Re: [ccp4bb] Current "best" software for computing volumes of active sites

[Christian Roth]

Well, I don't know if that is the newest appropriate piece of software, but
pdbsum does automatic calculation of clefts using MOLE I think. It does
provide jmol and rasmol scripts and volume and surface calculations.

Cheers
Christian

On Thu, Apr 4, 2019 at 8:24 AM Fred Vellieux 
wrote:

> Hi CCP4BBers,
>
> With software constantly changing, new versions arriving to us and new
> software reaching the intended audience, I am looking for the most
> appropriate piece(s) of software to compute the volume of active site
> "cavities" in related 3D structures.
>
> I have tried to use Voidoo however I do not know where to download an
> initial (and fairly comprehensive) cavity.lib file which I'd modify if
> need be. The links on the USF web site appear to be broken.
>
> I am running Linux.
>
> Thanks for the advice,
>
> Fred. Vellieux
>
> 
>
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[ccp4bb] Current "best" software for computing volumes of active sites

[Fred Vellieux]

Hi CCP4BBers,

With software constantly changing, new versions arriving to us and new 
software reaching the intended audience, I am looking for the most 
appropriate piece(s) of software to compute the volume of active site 
"cavities" in related 3D structures.


I have tried to use Voidoo however I do not know where to download an 
initial (and fairly comprehensive) cavity.lib file which I'd modify if 
need be. The links on the USF web site appear to be broken.


I am running Linux.

Thanks for the advice,

Fred. Vellieux



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[ccp4bb] Research Technician Position in NYC

[Karim Armache]

A research technician position is available in the laboratory of Dr.
Karim-Jean Armache, Assistant Professor in the Structural Biology Program
at the Skirball Institute of Biomedical Research—NYU Medical Center, New
York, USA.


We are looking for creative individuals with a strong interest in protein
and nucleic acid biochemistry. A commitment of at least 2 years is
required. Ideal candidates should be highly motivated and have obtained a
B.S. or M.S. degree with a background in biochemistry or molecular biology.
Experience in molecular cloning and protein expression, as well as an
ability to maintain organized records is essential. Experience with cell
culture would be a plus. The candidate must have an excellent command of
oral and written English. Applicants should send a single PDF file
containing their CV along with a summary of their previous research
experience, accomplishments, and experimental expertise.


They should also arrange for 2-3 letters of reference to be sent directly
to Dr. Karim-Jean Armache via e-mail at:


*kjarma...@gmail.com *


The position is open immediately and applications will be reviewed until
the position is filled.



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Re: [ccp4bb] select from a pdb file a sphere of atoms

[Oleg Sobolev]

Phenix?

phenix.pdb_atom_selection model.pdb "within(5, (resid 4 and name CA))"
where 5 - 5 Angstrom radius, (resid 4 and name CA) - selection of an atom.
Don't have to be a single atom. More docs on selection syntax is here:
https://www.phenix-online.org/documentation/reference/atom_selections.html

Expanding to include whole residues:
phenix.pdb_atom_selection model.pdb "residues_within(5, (resid 4 and name
CA))"

Dumping result to a .pdb file:
phenix.pdb_atom_selection model.pdb "residues_within(5, (resid 4 and name
CA))" --write-pdb-file selected.pdb

Best regards,
Oleg Sobolev.

On Wed, Apr 3, 2019 at 7:19 AM Stephen Cusack  wrote:

> Dear All,
>
>   I am looking for an accessible programme that allows selection of
> atoms from a PDB file
>
> within a sphere of inputted radius from a central atom.
>
> Thanks for any help,
>
> Stephen Cusack
>
> --
>
> **
> Dr. Stephen Cusack, FRS
> Head of Grenoble Outstation of the European Molecular Biology Laboratory
> (EMBL)
> Group leader in structural biology of protein-RNA complexes and viral
> proteins
> **
>
> Email:  cus...@embl.fr
> Website: http://www.embl.fr
> Tel:(33) 4 76 20 7238Secretary (33) 4 76 20 7123
>
> Fax:(33) 4 76 20 7199
> Postal address:   EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS
> 90181, 38042 Grenoble Cedex 9, France
> Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71
> Avenue des Martyrs, 38000 Grenoble, France
> **
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>



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Re: [ccp4bb] High Rfree - ice ring

[Eleanor Dodson]

Look at the plots for Rfactor for your last cycle.

