[ccp4bb] open pdb and mtz in qtRView1.16 interface

[Wei Ding]

Dear all,
As we know, when a modelbuild procedure finish(such as buccaneer),  we can open 
the input and output pdb/mtz file directly in qtRView interface by click the 
Coot/ccp4mg/Display button.
And now, I am revising the OASIS package and hope that  the intermediate 
results(e.g.: circle1.pdb, circle1.mtz, circle2.pdb,circle2.mtz...) can also 
display in qtRView interface.
How to achieve this?
Thank you for your time.






--

Wei Ding
P.O.Box 603
The Institute of Physics,Chinese Academy of Sciences
Beijing,China
100190
Tel: +86-10-82649083
E-mail: ding...@iphy.ac.cn

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

[Khoa Pham]

Dear All,

Thank you very much for your suggestions. 
I will refine the structure and keep you updated. 

Khoa

Re: [ccp4bb] Unknown Ligand Density

[Artem Evdokimov]

Flying spaghetti monster. Ramen!

Sorry. Could not resist.

Artem
www.harkerbio.com
"...touched by His Noodly Appendage"

On Jun 14, 2017 12:51 PM, "Nick Thomas"  wrote:

Dear CCP4bb,

I am refining a structure and have come across strong electron density for
an unknown ligand (image attached). Would someone be able to identify this
unknown ligand that somehow was co-purified with the protein.


The electron density shape does not match anything included in the
crystallization conditions.


The crystallization condition is
0.1M MES monohydrate, pH 6.5, 1.6 M Magnesium sulphate heptahydrate

Re: [ccp4bb] Unknown Ligand Density

[Eleanor Dodson]

First thing to check - is there any anomalous scatterer peak in the
density?
Easy to do an anom diff map from GUI2 - choose REFMAC and add - do anom
diff fourier, then follow with a diff peak search in COOT .
Eleanor

On 14 June 2017 at 18:04, Sanishvili, Ruslan  wrote:

> Difficult to guess from what is visible of the protein but is this density
> on a two-fold axis?
>
> Or, it could be Slimer the ghost...
>
> Cheers,
>
> Nukri
>
>
> Ruslan Sanishvili (Nukri), Ph.D.
> Macromolecular Crystallographer
> GM/CA@APS
> X-ray Science Division, ANL
> 9700 S. Cass Ave.
> Lemont, IL 60439
>
> Tel: (630)252-0665 <(630)%20252-0665>
> Fax: (630)252-0667 <(630)%20252-0667>
> rsanishv...@anl.gov
>
>
>
> --
> *From:* CCP4 bulletin board  on behalf of Nick
> Thomas 
> *Sent:* Wednesday, June 14, 2017 11:39 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Unknown Ligand Density
>
> Dear CCP4bb,
>
> I am refining a structure and have come across strong electron density for
> an unknown ligand (image attached). Would someone be able to identify
> this unknown ligand that somehow was co-purified with the protein.
>
>
> The electron density shape does not match anything included in the
> crystallization conditions.
>
>
> The crystallization condition is
> 0.1M MES monohydrate, pH 6.5, 1.6 M Magnesium sulphate heptahydrate
>

[ccp4bb] PhD fellowships, Biozentrum Basel, Switzerland

[Timm Maier]

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Re: [ccp4bb] Interaction of protein's glutamine sidechain nitrogen with a bound ligand's double bond

[Matthew Merski]

Yes, it very well could be, the distance is pretty typical for this kind of
weak, "non-cannonical" hydrogen bond.  However, directionality is an
important aspect of hydrogen bonding and its hard to say if this is a
reasonable bond without a  (small filesize so no one's inbox gets
overloaded) picture of the geometry.

Matthew Merski
University of Warsaw

On Wed, Jun 14, 2017 at 7:23 PM, Evan Waldron  wrote:

> Dear CCP4bb,
>
>I recently solved the 2.0 Å crystal structure of a small hydrophobic
> molecule bound to a protein. A glutamine sidechain nitrogen is positioned
> ~3.3-3.4 Å from a double bond in the small molecule acyl chain. Could this
> be a similar interaction to the X-H (where X-H is an H-bond donor) Pi
> bonding seen between aromatic residues and hydrogen bond donors, i.e., is
> this an interaction that could be contributing to the protein-ligand
> binding energy?
>
> I haven't found a precedent for X-H-Pi hydrogen bonding between amides and
> alkenes in the protein literature or my searches of the PDB; however, I did
> find several papers that consider the role of such interactions in small
> molecules:
>
> http://pubs.acs.org/doi/abs/10.1021/jp046031o
> http://pubs.acs.org/doi/pdf/10.1021/ja00288a034
> http://pubs.acs.org/doi/pdf/10.1021/ja0013531
>
> Thank you in advance for considering my question regarding this
> protein-ligand interaction. Any thoughts on this unusual interaction will
> be greatly appreciated.
>
> Sincerely,
> Evan Waldron
>
> Neiditch Lab Graduate Student
> Rutgers, NJMS
>

