Re: [ccp4bb] Unknown electron density blob

[Robbie Joosten]

PEG likes to hang around where it is unwelcome: 
http://onlinelibrary.wiley.com/doi/10.1002/pro.2923/full

Cheers,
Robbie

Sent from my Windows 10 phone

Van: Bernhard Rupp
Verzonden: dinsdag 24 januari 2017 23:20
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: Re: [ccp4bb] Unknown electron density blob

Some general remarks about PEG modelling and associated caveats:
http://journals.iucr.org/d/issues/2016/12/00/rr5136/index.html
Section 3.6.5.

Best, BR

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ana Luísa 
Moreira de Carvalho
Sent: Tuesday, January 24, 2017 10:11 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Unknown electron density blob

Just to add to this, in our group, we had a funny case where we found PEG 
around K:

https://drive.google.com/open?id=0B2DrnhrLgvwGSldLVl9pSEptakE
https://drive.google.com/open?id=0B2DrnhrLgvwGZlNiYTFoaktPUHc

Ana Luisa


On 24 Jan 2017, at 17:36, Artem Evdokimov 
> wrote:

PEG. It wraps around K or R residues just like you are showing.

Artem
www.harkerbio.com
"where every blob has candy inside"

On Jan 24, 2017 12:19 PM, "Uma Gabale" 
<0ebb5dcf3eaa-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Dear all,
While refining a structure at 2.5 A resolution, we observed a 
semi-circular/crescent shaped electron density blob as shown in the attached 
picture. We have been unable to identify it so far, and would appreciate any 
help in identification.
The protein was expressed in E. coli BL21(DE3), purified on Ni-NTA followed by 
gel filtration. The purification buffers included Tris and NaCl (no detergent/ 
other ingredients except for imidazole for Ni-NTA). Crystallization condition 
had HEPES and PEG3350; no cryoprotectant was used.
The blob is surrounded by residues Trp, Thr, Gln, Arg, and Phe.
Thanks and regards,
Uma.

--
Uma Gabale, PhD
Research Associate
Molecular and Cellular Biochemistry
Indiana University Bloomington

Research Assistant Professor at UCIBIO@REQUIMTE-FCT-NOVA
***
Biologia Estrutural - Cristalografia de Raios-X (Gab 6.34)
Dep. Quimica, FCT-UNL
2829-516 Caparica
Portugal
Phone: 00351212948300 (ext: Gab: 10940; Lab: 10962; X-ray Lab: 10915)
Fax: 00351212948550
http://docentes.fct.unl.pt/almc
http://sites.fct.unl.pt/xtal
https://www.facebook.com/XtalNOVA/
***
Single Crystal X-ray Structure Determination Service: 
http://www.dq.fct.unl.pt/en/single-crystal-x-ray-structure-determination

Re: [ccp4bb] Bad density for chains

[Debanu]

Hi Pooja,

Are you positive you have the correct space group and there are no other issues 
like twinning, etc?

If sure, did you define NCS groups in refinement? TLS refinement? Try different 
refinement programs?

How big is the molecule? Was it solved by MR or experimental phasing?

You can try superimposing A/B on C/D and refinement with tight NCS then adjust 
NCS restraints during model adjustments based on local differences or also see 
if phenix autobuild helps. 

Best,
Debanu 
--
Debanu Das
Accelero Biostructures 


> On Jan 24, 2017, at 8:42 PM, Pooja Kesari  wrote:
> 
> Dear All,
> 
> I have a 2.6 A resolution structure having four chains in an asymmetric unit.
> The chain A and B have density for almost all residues however we don't have 
> proper residue density in chain C and D.What can be tried to build chain C 
> and D ?
> 
> 
> 
> Many Thanks 
> Pooja

[ccp4bb] Bad density for chains

[Pooja Kesari]

Dear All,

I have a 2.6 A resolution structure having four chains in an asymmetric
unit.
The chain A and B have density for almost all residues however we don't
have proper residue density in chain C and D.What can be tried to build
chain C and D ?