Is there a blip at some resoution?

And also look at the plot of  v  v resolution-- again are
there blips?

People have put a lot of effort in generating informative graphs so use
them!
You should see ice ring effects in the Wilson plot too..

Eleanor

On Wed, 3 Apr 2019 at 19:41, Sam Tang  wrote:

> Hi everyone again
>
> Hmmm I think we have solved a structure in P1 space, to 2.5 A. However
> after refinement the Rfree stuck at 33%-35% with Rwork around 26%. The
> structure was solved by MR and current model seems to fit density well. In
> Refmac log I found that at the resolution corresponding to high R there may
> be a solvent/ice ring. Since imosflm should be able to exclude ice rings, I
> am not 100% sure whether it's the cause to high R. But if this is actually
> the case, is there a way I can exclude certain resolution bins during
> Refmac (and is it an appropriate way to do so?)
>
> PS - the data is not affected by twining or pseudosymmetry as checked by
> Xtriage.
>
> Many thanks!
>
> Sam
>
> --
>
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> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac5 problems with unnatural amino acid

[Eleanor Dodson]

Usually externaly provided has pecedent over library routine ..
you need to label any "amino-acid" as a peptide though to generate the
required links in the protein chain.
E

On Wed, 3 Apr 2019 at 16:09,  wrote:

> Dear Deniz,
>
>
>
> In the past, I had similar problems caused by the fact that when the
> residue was “known” to ccp4, it would use the cif file from the ccp4
> library instead of the cif I had created myself. You could check if this
> might be the case for you. You find the cif files under
> $CCP4/lib/data/monomers in the subdirectory with the first letter of the
> three-letter code of your ligand and check the CIF file with the same
> three-letter code as you are using.
>
> However, it is possible that the ccp4 developers have resolved this issue
> by letting an externally provided cif file override the internal cif file.
>
>
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *"Deniz Üresin"
> *Gesendet:* Mittwoch, 3. April 2019 13:15
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] [ccp4bb] refmac5 problems with unnatural amino acid
>
>
>
> Hello,
>
> I'm trying to refine the structure of a protein mutant that has an
> unnatural amino acid in it. I created a restraint file for the AA and the
> mutation worked fine in COOT. But when I use refmac5 for refinement, it
> always changes the bond angle in the sidechain (an azide group, which
> should have a bond angle of 180°). I set the SD of the angle to 0 but that
> didn't help (the "refined" bond angle ends up somewhere between 120 and
> 150°).
>
> Is there any other way to tell refmac5 to not alter that bond angle?
>
> Thanks in advance,
>
> Deniz Üresin
>
>
>
> _
>
> Deniz Üresin
>
> Institut für Biophysik
>
> Johann Wolfgang Goethe-Universität Frankfurt am Main
> http://www.biophys.uni-frankfurt.de/~bredenbeck/
> 
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> 
>
> --
>
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>



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[ccp4bb] High Rfree - ice ring

[Sam Tang]

Hi everyone again

Hmmm I think we have solved a structure in P1 space, to 2.5 A. However
after refinement the Rfree stuck at 33%-35% with Rwork around 26%. The
structure was solved by MR and current model seems to fit density well. In
Refmac log I found that at the resolution corresponding to high R there may
be a solvent/ice ring. Since imosflm should be able to exclude ice rings, I
am not 100% sure whether it's the cause to high R. But if this is actually
the case, is there a way I can exclude certain resolution bins during
Refmac (and is it an appropriate way to do so?)

PS - the data is not affected by twining or pseudosymmetry as checked by
Xtriage.

Many thanks!

Sam



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Re: [ccp4bb] (EXTERNAL) [ccp4bb] pseudo internal symmetry

[Edward A. Berry]

While I agree with testing in lower symmetry (and I'm sure you have), it is 
also possible that the asymmetry is too slight or doesn't affect the crystals 
contacts, so that the dimer would orient randomly as it packs into the crystal. 
In that case, taking the average over all asymmetric units, the crystal really 
does have the higher symmetry and you would have to use alternate conformations 
as you are doing. I believe a case of this is Mario Amzel's F1 ATPase (pdb 
1MAB) which crystallized in 1H32. The ATPase (ATP synthase we would call it 
today) catalytic subunits are known to form an asymmetric trimer but it 
apparently crystallized with that trimer axis on the 3-fold crystallographic 
axis. The data clearly justified The higher symmetry (according to the 
authors). Later structures with the entire assembly in the asymmetric unit give 
us a good picture of the three different protomers, and it would be interesting 
to go back and try to model it with 3 alternate conformations in each asym
m
etric unit of Amzel's structure.

