Re: [ccp4bb] ligand with out space group information

[Johannes Cramer]

Hi,

I had the same problem once. Some chemistry programs are not really good at
exporting to pdb. Check the file format definition of pdb files, here:
ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_A4.pdf
Most interesting for you is probably pp. 174.
Also make sure, there is an "END" at the end.
It might help, if you send a link to the ligand file.

Cheers,
Johannes

2017-03-30 19:41 GMT+02:00 Paul Emsley :

> On 30/03/17 14:59, chemocev marker wrote:
>
>> Hi
>>
>
> Hi.
>
> I have model of ligand molecule and it does not open in coot. Its not a
>> crystal structure. I can view it in the pymol or chimera but not in the
>> coot. It gives error that it does not have any space group information. Is
>> there is a way to open it in coot.
>>
>>
> If there is not a CRYST1 card in your pdb file, then Coot will warn you
> that your molecule does not have symmetry.  It is merely a warning, not an
> error.
>
> If coot can't read the pdb file it's likely (it seems to me) that it's not
> actually a (specifications-compliant) pdb file.  Coot should give you an
> error about any line that it particularly doesn't like.
>
>
> Paul.
>

Re: [ccp4bb] ligand with out space group information

[Tim Gruene]

Dear Paul,

a promising way to fix the problem is the program pdbset (or pdbcur), both 
available with ccp4.

You can place the molecule into a P1 cell large enough to hold all 
coordinates, e.g. from the command line

pdbset XYZIN yourbroken.pdb XYZOUT yourfixed.pdb << eof
SPACEGROUP P1
CELL 25 25 25 90 90 90
END
eof

the cell is arbitrary, just make it sufficiently big.

Kindly,
Tim

On Friday 31 March 2017 09:11:17 AM Johannes Cramer wrote:
> Hi,
> 
> I had the same problem once. Some chemistry programs are not really good at
> exporting to pdb. Check the file format definition of pdb files, here:
> ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_A4.pdf
> Most interesting for you is probably pp. 174.
> Also make sure, there is an "END" at the end.
> It might help, if you send a link to the ligand file.
> 
> Cheers,
> Johannes
> 
> 2017-03-30 19:41 GMT+02:00 Paul Emsley :
> > On 30/03/17 14:59, chemocev marker wrote:
> >> Hi
> > 
> > Hi.
> > 
> > I have model of ligand molecule and it does not open in coot. Its not a
> > 
> >> crystal structure. I can view it in the pymol or chimera but not in the
> >> coot. It gives error that it does not have any space group information.
> >> Is
> >> there is a way to open it in coot.
> > 
> > If there is not a CRYST1 card in your pdb file, then Coot will warn you
> > that your molecule does not have symmetry.  It is merely a warning, not an
> > error.
> > 
> > If coot can't read the pdb file it's likely (it seems to me) that it's not
> > actually a (specifications-compliant) pdb file.  Coot should give you an
> > error about any line that it particularly doesn't like.
> > 
> > 
> > Paul.
-- 
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Principal Investigator
Biology and Chemistry
OFLC/104
CH-5232 Villigen PSI

Phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A



signature.asc
Description: This is a digitally signed message part.

[ccp4bb] Ligand electron density

[Bernhard Rupp]

Hi Fellows,

 

due to the change of month on Sa I am releasing already today

the first page of an until Sa embargoed reprint on concerns 

about theoretical principles of electron density reconstruction. 

 

The paper is available on my dropbox (full paper after Sa):  

https://dl.dropboxusercontent.com/u/30662912/Rupp_2017_Phys_Rev_Letters_Elec
tron_Density.pdf

 

Best wishes, BR

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

http://www.hofkristallamt.org/

b...@hofkristallamt.org  

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

[ccp4bb] Spam : Re: [ccp4bb] Protein Ligand interaction using SPR technique

[Debasish Kumar Ghosh]

Debasish Kumar Ghosh

CSIR- Senior Research Fellow (PhD Scholar)
C/o: Dr. Akash Ranjan
Computational and Functional Genomics Group
Centre for DNA Fingerprinting and Diagnostics
Hyderabad, INDIA

Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com
Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab)
Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html



- Original Message -
From: Praveen Tripathi 
To: CCP4BB@JISCMAIL.AC.UK
Sent: Fri, 31 Mar 2017 10:31:43 +0530 (IST)
Subject: [ccp4bb] Protein Ligand interaction using SPR technique

Dear all,
Sorry for off-topic question.
I want to study protein interaction with few small molecules using SPR
(Machine- *BIACORE 3000*).

The recombinant protein expressed in bacterial expression system is of 92
kDa (with His tag), pI= 9.

*Question-*
1. What should be the chip of choice- *NTA chip or CM5 chip* of GE
healthcare?
2. Is there any alternative available for chips and machine?

Thanks in advance.