Many Thanks
Pooja

Re: [ccp4bb] add ligand solution onto drop directly

[Bernhard Rupp]

The truth is in the map. Ergo, zap it and rationalize why it worked or not 
later.

 

Cheers, BR

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Markus 
Heckmann
Sent: Tuesday, January 24, 2017 6:23 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] add ligand solution onto drop directly

 

Dear all,

I wondered if it is OK to pipette ligand soln (X-CoA) *directly* to the drop 
with crystal (1:1 ratio of protein:precipitant 2µl) instead of dissolving it in 
precipitant solution and transferring the crystal to this ligand containing 
precipitant solution. The crystals survive this as I add the ligand solution to 
the edge of the drop and gently mix the two solutions. Since I collected my 
datasets I wonder if it is OK?

Many thanks,

Markus

[ccp4bb] add ligand solution onto drop directly

[Markus Heckmann]

Dear all,
I wondered if it is OK to pipette ligand soln (X-CoA) *directly* to the
drop with crystal (1:1 ratio of protein:precipitant 2µl) instead of
dissolving it in precipitant solution and transferring the crystal to this
ligand containing precipitant solution. The crystals survive this as I add
the ligand solution to the edge of the drop and gently mix the two
solutions. Since I collected my datasets I wonder if it is OK?

Many thanks,
Markus

Re: [ccp4bb] SHELXL refinement with TYR on special position

[George Sheldrick]

Dear Francis,

You need to put the atoms starting with CG into PART -1 to prevent them 
clashing, and reset the occupancies to 10.5 (i.e. fixed at 0.5). There 
must be another disorder component pointing somewhere else (also with 
half occupancy).


SHELXPRO has been made obsolete by Anna Luebben's PDB2INS.

Best wishes, George


On 01/24/2017 11:09 PM, Francis Reyes wrote:

Hi all

I'm trying to refine a structure with a tyrosine sitting on a special position 
, or maybe it's some disorder.. or  Suggestions?

https://i.imgsafe.org/7cfbf83a38.jpg


Using just FLAT, CHIV,DFIX, and DANG from shelxpro doesn't work.

Thanks,

Francis




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] Unknown electron density blob

[Bernhard Rupp]

Some general remarks about PEG modelling and associated caveats:

http://journals.iucr.org/d/issues/2016/12/00/rr5136/index.html

Section 3.6.5.

 

Best, BR

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ana
Luísa Moreira de Carvalho
Sent: Tuesday, January 24, 2017 10:11 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Unknown electron density blob

 

Just to add to this, in our group, we had a funny case where we found PEG
around K:

 

https://drive.google.com/open?id=0B2DrnhrLgvwGSldLVl9pSEptakE

https://drive.google.com/open?id=0B2DrnhrLgvwGZlNiYTFoaktPUHc

 

Ana Luisa

 

 

On 24 Jan 2017, at 17:36, Artem Evdokimov  > wrote:

 

PEG. It wraps around K or R residues just like you are showing.

 

Artem

www.harkerbio.com  

"where every blob has candy inside"

 

On Jan 24, 2017 12:19 PM, "Uma Gabale"
<0ebb5dcf3eaa-dmarc-requ...@jiscmail.ac.uk
 > wrote:

Dear all,

While refining a structure at 2.5 A resolution, we observed a
semi-circular/crescent shaped electron density blob as shown in the attached
picture. We have been unable to identify it so far, and would appreciate any
help in identification.

The protein was expressed in E. coli BL21(DE3), purified on Ni-NTA followed
by gel filtration. The purification buffers included Tris and NaCl (no
detergent/ other ingredients except for imidazole for Ni-NTA).
Crystallization condition had HEPES and PEG3350; no cryoprotectant was used.

The blob is surrounded by residues Trp, Thr, Gln, Arg, and Phe.

Thanks and regards,

Uma.