On 04/03/2019 04:36 AM, Daniele de Sanctis wrote:

Hi all,

we have a structure with a pseudo internal symmetry along a 2-fold axis that 
sits on a 2-fold crystallographic axis. For refinement purposes we have modeled 
the parts that differ with 50% occupancy, but before depositing the structure 
we wanted to make sure that this is the best way to deal with it and it is in 
agreement with PDB standards.

Did anyone deal with similar cases in the past?

Cheers

Daniele


--

ἀρετή
---
Daniele de Sanctis
Structural Biology Group
ESRF - The European Synchrotron
Grenoble, France
Tel 33 (0)4 76 88 2869

http://www.esrf.eu/id29 


--

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Re: [ccp4bb] select from a pdb file a sphere of atoms

[Tristan Croll]

In ChimeraX, you can promote a selection to whole residues with:

select up

Repeating the command will expand to whole secondary structure elements, 
then whole chains, then whole models. You can reverse this with:


select down


On 2019-04-03 16:13, Gianluca Santoni wrote:

I could be useful to then expand the selection to include the full
residues and not just the atoms within the sphere:

byres S1


On 4/3/19 4:21 PM, Steiner, Roberto wrote:

pymol?

example
S1 around 12.3  a.  Atoms with centers within 12.3 Angstroms of 
the center of any atom in S1

Best wishes
Roberto

On 3 Apr 2019, at 15:18, Stephen Cusack 
mailto:cus...@embl.fr>> wrote:


Dear All,

  I am looking for an accessible programme that allows selection of 
atoms from a PDB file


within a sphere of inputted radius from a central atom.

Thanks for any help,

Stephen Cusack

--

**
Dr. Stephen Cusack, FRS
Head of Grenoble Outstation of the European Molecular Biology 
Laboratory (EMBL)
Group leader in structural biology of protein-RNA complexes and viral 
proteins

**

Email: cus...@embl.fr
Website: 
https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.embl.fr&data=01%7C01%7Croberto.steiner%40KCL.AC.UK%7C741d46af65624537240e08d6b83f5ac5%7C8370cf1416f34c16b83c724071654356%7C0&sdata=he7%2BNc8OllNF1sHbwnp6VcqkEbXUHohZNp9UgrhHMUc%3D&reserved=0

Tel: (33) 4 76 20 7238Secretary (33) 4 76 20 7123
Fax:(33) 4 76 20 7199
Postal address:   EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 
90181, 38042 Grenoble Cedex 9, France
Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 
Avenue des Martyrs, 38000 Grenoble, France

**



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Professor Roberto Steiner
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London










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Re: [ccp4bb] select from a pdb file a sphere of atoms

[Petr Kolenko]

This is easy to do in Pymol again. If you have atoms in selection "nameX", the 
command is "select nameX, br. nameX". Very simple.
Best regards,
Petr


From: CCP4 bulletin board  on behalf of Gianluca Santoni 

Sent: Wednesday, April 3, 2019 5:13:59 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] select from a pdb file a sphere of atoms

I could be useful to then expand the selection to include the full
residues and not just the atoms within the sphere:

byres S1


On 4/3/19 4:21 PM, Steiner, Roberto wrote:
> pymol?
>
> example
> S1 around 12.3  a.  Atoms with centers within 12.3 Angstroms of the 
> center of any atom in S1
> Best wishes
> Roberto
>
> On 3 Apr 2019, at 15:18, Stephen Cusack 
> mailto:cus...@embl.fr>> wrote:
>
> Dear All,
>
>   I am looking for an accessible programme that allows selection of atoms 
> from a PDB file
>
> within a sphere of inputted radius from a central atom.
>
> Thanks for any help,
>
> Stephen Cusack
>
> --
>
> **
> Dr. Stephen Cusack, FRS
> Head of Grenoble Outstation of the European Molecular Biology Laboratory 
> (EMBL)
> Group leader in structural biology of protein-RNA complexes and viral proteins
> **
>
> Email: cus...@embl.fr
> Website: 
> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.embl.fr&data=01%7C01%7Croberto.steiner%40KCL.AC.UK%7C741d46af65624537240e08d6b83f5ac5%7C8370cf1416f34c16b83c724071654356%7C0&sdata=he7%2BNc8OllNF1sHbwnp6VcqkEbXUHohZNp9UgrhHMUc%3D&reserved=0
> Tel: (33) 4 76 20 7238Secretary (33) 4 76 20 7123
> Fax:(33) 4 76 20 7199
> Postal address:   EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 
> 38042 Grenoble Cedex 9, France
> Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue 
> des Martyrs, 38000 Grenoble, France
> **
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
> Professor Roberto Steiner
> Randall Centre for Cell and Molecular Biophysics
> Faculty of Life Sciences and Medicine
> King's College London
>
> roberto.stei...@kcl.ac.uk
> Phone 0044 20 78488216
> Fax0044 20 78486435
>
> Room 3.10A
> New Hunt's House
> Guy's Campus
> SE1 1UL
> London
>
>
>
>
>
>
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>

--
Gianluca SANTONI,
Serial crystallography data scientist
ESRF 71 av. des Martyrs
38027 Grenoble (France)



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Re: [ccp4bb] select from a pdb file a sphere of atoms

[Gianluca Santoni]

I could be useful to then expand the selection to include the full 
residues and not just the atoms within the sphere:


byres S1


On 4/3/19 4:21 PM, Steiner, Roberto wrote:

pymol?

example
S1 around 12.3  a.  Atoms with centers within 12.3 Angstroms of the center 
of any atom in S1
Best wishes
Roberto

On 3 Apr 2019, at 15:18, Stephen Cusack mailto:cus...@embl.fr>> 
wrote:

Dear All,

  I am looking for an accessible programme that allows selection of atoms from 
a PDB file

within a sphere of inputted radius from a central atom.

Thanks for any help,

Stephen Cusack

--

**
Dr. Stephen Cusack, FRS
Head of Grenoble Outstation of the European Molecular Biology Laboratory (EMBL)
Group leader in structural biology of protein-RNA complexes and viral proteins
**

Email: cus...@embl.fr
Website: 
https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.embl.fr&data=01%7C01%7Croberto.steiner%40KCL.AC.UK%7C741d46af65624537240e08d6b83f5ac5%7C8370cf1416f34c16b83c724071654356%7C0&sdata=he7%2BNc8OllNF1sHbwnp6VcqkEbXUHohZNp9UgrhHMUc%3D&reserved=0
Tel: (33) 4 76 20 7238Secretary (33) 4 76 20 7123
Fax:(33) 4 76 20 7199
Postal address:   EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 
38042 Grenoble Cedex 9, France
Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue 
des Martyrs, 38000 Grenoble, France
**



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Professor Roberto Steiner
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London










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--
Gianluca SANTONI,
Serial crystallography data scientist
ESRF 71 av. des Martyrs
38027 Grenoble (France)



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[ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac5 problems with unnatural amino acid

[Herman . Schreuder]

Dear Deniz,

In the past, I had similar problems caused by the fact that when the residue 
was “known” to ccp4, it would use the cif file from the ccp4 library instead of 
the cif I had created myself. You could check if this might be the case for 
you. You find the cif files under $CCP4/lib/data/monomers in the subdirectory 
with the first letter of the three-letter code of your ligand and check the CIF 
file with the same three-letter code as you are using.
However, it is possible that the ccp4 developers have resolved this issue by 
letting an externally provided cif file override the internal cif file.

Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von "Deniz 
Üresin"
Gesendet: Mittwoch, 3. April 2019 13:15
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] refmac5 problems with unnatural amino acid

Hello,
I'm trying to refine the structure of a protein mutant that has an unnatural 
amino acid in it. I created a restraint file for the AA and the mutation worked 
fine in COOT. But when I use refmac5 for refinement, it always changes the bond 
angle in the sidechain (an azide group, which should have a bond angle of 
180°). I set the SD of the angle to 0 but that didn't help (the "refined" bond 
angle ends up somewhere between 120 and 150°).
Is there any other way to tell refmac5 to not alter that bond angle?
Thanks in advance,
Deniz Üresin

_
Deniz Üresin
Institut für Biophysik
Johann Wolfgang Goethe-Universität Frankfurt am Main
http://www.biophys.uni-frankfurt.de/~bredenbeck/




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Re: [ccp4bb] select from a pdb file a sphere of atoms

[Petr Kolenko]

Dear Stephen,
PyMOL can do it. You have to choose your atom and then use following command: 
select your-name, (sele) expand 10; where (sele) is your selection - atom or a 
group of atoms and 10 is the radius in AA.
Best regards,
Petr


From: CCP4 bulletin board  on behalf of Stephen Cusack 

Sent: Wednesday, April 3, 2019 4:18:49 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] select from a pdb file a sphere of atoms

Dear All,

  I am looking for an accessible programme that allows selection of
atoms from a PDB file

within a sphere of inputted radius from a central atom.

Thanks for any help,

Stephen Cusack

--

**
Dr. Stephen Cusack, FRS
Head of Grenoble Outstation of the European Molecular Biology Laboratory (EMBL)
Group leader in structural biology of protein-RNA complexes and viral proteins
**

Email:  cus...@embl.fr
Website: http://www.embl.fr
Tel:(33) 4 76 20 7238Secretary (33) 4 76 20 7123
Fax:(33) 4 76 20 7199
Postal address:   EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 
38042 Grenoble Cedex 9, France
Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue 
des Martyrs, 38000 Grenoble, France
**



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Re: [ccp4bb] select from a pdb file a sphere of atoms

[Tristan Croll]

In ChimeraX:

ctrl-click to select your atom, then in the command line below:

select zone sel 

Best regards,

Tristan

On 2019-04-03 15:18, Stephen Cusack wrote:

Dear All,

 I am looking for an accessible programme that allows selection of
atoms from a PDB file

within a sphere of inputted radius from a central atom.

Thanks for any help,

Stephen Cusack

--

**
Dr. Stephen Cusack, FRS
Head of Grenoble Outstation of the European Molecular Biology 
Laboratory (EMBL)
Group leader in structural biology of protein-RNA complexes and viral 
proteins

**

Email:  cus...@embl.fr
Website: http://www.embl.fr
Tel:(33) 4 76 20 7238Secretary (33) 4 76 20 7123
Fax:(33) 4 76 20 7199
Postal address:   EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS
90181, 38042 Grenoble Cedex 9, France
Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71
Avenue des Martyrs, 38000 Grenoble, France
**



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Re: [ccp4bb] select from a pdb file a sphere of atoms

[Steiner, Roberto]

pymol?

example
S1 around 12.3  a.  Atoms with centers within 12.3 Angstroms of the center 
of any atom in S1
Best wishes
Roberto

On 3 Apr 2019, at 15:18, Stephen Cusack mailto:cus...@embl.fr>> 
wrote:

Dear All,

 I am looking for an accessible programme that allows selection of atoms from a 
PDB file

within a sphere of inputted radius from a central atom.

Thanks for any help,

Stephen Cusack

--

**
Dr. Stephen Cusack, FRS
Head of Grenoble Outstation of the European Molecular Biology Laboratory (EMBL)
Group leader in structural biology of protein-RNA complexes and viral proteins
**

Email: cus...@embl.fr
Website: 
https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.embl.fr&data=01%7C01%7Croberto.steiner%40KCL.AC.UK%7C741d46af65624537240e08d6b83f5ac5%7C8370cf1416f34c16b83c724071654356%7C0&sdata=he7%2BNc8OllNF1sHbwnp6VcqkEbXUHohZNp9UgrhHMUc%3D&reserved=0
Tel: (33) 4 76 20 7238Secretary (33) 4 76 20 7123
Fax:(33) 4 76 20 7199
Postal address:   EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 
38042 Grenoble Cedex 9, France
Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue 
des Martyrs, 38000 Grenoble, France
**



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Professor Roberto Steiner
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
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SE1 1UL
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[ccp4bb] select from a pdb file a sphere of atoms

[Stephen Cusack]

Dear All,

 I am looking for an accessible programme that allows selection of 
atoms from a PDB file


within a sphere of inputted radius from a central atom.