[ccp4bb] Interaction of protein's glutamine sidechain nitrogen with a bound ligand's double bond

[Evan Waldron]

Dear CCP4bb,

   I recently solved the 2.0 Å crystal structure of a small hydrophobic
molecule bound to a protein. A glutamine sidechain nitrogen is positioned
~3.3-3.4 Å from a double bond in the small molecule acyl chain. Could this
be a similar interaction to the X-H (where X-H is an H-bond donor) Pi
bonding seen between aromatic residues and hydrogen bond donors, i.e., is
this an interaction that could be contributing to the protein-ligand
binding energy?

I haven't found a precedent for X-H-Pi hydrogen bonding between amides and
alkenes in the protein literature or my searches of the PDB; however, I did
find several papers that consider the role of such interactions in small
molecules:

http://pubs.acs.org/doi/abs/10.1021/jp046031o
http://pubs.acs.org/doi/pdf/10.1021/ja00288a034
http://pubs.acs.org/doi/pdf/10.1021/ja0013531

Thank you in advance for considering my question regarding this
protein-ligand interaction. Any thoughts on this unusual interaction will
be greatly appreciated.

Sincerely,
Evan Waldron

Neiditch Lab Graduate Student
Rutgers, NJMS

Re: [ccp4bb] Unknown Ligand Density

[Sanishvili, Ruslan]

Difficult to guess from what is visible of the protein but is this density on a 
two-fold axis?

Or, it could be Slimer the ghost...

Cheers,

Nukri


Ruslan Sanishvili (Nukri), Ph.D.
Macromolecular Crystallographer
GM/CA@APS
X-ray Science Division, ANL
9700 S. Cass Ave.
Lemont, IL 60439

Tel: (630)252-0665
Fax: (630)252-0667
rsanishv...@anl.gov




From: CCP4 bulletin board  on behalf of Nick Thomas 

Sent: Wednesday, June 14, 2017 11:39 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unknown Ligand Density

Dear CCP4bb,

I am refining a structure and have come across strong electron density for an 
unknown ligand (image attached). Would someone be able to identify this unknown 
ligand that somehow was co-purified with the protein.

The electron density shape does not match anything included in the 
crystallization conditions.

The crystallization condition is
0.1M MES monohydrate, pH 6.5, 1.6 M Magnesium sulphate heptahydrate

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

[benjamin bax]

Hi Khoa,

  How many rounds of refine and rebuild have you gone through on the graphics?

Have you tried Lorestr in CCP4 (Automated refinement of macromolecular 
structures at low resolution using prior information, Oleg Kovalevskiy, Robert 
A. Nicholls and Garib N. Murshudov). 

Ben 

[At 2.9A resolution traditionallly I would calculate maps with refmac, phenix 
and buster with and without tls refinement.
Then go through the structure looking at all maps and rebuilding. 
Information content at 2.9A is sometimes limited and structural changes only 
appear slowly with careful refinement (5-10 rounds).]


On 14 Jun 2017, at 14:09, Khoa Pham  wrote:

Dear CCP4 members,

I am refining a structure with a resolution of ~ 2.9 A and the Rwork/Rfree are 
are 0.34/0.37, respectively. 
My question is that these Rwork/Rfree are acceptable for publication. If not, 
how can I reduce them?

Thank you.

Khoa

The table of statics.
Space group
C121

Resolution (Å)
29.69-2.92
No of unique reflections
61569 (8747)
Rmerge (%)
20 (350)
Rpim (%)
11 (198)
I/s(I)
8.3 (0.5)
CC1/2
0.99 (0.33)
CCanomalous
N/A
Completeness (%)
98.5 (95.8)
Redundancy
4.2 (4.0)
 
 
Refinement
 
Resolution (Å)
29.69-2.92
No of reflections
58394 (4069)
Rwork/Rfree
0.3380/0.3689

R.m.s. deviations
 
   Bond lengths (Å)
0.0073
   Bond angles (o)
1.1062


Dr Ben Bax

York Structural Biology Laboratory, 
Department of Chemistry, 
University of York,
York YO10 5DD

ben.d.v@gmail.com

 

 

Re: [ccp4bb] Shape similarity of ligand binding sites

[Avinash Punekar]

Hi Steve,

Have you tried CASTp server (http://sts.bioe.uic.edu/castp/). That should help 
you to compare the shape of the ligand-binding sites.