 

--

Uma Gabale, PhD

Research Associate

Molecular and Cellular Biochemistry
Indiana University Bloomington

 

Research Assistant Professor at UCIBIO@REQUIMTE-FCT-NOVA

***
Biologia Estrutural - Cristalografia de Raios-X (Gab 6.34)
Dep. Quimica, FCT-UNL
2829-516 Caparica
Portugal
Phone: 00351212948300 (ext: Gab: 10940; Lab: 10962; X-ray Lab: 10915)
Fax: 00351212948550
  http://docentes.fct.unl.pt/almc
http://sites.fct.unl.pt/xtal

https://www.facebook.com/XtalNOVA/
***

Single Crystal X-ray Structure Determination Service:
http://www.dq.fct.unl.pt/en/single-crystal-x-ray-structure-determination

 

[ccp4bb] SHELXL refinement with TYR on special position

[Francis Reyes]

Hi all

I'm trying to refine a structure with a tyrosine sitting on a special position 
, or maybe it's some disorder.. or  Suggestions?

https://i.imgsafe.org/7cfbf83a38.jpg


Using just FLAT, CHIV,DFIX, and DANG from shelxpro doesn't work. 

Thanks,

Francis

Re: [ccp4bb] Unknown electron density blob

[Ana Luísa Moreira de Carvalho]

Just to add to this, in our group, we had a funny case where we found PEG 
around K:

https://drive.google.com/open?id=0B2DrnhrLgvwGSldLVl9pSEptakE
https://drive.google.com/open?id=0B2DrnhrLgvwGZlNiYTFoaktPUHc

Ana Luisa


> On 24 Jan 2017, at 17:36, Artem Evdokimov  wrote:
> 
> PEG. It wraps around K or R residues just like you are showing.
> 
> Artem
> www.harkerbio.com 
> "where every blob has candy inside"
> 
> On Jan 24, 2017 12:19 PM, "Uma Gabale" 
> <0ebb5dcf3eaa-dmarc-requ...@jiscmail.ac.uk 
> > wrote:
> Dear all,
> While refining a structure at 2.5 A resolution, we observed a 
> semi-circular/crescent shaped electron density blob as shown in the attached 
> picture. We have been unable to identify it so far, and would appreciate any 
> help in identification.
> The protein was expressed in E. coli BL21(DE3), purified on Ni-NTA followed 
> by gel filtration. The purification buffers included Tris and NaCl (no 
> detergent/ other ingredients except for imidazole for Ni-NTA). 
> Crystallization condition had HEPES and PEG3350; no cryoprotectant was used.
> The blob is surrounded by residues Trp, Thr, Gln, Arg, and Phe.
> Thanks and regards,
> Uma.
> 
> --
> Uma Gabale, PhD
> Research Associate
> Molecular and Cellular Biochemistry
> Indiana University Bloomington

Research Assistant Professor at UCIBIO@REQUIMTE-FCT-NOVA
***
Biologia Estrutural - Cristalografia de Raios-X (Gab 6.34)
Dep. Quimica, FCT-UNL
2829-516 Caparica
Portugal
Phone: 00351212948300 (ext: Gab: 10940; Lab: 10962; X-ray Lab: 10915)
Fax: 00351212948550
http://docentes.fct.unl.pt/almc 
http://sites.fct.unl.pt/xtal
https://www.facebook.com/XtalNOVA/
***
Single Crystal X-ray Structure Determination Service: 
http://www.dq.fct.unl.pt/en/single-crystal-x-ray-structure-determination

Re: [ccp4bb] Unknown electron density blob

[Vivoli, Mirella]

Hi there,

I think it is PEG, very common to have PEG in horseshoe shape with arginine 
pointing toward to it.