Thanks for any help,

Stephen Cusack

--

**
Dr. Stephen Cusack, FRS
Head of Grenoble Outstation of the European Molecular Biology Laboratory (EMBL)
Group leader in structural biology of protein-RNA complexes and viral proteins
**

Email:  cus...@embl.fr  
Website: http://www.embl.fr 
Tel:(33) 4 76 20 7238Secretary (33) 4 76 20 7123

Fax:(33) 4 76 20 7199   
Postal address:   EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 
38042 Grenoble Cedex 9, France
Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue 
des Martyrs, 38000 Grenoble, France
**



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Re: [ccp4bb] refmac5 problems with unnatural amino acid

[Eleanor Dodson]

Qs..
1) You are using the same dictionaries for both REFMAC and COOT?

2) What happens in refmac if you just use REFI IDEALISE?
And turn on the option for REFMAC to
MONITOR MANY - it might tell you if there is some clash which is overriding
the geometry restraints..
Eleanor

On Wed, 3 Apr 2019 at 12:24, "Deniz Üresin"  wrote:

> Hello,
> I'm trying to refine the structure of a protein mutant that has an
> unnatural amino acid in it. I created a restraint file for the AA and the
> mutation worked fine in COOT. But when I use refmac5 for refinement, it
> always changes the bond angle in the sidechain (an azide group, which
> should have a bond angle of 180°). I set the SD of the angle to 0 but that
> didn't help (the "refined" bond angle ends up somewhere between 120 and
> 150°).
> Is there any other way to tell refmac5 to not alter that bond angle?
> Thanks in advance,
> Deniz Üresin
>
> _
> Deniz Üresin
> Institut für Biophysik
> Johann Wolfgang Goethe-Universität Frankfurt am Main
> http://www.biophys.uni-frankfurt.de/~bredenbeck/
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] refmac5 problems with unnatural amino acid

[Deniz Üresin]

Hello,

I'm trying to refine the structure of a protein mutant that has an unnatural amino acid in it. I created a restraint file for the AA and the mutation worked fine in COOT. But when I use refmac5 for refinement, it always changes the bond angle in the sidechain (an azide group, which should have a bond angle of 180°). I set the SD of the angle to 0 but that didn't help (the "refined" bond angle ends up somewhere between 120 and 150°).

Is there any other way to tell refmac5 to not alter that bond angle?

Thanks in advance,

Deniz Üresin

 

_

Deniz Üresin

Institut für Biophysik

Johann Wolfgang Goethe-Universität Frankfurt am Main
http://www.biophys.uni-frankfurt.de/~bredenbeck/

 


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Re: [ccp4bb] AW: [ccp4bb] pseudo internal symmetry

[Harry Powell]

Hi

One way to test if the data processing software has imposed too much symmetry 
is to actually look at the images themselves using one of the processing 
packages, or process in a lower symmetry and use "viewhkl" (or even "hklview" 
if you're old-fashioned...) to view sections of the integrated data down 
principal axes. The human eye/brain combination takes a lot of beating.

Harry

On 3 Apr 2019, at 11:03, herman.schreu...@sanofi.com wrote:

> I agree. The data processing software might have been confused by the NC 
> 2-fold and thought that it was crystallographic and of course, after merging 
> the data, the NC axis will have been made “crystallographic” with 
> superimposed A and B conformations at 50% occupancy. In this case, 
> reprocessing in the true, lower symmetry space group, would bring better 
> stats, but also much clearer and much easier interpretable electron density 
> maps. However, if the distribution of you’re A and B conformations is truly 
> random you could submit the structure as it is now.
> Best, Herman
>  
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von David 
> Briggs
> Gesendet: Mittwoch, 3. April 2019 10:46
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [EXTERNAL] Re: [ccp4bb] pseudo internal symmetry
>  
> Hi, 
>  
> This doesn't answer your question directly, but I'd be tempted to reduce the 
> symmetry and re-refine in a space group lacking that 2-fold axis.
> I'd hope that the scaling in the lower space group would give you better 
> stats as well, but maybe the differences in your case are too subtle?
>  
> I don't know what PDB rules and regs are though. 
>  
> HTH,
>  
> Dave
> From: CCP4 bulletin board  on behalf of Daniele de 
> Sanctis 
> Sent: 03 April 2019 09:36
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] pseudo internal symmetry
>  
> Hi all,
>  
> we have a structure with a pseudo internal symmetry along a 2-fold axis that 
> sits on a 2-fold crystallographic axis. For refinement purposes we have 
> modeled the parts that differ with 50% occupancy, but before depositing the 
> structure we wanted to make sure that this is the best way to deal with it 
> and it is in agreement with PDB standards.
>  
> Did anyone deal with similar cases in the past?
>  
> Cheers
>  
> Daniele
> 
> 
> --
>  
> ἀρετή
> ---
> Daniele de Sanctis
> Structural Biology Group
> ESRF - The European Synchrotron
> Grenoble, France
> Tel 33 (0)4 76 88 2869
> 
> http://www.esrf.eu/id29
>  
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> The Francis Crick Institute Limited is a registered charity in England and 
> Wales no. 1140062 and a company registered in England and Wales no. 06885462, 
> with its registered office at 1 Midland Road London NW1 1AT
>  
> To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] AW: [ccp4bb] pseudo internal symmetry

[Herman . Schreuder]

I agree. The data processing software might have been confused by the NC 2-fold 
and thought that it was crystallographic and of course, after merging the data, 
the NC axis will have been made “crystallographic” with superimposed A and B 
conformations at 50% occupancy. In this case, reprocessing in the true, lower 
symmetry space group, would bring better stats, but also much clearer and much 
easier interpretable electron density maps. However, if the distribution of 
you’re A and B conformations is truly random you could submit the structure as 
it is now.
Best, Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von David 
Briggs
Gesendet: Mittwoch, 3. April 2019 10:46
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] pseudo internal symmetry

Hi,

This doesn't answer your question directly, but I'd be tempted to reduce the 
symmetry and re-refine in a space group lacking that 2-fold axis.
I'd hope that the scaling in the lower space group would give you better stats 
as well, but maybe the differences in your case are too subtle?

I don't know what PDB rules and regs are though.

HTH,

Dave

From: CCP4 bulletin board  on behalf of Daniele de 
Sanctis 
Sent: 03 April 2019 09:36
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] pseudo internal symmetry

Hi all,

we have a structure with a pseudo internal symmetry along a 2-fold axis that 
sits on a 2-fold crystallographic axis. For refinement purposes we have modeled 
the parts that differ with 50% occupancy, but before depositing the structure 
we wanted to make sure that this is the best way to deal with it and it is in 
agreement with PDB standards.

Did anyone deal with similar cases in the past?

Cheers

Daniele


--

ἀρετή
---
Daniele de Sanctis
Structural Biology Group
ESRF - The European Synchrotron
Grenoble, France
Tel 33 (0)4 76 88 2869

http://www.esrf.eu/id29



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Re: [ccp4bb] pseudo internal symmetry

[Eleanor Dodson]

Yes - I have had cases like that where reducing the spacegroup symmetry
improved the model a lot!
Eleanor

On Wed, 3 Apr 2019 at 09:47, David Briggs  wrote:

> Hi,
>
> This doesn't answer your question directly, but I'd be tempted to reduce
> the symmetry and re-refine in a space group lacking that 2-fold axis.
> I'd hope that the scaling in the lower space group would give you better
> stats as well, but maybe the differences in your case are too subtle?
>
> I don't know what PDB rules and regs are though.
>
> HTH,
>
> Dave
> --
> *From:* CCP4 bulletin board  on behalf of Daniele
> de Sanctis 
> *Sent:* 03 April 2019 09:36
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] pseudo internal symmetry
>
> Hi all,
>
> we have a structure with a pseudo internal symmetry along a 2-fold axis
> that sits on a 2-fold crystallographic axis. For refinement purposes we
> have modeled the parts that differ with 50% occupancy, but before
> depositing the structure we wanted to make sure that this is the best way
> to deal with it and it is in agreement with PDB standards.
>
> Did anyone deal with similar cases in the past?
>
> Cheers
>
> Daniele
>
>
> --
>
> ἀρετή
> ---
> Daniele de Sanctis
> Structural Biology Group
> ESRF - The European Synchrotron
> Grenoble, France
> Tel 33 (0)4 76 88 2869
>
> http://www.esrf.eu/id29
> 
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> 
>
> The Francis Crick Institute Limited is a registered charity in England and
> Wales no. 1140062 and a company registered in England and Wales no.
> 06885462, with its registered office at 1 Midland Road London NW1 1AT
>
> --
>
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[ccp4bb] Job opportunity in Berlin - HZB and Humboldt University advertise a postdoc position