Regards

Praveen

[ccp4bb] Spam : Re: [ccp4bb] Protein Ligand interaction using SPR technique

[Debasish Kumar Ghosh]

Dear Praveen,

We have very good experience with protein ligand interaction with Biacore 3000 
using CM5 chip. The NTA chip is prone to nonspecific interactions and give 
erroneous results. However the gold standard is ITC since it is more sensitive 
than Biacore 3000. 
One quick note for using Biacore 3000 is to optimize the buffer. HBS appeared 
nice for us.
Hope that helps.

Cheers!!



Debasish

CSIR- Senior Research Fellow (PhD Scholar)
C/o: Dr. Akash Ranjan
Computational and Functional Genomics Group
Centre for DNA Fingerprinting and Diagnostics
Hyderabad, INDIA

Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com
Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab)
Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html



- Original Message -
From: Praveen Tripathi 
To: CCP4BB@JISCMAIL.AC.UK
Sent: Fri, 31 Mar 2017 10:31:43 +0530 (IST)
Subject: [ccp4bb] Protein Ligand interaction using SPR technique

Dear all,
Sorry for off-topic question.
I want to study protein interaction with few small molecules using SPR
(Machine- *BIACORE 3000*).

The recombinant protein expressed in bacterial expression system is of 92
kDa (with His tag), pI= 9.

*Question-*
1. What should be the chip of choice- *NTA chip or CM5 chip* of GE
healthcare?
2. Is there any alternative available for chips and machine?

Thanks in advance.

Regards

Praveen

[ccp4bb] AstraZeneca postdoc postion

[Edman, Karl]

Dear all,
We're looking for a talented scientist to join the AstraZeneca Post Doc 
Programme to study the structure and function of a full-length transcription 
factor in complex with novel ligands and link this information to broader mode 
of action studies for active clinical projects. You will work in a highly 
dynamic environment with input from many different functions across the 
company. For full details about the position, requirements and how to apply, 
please follow the link below.
Best regards
Karl Edman

https://job-search.astrazeneca.com/job/gothenburg/postdoc-fellow-structure-and-biophysics-gothenburg-sweden/7684/4031185




Confidentiality Notice: This message is private and may contain confidential 
and proprietary information. If you have received this message in error, please 
notify us and remove it from your system and note that you must not copy, 
distribute or take any action in reliance on it. Any unauthorized use or 
disclosure of the contents of this message is not permitted and may be unlawful.

[ccp4bb] Scientist Position: HT crystallography at EMBL Grenoble

[Jose A. Marquez]

Dear colleagues,

We are looking for a experienced crystallographer for an Industrial
Liaison Scientist position at the EMBL Grenoble Outstation. Those
interested please, see the link below.

https://www.embl.fr/jobs/searchjobs/index.php?ref=GR_00107&newlang=1&b=%2Fjobs%2Fsearchjobs%2Findex.php%3Fsrch_trm%3D%26list%3DGo

Applications from scientists in either academia or industry are encouraged.

Best regards

Josan

_

Jose A. Marquez Ph.D.
Team Leader, Head of the Crystallization Facility
EMBL Grenoble Outstation
Postal address: European Molecular Biology Laboratory
71, Avenue des Martyrs
CS 90181 38042 Grenoble Cedex 9, France
Delivery address: European Molecular Biology Laboratory
71, Avenue des Martyrs
38000 Grenoble, France
Phone +33 (0)476 20 74 25
Fax. +33 (0)476 20 71 99
https://embl.fr/htxlab/
_

<>

[ccp4bb] Post-Doctoral position at EMBL Grenoble

[Jose A. Marquez]

A Post-doctoral position is available at the EMBL Grenoble  Outstation.
Please see

https://www.embl.fr/jobs/searchjobs/index.php?ref=GR_00105&newlang=1&b=%2Fjobs%2Fsearchjobs%2Findex.php%3Fsrch_trm%3D%26list%3DGo

Best regards

Josan

-- 
_

Jose A. Marquez Ph.D.
Team Leader, Head of the Crystallization Facility
EMBL Grenoble Outstation
Postal address: European Molecular Biology Laboratory
71, Avenue des Martyrs
CS 90181 38042 Grenoble Cedex 9, France
Delivery address: European Molecular Biology Laboratory
71, Avenue des Martyrs
38000 Grenoble, France
Phone +33 (0)476 20 74 25
Fax. +33 (0)476 20 71 99
https://embl.fr/htxlab/
_

<>

Re: [ccp4bb] Proline derivatives

[Lakshmi SwarnaMukhi Pidugu]

You could try scifinder.