Cheers,


Mirella


Vivoli Mirella

Associate Research Fellow
Biocatalysis Centre, Henry Wellcome Building
College of Life and Environmental Sciences,
University of Exeter
Stocker Road
Exeter
Ex4 4QD
Tel: + 44 (0)1392 726121
Email: m.viv...@exeter.ac.uk

"I don't want to believe. I want to know". [C. Sagan]

From: CCP4 bulletin board  on behalf of Paul Emsley 

Sent: 24 January 2017 17:32:35
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Unknown electron density blob

On 24/01/2017 17:19, Uma Gabale wrote:

> While refining a structure at 2.5 A resolution, we observed a 
> semi-circular/crescent shaped
> electron density blob as shown in the attached picture. We have been unable 
> to identify it
> so far, and would appreciate any help in identification.

If you have Coot:

Extensions->Modelling->Add Other Solvent Molecules->Add New Residue 
Type->"PG4"->Add
then click "PG4 Tetraethylene Glycol"

Re: [ccp4bb] Unknown electron density blob

[Artem Evdokimov]

PEG. It wraps around K or R residues just like you are showing.

Artem
www.harkerbio.com
"where every blob has candy inside"

On Jan 24, 2017 12:19 PM, "Uma Gabale" <
0ebb5dcf3eaa-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear all,
> While refining a structure at 2.5 A resolution, we observed a
> semi-circular/crescent shaped electron density blob as shown in the
> attached picture. We have been unable to identify it so far, and would
> appreciate any help in identification.
> The protein was expressed in *E. coli* BL21(DE3), purified on Ni-NTA
> followed by gel filtration. The purification buffers included Tris and NaCl
> (no detergent/ other ingredients except for imidazole for Ni-NTA).
> Crystallization condition had HEPES and PEG3350; no cryoprotectant was used.
> The blob is surrounded by residues Trp, Thr, Gln, Arg, and Phe.
> Thanks and regards,
> Uma.
>
> --
> Uma Gabale, PhD
> Research Associate
> Molecular and Cellular Biochemistry
> Indiana University Bloomington
>

Re: [ccp4bb] Unknown electron density blob

[Parthasarathy Sampathkumar]

Hi Uma,

It is risky to guess based on one-view of of the density from 2-dimensional
images. What is the contour-level of 2mFo-DFc (blue) map displayed here?!!
If 2mFo-DFc density is continuous from Arg, say at 0.8 sigma, then could it
be an alternate conformation of the Arg side-chain. One could build, and
re-refine and see if negative mFo-DFc features shows up.

Hope this helps,
Partha

On Tue, Jan 24, 2017 at 12:19 PM, Uma Gabale <
0ebb5dcf3eaa-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear all,
> While refining a structure at 2.5 A resolution, we observed a
> semi-circular/crescent shaped electron density blob as shown in the
> attached picture. We have been unable to identify it so far, and would
> appreciate any help in identification.
> The protein was expressed in *E. coli* BL21(DE3), purified on Ni-NTA
> followed by gel filtration. The purification buffers included Tris and NaCl
> (no detergent/ other ingredients except for imidazole for Ni-NTA).
> Crystallization condition had HEPES and PEG3350; no cryoprotectant was used.
> The blob is surrounded by residues Trp, Thr, Gln, Arg, and Phe.
> Thanks and regards,
> Uma.
>
> --
> Uma Gabale, PhD
> Research Associate
> Molecular and Cellular Biochemistry
> Indiana University Bloomington
>

[ccp4bb] 2 year PDRA position in University of Liverpool UK

[Antonyuk, Svetlana]

