 at 12:44 PM Frank von Delft <
>> frank.vonde...@cmd.ox.ac.uk> 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
>>>
>>> 
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>>
>>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
>>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
>>> available at https://www.jiscmail.ac.uk/policyandsecurity/
>>>
>>



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Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

2021-05-25 Thread Debanu Das 
Easy way to do it online: https://www.ebi.ac.uk/pdbe/pisa/
or here: http://www.ccp4.ac.uk/pisa/

Best,
Debanu

On Tue, May 25, 2021 at 1:04 PM Frank Von Delft 
wrote:

> Yes I thought so too, but discovered I am too stupid to decode the highly
> parsimonious manual on the ccp4 pages.
>
> What I need is a command line that always works. Presumably that's a well
> defined problem...?
>
>
>
> Sent from tiny silly touch screen <http://www.9folders.com/>
> --
> *From:* Debanu Das 
> *Sent:* Tuesday, 25 May 2021 20:55
> *To:* Frank Von Delft
> *Cc:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] writing coordinates of full biomol into one (PDB)
> file
>
> Hi Frank,
> PISA is your friend here.
> Thanks,
> Debanu
>
> On Tue, May 25, 2021 at 12:44 PM Frank von Delft <
> frank.vonde...@cmd.ox.ac.uk> 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
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
>> available at https://www.jiscmail.ac.uk/policyandsecurity/
>>
>



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Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

2021-05-25 Thread Frank Von Delft 
Yes I thought so too, but discovered I am too stupid to decode the highly 
parsimonious manual on the ccp4 pages.

What I need is a command line that always works. Presumably that's a well 
defined problem...?



Sent from tiny silly touch screen<http://www.9folders.com/>

From: Debanu Das 
Sent: Tuesday, 25 May 2021 20:55
To: Frank Von Delft
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

Hi Frank,
PISA is your friend here.
Thanks,
Debanu

On Tue, May 25, 2021 at 12:44 PM Frank von Delft 
mailto:frank.vonde...@cmd.ox.ac.uk>> 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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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

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Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

2021-05-25 Thread Debanu Das 
Hi Frank,
PISA is your friend here.
Thanks,
Debanu

On Tue, May 25, 2021 at 12:44 PM Frank von Delft <
frank.vonde...@cmd.ox.ac.uk> 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
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>



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[ccp4bb] writing coordinates of full biomol into one (PDB) file

2021-05-25 Thread Frank von Delft 

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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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

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