[Manfred S. Weiss]

The Helmholtz Zentrum Berlin für Materialien und Energie, the 
Max-Delbrück-Center for Molecular Medicine, the Freie Universität Berlin, the 
Chariteand the Humboldt Universität zu Berlin jointly operate three 
experimental stations for bio-macromolecular crystallography at BESSY II, one 
of the world’s most modern synchrotron radiation sources for VUV and soft 
X-rays.
(https://www.helmholtz-berlin.de/forschung/oe/np/gmx/index_en.html)

The Humboldt University zu Berlin is seeking a

Post Doctoral Research Assistant

to work on and support research topics in the field of structural enzymology 
(e.g. control of chemical reactions in macromolecular crystals, combination of 
UV/Vis absorption spectroscopy and crystallography, etc.) originating from the 
group of Prof. Dr. Holger Dobbek. The successful candidate will also be 
involved in the operation of the BESSY II bio-macromolecular crystallography 
beamlines (headed by Dr. Manfred S. Weiss) including supporting external users 
at the beamlines and will take part in graduate student education.

Initially, a contract lasting until 31.12.2020 will be offered to the 
successful candidate with the possibility for an extension. The salary will be 
based on German Federal TVöD. The position is available immediately.

Applicants should hold a Ph.D. in the biological, chemical or physical sciences 
and have a solid background in biochemical methods, in bio-macromolecular 
crystallography and/or related fields. The position also requires the 
documented ability to conduct independent research as well as excellent 
communication and interpersonal skills.

Please send applications (CV, list of publications, two references, .pdf-file 
format) citing the reference number AN/106/19 in electronic form until 
25.04.2019 to:

Dr. Manfred Weiss 
(mswe...@helmholtz-berlin.de)

Here is the link to the advertisement (in German):
https://www.personalabteilung.hu-berlin.de/de/stellenausschreibungen/wissenschaftlicher-mitarbeiter-m-w-d-befristet-bis-31-12-2020-e-13-tv-l-hu


--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. 
Jutta Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (kommissarisch), Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin



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Re: [ccp4bb] pseudo internal symmetry

[David Briggs]

Hi,

This doesn't answer your question directly, but I'd be tempted to reduce the 
symmetry and re-refine in a space group lacking that 2-fold axis.
I'd hope that the scaling in the lower space group would give you better stats 
as well, but maybe the differences in your case are too subtle?

I don't know what PDB rules and regs are though.

HTH,

Dave

From: CCP4 bulletin board  on behalf of Daniele de 
Sanctis 
Sent: 03 April 2019 09:36
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] pseudo internal symmetry

Hi all,

we have a structure with a pseudo internal symmetry along a 2-fold axis that 
sits on a 2-fold crystallographic axis. For refinement purposes we have modeled 
the parts that differ with 50% occupancy, but before depositing the structure 
we wanted to make sure that this is the best way to deal with it and it is in 
agreement with PDB standards.

Did anyone deal with similar cases in the past?

Cheers

Daniele


--

ἀρετή
---
Daniele de Sanctis
Structural Biology Group
ESRF - The European Synchrotron
Grenoble, France
Tel 33 (0)4 76 88 2869

http://www.esrf.eu/id29



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[ccp4bb] pseudo internal symmetry

[Daniele de Sanctis]

Hi all,

we have a structure with a pseudo internal symmetry along a 2-fold axis
that sits on a 2-fold crystallographic axis. For refinement purposes we
have modeled the parts that differ with 50% occupancy, but before
depositing the structure we wanted to make sure that this is the best way
to deal with it and it is in agreement with PDB standards.

Did anyone deal with similar cases in the past?

Cheers

Daniele


-- 

ἀρετή
---
Daniele de Sanctis
Structural Biology Group
ESRF - The European Synchrotron
Grenoble, France
Tel 33 (0)4 76 88 2869

http://www.esrf.eu/id29



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