THE UNIVERSITY OF LIVERPOOL
FACULTY OF HEALTH AND LIFE SCIENCES
INSTITUTE OF INTEGRATIVE BIOLOGY
DEPARTMENT OF BIOCHEMISTRY
 POSTDOCTORAL RESEARCH ASSOCIATE GRADE 7
 £32,958 - £34,956 pa
An exciting opportunity has emerged in the Molecular 
Biophysics group to work on a BBSRC-supported 
project on structure-function-mechanism studies of Cu-nitrite reductase and 
membrane bound nitric oxide (NO) reductase and the role of metabolon complex 
formation in controlling levels of cytotoxic NO. The project will link 
crystallographic studies with techniques to probe factors that control delivery 
of electrons and protons to the active site of these enzymes. You will be 
responsible for using established molecular biology procedures underpinning the 
overexpression and purification of a number of enzymes and their mutants 
including membrane proteins and undertake crystallographic, spectroscopic and 
mechanistic aspects of the programme. You will have the opportunity  to spend 
up to 4 weeks in the RIKEN laboratories in Japan as part of a collaborative 
programme alongside two PhD students working on membrane-bound nitric oxide 
reductases
You should have a PhD in the area of physics, chemistry, biological sciences or 
biophysics, with experience in protein crystallography and practical knowledge 
of molecular biology preferably with experience in membrane proteins. Excellent 
verbal and written communication skills are essential. The post is available 
until 31 March 2019.

Job Ref: 005185 
  Closing Date: 23 February 2017

For full details and to apply online, please visit: 
https://recruit.liverpool.ac.uk

Dr. Svetlana Antonyuk
Senior Lecturer
Co-Director of Barkla X-ray Laboratory of Biophysics
Institute of Integrative Biology
Faculty of Health and Life Sciences
University of Liverpool
Life Sciences Building
Liverpool
L69 7ZB
--
Phone:   +44(0)151-795 5145
Email:   s.anton...@liverpool.ac.uk

http://www.biophysics.liv.ac.uk/

Re: [ccp4bb] Unknown electron density blob

[Paul Emsley]

On 24/01/2017 17:32, Paul Emsley wrote:

On 24/01/2017 17:19, Uma Gabale wrote:


While refining a structure at 2.5 A resolution, we observed a 
semi-circular/crescent shaped
electron density blob as shown in the attached picture. We have been unable to 
identify it
so far, and would appreciate any help in identification.


If you have Coot:

Extensions->Modelling->Add Other Solvent Molecules->Add New Residue 
Type->"PG4"->Add
then click "PG4 Tetraethylene Glycol"


Delete the water first, obviously.

Re: [ccp4bb] Unknown electron density blob

[Paul Emsley]

On 24/01/2017 17:19, Uma Gabale wrote:


While refining a structure at 2.5 A resolution, we observed a 
semi-circular/crescent shaped
electron density blob as shown in the attached picture. We have been unable to 
identify it
so far, and would appreciate any help in identification.


If you have Coot:

Extensions->Modelling->Add Other Solvent Molecules->Add New Residue 
Type->"PG4"->Add
then click "PG4 Tetraethylene Glycol"

Re: [ccp4bb] Unknown electron density blob

[Boaz Shaanan]

Hi,


Could it be a segment of peg3350?


  Cheers,


              Boaz


 
 
Boaz Shaanan, Ph.D.

Dept. of Life Sciences  
Ben-Gurion University of the Negev  
Beer-Sheva 84105    
Israel  
    
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan  
Fax:   972-8-647-2992 or 972-8-646-1710
 
 








From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Uma Gabale [0ebb5dcf3eaa-dmarc-requ...@jiscmail.ac.uk]
Sent: Tuesday, January 24, 2017 7:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unknown electron density blob





Dear all,
While refining a structure at 2.5 A resolution, we observed a semi-circular/crescent shaped electron density blob as shown in the attached picture. We have been unable to identify it so far, and would
 appreciate any help in identification.
The protein was expressed in
E. coli BL21(DE3), purified on Ni-NTA followed by gel filtration. The purification buffers included Tris and NaCl (no detergent/ other ingredients except for imidazole for Ni-NTA). Crystallization condition
 had HEPES and PEG3350; no cryoprotectant was used.
The blob is surrounded by residues Trp,
Thr,
Gln,
Arg, and Phe.
Thanks and regards,
Uma.