Swarna

On Wed, Mar 29, 2017 at 6:07 PM, Jan van Agthoven  wrote:

> Hi Everyone,
> Does anyone know what’s the fastest way the find all commercially
> available proline derivatives on carbon gamma?
> Thanks,
> Jan

Re: [ccp4bb] ligand with out space group information

[laksdhamu]

Send xaxa2,from my Samsung Galaxy smartphone.
 Original message From: chemocev marker  
Date: 3/30/17  9:59 AM  (GMT-05:00) To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] 
ligand with out space group information 
HiI have model of ligand molecule and it does not open in coot. Its not a 
crystal structure. I can view it in the pymol or chimera but not in the coot. 
It gives error that it does not have any space group information. Is there is a 
way to open it in coot.
best
Jiri

[ccp4bb] RES: [ccp4bb] Large number of outliers in the dataset

[Juliana Ferreira de Oliveira]

Thank you very much for all comments. Certainly it will help me a lot!
I will compare the maps at different resolutions, reprocess the data with 
another program, looking out the mosaicity and multiplicity, and I will try to 
use all data if it is possible.
Some answers: there is no ice on crystal; I had a good prediction of the spots 
in the indexed patterns (but I will process the data again with another program 
and observe it better); Xtriage said that I don´t have twinning; I run Zanuda 
due to the possibility of pseudo translation, but it said that the space group 
seems to be correct; the multiplicity is Overall- 10.3  InnerShell - 9.5 
OuterShell - 10.2; the diffraction spots are smeared.
Bests regards,
Juliana

Juliana Ferreira de Oliveira
Brazilian Laboratory of Biosciences - LNBio
Brazilian Center for Research in Energy and Materials - CNPEM
Campinas-SP, Brazil


De: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Em nome de Xiao Lei
Enviada em: quinta-feira, 30 de março de 2017 08:44
Para: CCP4BB@JISCMAIL.AC.UK
Assunto: Re: [ccp4bb] Large number of outliers in the dataset

This case is encouraging to me that a structure can be solved with such high 
mosaicity (in your report is 1.9). I wonder how the diffraction looks like (I 
imagine spots smearing or streak). With such high mosaicity, the unit cell 
dimension and space group determination is highly likely not accurate. I 
usually lose hope of a dataset with average mosaicity above 1.3 and I would not 
process any high mosaic data, but from your case it seems 2.6A cutoff you get a 
very nice solution.  It seems the  data processing software (Imosflm or XDS) 
nowadays can handle with high mosaic data well.





On Wed, Mar 29, 2017 at 11:00 AM, Gianluca Santoni 
mailto:gianluca.sant...@esrf.fr>> wrote:
In addition to what Nicolas has pointed out, is it quite suspicious to me that 
you have the same multiplicity in the high resolution shell as in the low 
resolution.

On Mar 29, 2017 18:17, Nicolas FOOS 
mailto:nicolas.f...@esrf.fr>> wrote:

Dear Juliana,

all the statistics presented here looks good in terms of resolution cut (maybe 
I will be less sever). For me the point is about the mosaicity you report 1.90 
it's high in my opinion. How looks you images? I am wondering if the indexation 
is really right. And maybe the complain of Xtriage about outlier is due to this 
high mosaicity. What is the diagnostic of Xtriage in terms of possible 
twinning? I am also wondering about a pseudo translation.
Maybe try to re-processed your data in this direction.

Hope to help.

Nicolas

Nicolas Foos

PhD

Structural Biology Group

European Synchrotron Radiation Facility (E.S.R.F)

71, avenue des Martyrs

CS 40220

38043 GRENOBLE Cedex 9

+33 (0)6 76 88 14 87

+33 (0)4 76 88 45 19
On 29/03/2017 17:56, Mark J van Raaij wrote:
To be really convinced I think you should also compare the maps at 2.6 and 2.3 
Å. If the 2.3 Å map looks better, go for it. If it doesn’t look better, perhaps 
you are adding noise, but the I/sigma and CC1/2 values suggest you aren’t.
Perhaps try 2.5 and 2.4 Å also.
And perhaps remove a well-ordered aa from the input model, refine at different 
resolutions and compare the difference maps for that aa. Or calculate omit maps 
at different resolutions and compare those.

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser.cnb.csic.es/~mjvanraaij

On 29 Mar 2017, at 17:44, Phil Evans 
mailto:p...@mrc-lmb.cam.ac.uk>> wrote:

It is not clear to me why you believe that cutting the resolution of the data 
would improve your model (which after all is the aim of refinement). At the 
edge CC(1/2) and I/sigI are perfectly respectable, and there doesn’t seem to be 
anything wrong with the Wilson plot. Th R-factor will of course be higher if 
you include more weak data, but minimising R is _not_ the aim of refinement. 
You should keep all the data

I don’t know what xtriage means by “large number of outliers”: perhaps someone 
else can explain

Phil


On 29 Mar 2017, at 14:54, Juliana Ferreira de Oliveira 
mailto:juliana.olive...@lnbio.cnpem.br>> wrote:

Hello,
I have one dataset at 2.3 Å (probably it can be better, I/σ = 2.1 and CC1/2 = 
0.779, the summary data is below), but when I perform Xtriage analysis it says 
that “There are a large number of outliers in the data”. The space group is 
P212121. When I refine the MR solution the Rfree stops around 30% and it 
doesn´t decrease (in fact if I continue refining it starts to increase).
The Wilson plot graph is not fitting very well between 2.3 and 2.6 Å:



So I decided to cut the data at 2.6A and Xtriage analysis doesn’t notify about 
outliers anymore. I could refine the MR solution very well, the final Rwork is 
0.2427 and Rfree = 0.2730 and validation on Phenix results in a good structure.
I run Zanuda to confirm the space group and i