--
Uma Gabale, PhD

Research Associate

Molecular and Cellular Biochemistry
Indiana University Bloomington

Re: [ccp4bb] rigid flexible analysis

[Pavel Afonine]

Hi,

can't you infer this from refined atomic displacement parameters (ADPs;
also knowns as B-factors)?

Or run a 100 or so SA refinement jobs, each starting with a different
random seed. This will generate an ensemble of models with some atoms
occupying more conserved positions than the others.

Pavel

On Tue, Jan 24, 2017 at 3:46 AM, Gauri Misra  wrote:

> Hi everyone!
>
> I would like to know the current online servers available for analyzing
> the rigid and flexible regions of proteins.Looking forward for precious
> inputs from the community.
>
> Sincerely,
> Dr. Gauri Misra
>
> Assistant Professor
> Amity Institute of Biotechnology
> Amity University
> Noida (U.P.) India
>

Re: [ccp4bb] Modelling of ligand and Refmac5

[Sam Tang]

Dear Dr Emsley

Many thanks for your reply.

I have now updated my Coot and am able to run refmac refinement using my
ligand PDB and CIF generated from elbow2 under Phenix.

This is indeed a lesson on the importance of keeping all softwares updated!

Kind regards

Sam

On 24 January 2017 at 18:29, Paul Emsley  wrote:

> On 24/01/2017 08:04, Sam Tang wrote:
>
>>
>> I am trying to fit a small molecule ligand into a protein complex using
>> Coot. The data was
>> processed to P212121, at 2.6 A.  What I did was to input a SMILES string,
>> fit the ligand,
>> merge the ligand into the protein molecule using 'Merge Molecules' and
>> save coordinates.
>>
>> After fitting the ligand (now as chain O) I ran restrained refinement in
>> Refmac5 and the
>> following error returns:
>>
>>
> Into what did you input a SMILES? If the answer is Coot, then you have an
> Old Coot and will be lead down the garden path.
>
> > I believe it is due to the nomenclature of the ligand wherein Refmac
> mistook atoms as DUM
>
> I think that you're more or less right.
>
> The modern approach is to use Acedrg to generate the ligand either via a
> GUI or the command line. That will give you a PDB file which you can fit,
> and a dictionary that you can use in Refmac, Coot (and, I believe, Phenix).
>
> Paul.
>

[ccp4bb] rigid flexible analysis

[Gauri Misra]

Hi everyone!

I would like to know the current online servers available for analyzing the
rigid and flexible regions of proteins.Looking forward for precious inputs
from the community.

Sincerely,
Dr. Gauri Misra

Assistant Professor
Amity Institute of Biotechnology
Amity University
Noida (U.P.) India

[ccp4bb] Postdoctoral Research Scientist in Division of Structural Biology, University of Oxford

[Jonathan Grimes]

Dear All,

  Post-doc positions are available in the laboratory of Dr Jon Grimes, in the 
  Division of Structural Biology (STRUBI)  in the Nuffield Department of 
Clinical 
  Medicine at the University of Oxford. 
  Dr Grimes's group incorporates structural biology and multidisciplinary 
  bio-imaging approaches to characterize Influenza virus replication and 
transcription. 
  Key to viral replication is the viral polymerase that copies the viral genome 
and 
  produces viral messenger RNA which is then used to make building blocks for 
  new virus particles. Specifically, the group aims to understand in molecular 
level 
  detail the mechanisms and dynamics of viral replication and transcription. 
  

  The position is funded by The Wellcome Trust and is available immediately for 
a period of upto 5 years. 
  The start date is flexible but must be before September 2017. The deadline 
for applications is 6th February 2017.

   More information about the position can be found here

  
https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.display_form?p_display_in_irish=N_company=10_refresh_search=Y_process_type=_recruitment_id=126664_form_profile_detail=_display_apply_ind=Y_internal_external=E_applicant_no=


  Thanks
  Jon

Assoc Prof. Jonathan M. Grimes, 
NDM Senior Reseach Fellow
DIAMOND Research Fellow

Division of Structural Biology
Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive,
Oxford OX3 7BN, UK

Email: jonat...@strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk 
Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547   

Re: [ccp4bb] Modelling of ligand and Refmac5

[Paul Emsley]

On 24/01/2017 08:04, Sam Tang wrote:


I am trying to fit a small molecule ligand into a protein complex using Coot. 
The data was
processed to P212121, at 2.6 A.  What I did was to input a SMILES string, fit 
the ligand,
merge the ligand into the protein molecule using 'Merge Molecules' and save 
coordinates.

After fitting the ligand (now as chain O) I ran restrained refinement in 
Refmac5 and the
following error returns:



Into what did you input a SMILES? If the answer is Coot, then you have an Old Coot and will 
be lead down the garden path.


> I believe it is due to the nomenclature of the ligand wherein Refmac mistook 
atoms as DUM

I think that you're more or less right.

The modern approach is to use Acedrg to generate the ligand either via a GUI or the command 
line. That will give you a PDB file which you can fit, and a dictionary that you can use in 
Refmac, Coot (and, I believe, Phenix).


Paul.

[ccp4bb]

[Philip Walker]

Dear Colleagues 

A reminder: applications close on 31 Jan 2017. 

Dear colleagues, Applications are open for a cryo-electron microscopy scientist 
at the Francis Crick Institute in London to work in the Structural Biology 
Science Technology Platform. 
We are looking for a motivated, skilled electron microscopist who enjoys 
interacting with other scientists and will help with single-particle and 
tomography projects on our two recently acquired Titan Krios electron 
microscopes. 
Details pasted below and link found here:
https://goo.gl/XI6NLb
For any questions, please contact Peter Rosenthal (Group Leader; 
peter.rosent...@crick.ac.uk ), Alessandro Costa (Group Leader; 
alessandro.co...@crick.ac.uk ) or Phil Walker (Head, SB STP; 
philip.wal...@crick.ac.uk) Phil WalkerPeter RosenthalAlessandro Costa   Senior 
Laboratory Research Scientist – Cryo-electron Microscopy ScientistReports to 
Head, Structural Biology Science Technology PlatformSalary: Competitive with 
benefits, subject to skills and experienceThis is a 5 year fixed term position 
on Crick Terms and Conditions of Employment. There are excellent opportunities 
for career advancement.
SUMMARYThe Francis Crick Institute seeks to recruit a cryo-electron microscopy 
(cryo-EM) scientist to support single-particle and tomography projects.The 
research scientist will be appointed to the Structural Biology Science 
Technology Platform (SB STP), which supports the Crick in the areas of protein 
science (expression and purification), biophysics, X-ray crystallography, 
cryo-EM and related areas.The post-holder will build on existing strengths at 
the Crick Institute in cryo-EM by interacting with members of the technology 
platform, research groups in cryo-EM, and other structural biology 
laboratories. There are excellent opportunities for career advancement.The 
Francis Crick Institute is building a state-of-the-art facility for electron 
microscopy and computation and the post will consolidate excellence in these 
areas. Two FEI Titan Krios microscopes have recently been purchased and the 
installation and commissioning of the first of these should be completed in 
2016.There are excellent facilities for computing and expertise in experimental 
and computational aspects of cryoEM being developed through the structural 
biology platform.
KEY RESPONSIBILITIESThese include but not limited to; • Support a range of 
cryo-EM research activities through interaction with Crick scientists including 
cryo-EM scientists and other structural biologists interested in cryo-EM.• 
Contribute to management and maintenance of high-end cryo-electron microscopes• 
Support experimental design including sample preparation and imaging of 
biological specimens. • Provide expertise and support in computational image 
analysis.• Provide training in both experimental and computational aspects of 
cryo-EM.
ABOUT USThe Francis Crick Institute (the Crick) is a partnership between the 
Medical Research Council (MRC), Cancer Research UK (CRUK), the Wellcome Trust, 
University College London (UCL), Imperial College London and King’s College 
London. It is a registered charity whose purpose is to conduct biomedical 
research into all aspects of human health and disease.The institute aspires to 
be a world-leading centre of biomedical research and innovation. It will 
promote connections between researchers and disciplines and between academic 
institutions, healthcare organisations and businesses. Dedicated to research 
excellence, the institute will have the scale, vision and expertise to tackle 
the most challenging scientific questions underpinning health and disease. It 
will be world-class with a strong national role — training scientists and 
developing ideas for public good.
KEY EXPERIENCE AND COMPETENCIESThe post holder should embody and demonstrate 
our core Crick values: Bold, Imaginative, Open, Dynamic and Collegial, in 
addition to the following:
Essential• A higher degree in biological, physical, or engineering sciences. • 
Research experience and expertise in electron microscopy.• Specialist knowledge 
of cryo-electron microscope operation and high-resolution data collection.• 
Proven track record in three-dimensional electron microscopy.• Excellent 
communication skills within a research environment, building highly effective 
working relationships with scientists and support staff.• Plan time efficiently 
and be able to work both independently and in a team setting.
Desirable• PhD in Structural Biology or related areas.• Experience in data 
analysis single particle images and/or tomography data.• Experience with field 
emission gun microscopes and direct electron detectors.• Postdoctoral 
experience in conducting cutting-edge research in cryo-EM.• Authorship in 
peer-reviewed publications in internationally recognized scientific journals.• 
Specialist knowledge of cryo-EM reconstruction software. • Knowledge of 
scientific computing including Unix shell scripting, 

[ccp4bb] Tenure Track Research Group Leader Position “Cryo-Electron Microscopy of Membrane Protein Complexes”

[Christoph Parthier]

Dear ccp4 community,

I just would like to call your attention about this opening at the
Martin-Luther-University Halle-Wittenberg, Germany. Further information can
be found in the attached PDF.

Kind regards,
Christoph


HALOmem_8p138x255_09-01-17_s1.pdf
Description: Adobe PDF document

[ccp4bb] Modelling of ligand and Refmac5

[Sam Tang]

Dear all

I am trying to fit a small molecule ligand into a protein complex using
Coot. The data was processed to P212121, at 2.6 A.  What I did was to input
a SMILES string, fit the ligand, merge the ligand into the protein molecule
using 'Merge Molecules' and save coordinates.

After fitting the ligand (now as chain O) I ran restrained refinement in
Refmac5 and the following error returns:

Input file :C:/20161226_1.1_refmac1-coot-1.pdb

  --

  ---  LIBRARY OF MONOMERS   ---

 _lib_name mon_lib

 _lib_version  5.44

 _lib_update   30/05/14

  --

  NUMBER OF MONOMERS IN THE LIBRARY  : 13409

with complete description: 13409

  NUMBER OF MODIFICATIONS:63

  NUMBER OF LINKS:73

  I am reading libraries. Please wait.

  - energy parameters

  - monomer"s description (links & mod )


FORMATTED  OLD file opened on unit  45



Logical name: ATOMSF, Filename: C:\CCP4-7\7.0\lib\data\atomsf.lib




  Number of atoms:   19934

  Number of residues :2577

  Number of chains   :  15

  I am reading library. Please wait.

mon_lib.cif


ERROR : DUM : duplicated atom_name : "DUM ".

  chain: OO   residue:1


(And the error repeats itself for >100 times)


I believe it is due to the nomenclature of the ligand wherein Refmac
mistook atoms as DUM.  (Also, the chain ID O was identified as OO?)  In a
test run I carried out rigid body refinement and the programme finished
without issues.

Is there a way I could rectify the above problem? Thanks in advance for
your attention and input.

Kind regards


Sam Tang
Biochemistry Programme, School of Life Sciences, CUHK