Best wishes,
Avinash

Re: [ccp4bb] Antw: Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

[Eleanor Dodson]

The R factors may be high because the structure is imperfect - almost
inevitable at that resolution - but also there are often serious
difficulties with scaling at this resolution . If you are using REFMAC look
at the  v  wrt resolution plot at the end of refinement (follows R
and Rfree plot v resolution 0. You may see there is a large discrepancy..
Never sure what to do about it - the higher resolution data you can use the
more reliable the scaling so maybe you can extend the resolution by
accepting CC1/2 < 0.5 or whatever your data cut off is based on..
REFMAC offers various scaling options, trying to deal with the bulk
solvent.

But maybe your scaling is OK - just check it as a matter of course!1

Eleanor



On 14 June 2017 at 15:32, Matthias Barone  wrote:

> If you dont use Phenix, print the figures of
> https://doi.org/10.1016/S0969-2126(02)00743-8
> and use them beside your screen. Helps a lot if you wanna have a quick
> look at Rfact distributions..
>
>
> >>> Paul Emsley  14.06.17 15.25 Uhr >>>
> On 14/06/2017 14:09, Khoa Pham wrote:
> > Dear CCP4 members,
> >
> > I am refining a structure with a resolution of ~ 2.9 A and the
> Rwork/Rfree are are
> > 0.34/0.37, respectively.
> > My question is that these Rwork/Rfree are acceptable for publication.
>
> If you have Phenix, try POLYGON. That will give you a good clue.
>
> >If not, how can I
> > reduce them?
> >
>
> That is more complicated to answer.
>
>
> Paul.
>

Re: [ccp4bb] Shape similarity of ligand binding sites

[Chris Fage]

Hi Stephen,

I've had some luck calculating ligand-binding cavity volume with the 3v
website (http://3vee.molmovdb.org/). You might want to give it a shot.

Best,
Chris

On Wed, Jun 14, 2017 at 12:42 PM,  <
stephen.c...@rc-harwell.ac.uk> wrote:

> Dear ccp4bb,
>
> I am trying to compare the shape of a ligand binding site in my protein
> with that of some homologues and mutants and was wondering how others go
> about this?  I specifically want to compare the shapes of the surface
> (similar to an sc analysis of an interface) rather than the positions of
> the atoms in the residues that make up the site.  I have come across
> PESDserv, but this doesn't do quite what I would like.  Any suggestions
> would be very welcome.
>
> Best wishes,
>
> Steve
>
> Dr Stephen Carr
> Research Complex at Harwell (RCaH)
> Rutherford Appleton Laboratory
> Harwell Oxford
> Didcot
> Oxon OX11 0FA
> United Kingdom
> Email stephen.c...@rc-harwell.ac.uk
> tel 01235 567717
>
> This email and any attachments may contain confidential, copyright and or
> privileged material, and are for the use of the intended addressee only. If
> you are not the intended addressee or an authorized recipient of the
> addressee, please notify us of receipt by returning the e-mail and do not
> use, copy, retain, distribute or disclose the information in or attached to
> this email.
>
> Any views or opinions presented are solely those of the author and do not
> necessarily represent those of the Research Complex at Harwell.
>
> There is no guarantee that this email or any attachments are free from
> viruses and we cannot accept liability for any damage which you may sustain
> as a result of software viruses which may be transmitted in or with the
> message.
>
> We use an electronic filing system. Please send electronic versions of
> documents, unless paper is specifically requested.
>
> This email may have a protective marking, for an explanation, please see:
> http://www.mrc.ac.uk/About/informationandstandards/
> documentmarking/index.htm.
>

[ccp4bb] Antw: Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

[Matthias Barone]

If you dont use Phenix, print the figures of 
https://doi.org/10.1016/S0969-2126(02)00743-8
and use them beside your screen. Helps a lot if you wanna have a quick look at 
Rfact distributions..




>>> Paul Emsley  14.06.17 15.25 Uhr >>>
On 14/06/2017 14:09, Khoa Pham wrote:
> Dear CCP4 members,
> 
> I am refining a structure with a resolution of ~ 2.9 A and the Rwork/Rfree 
> are are 
> 0.34/0.37, respectively.
> My question is that these Rwork/Rfree are acceptable for publication. 

If you have Phenix, try POLYGON. That will give you a good clue.

 >If not, how can I
> reduce them?
> 

That is more complicated to answer.


Paul.

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

[Paul Emsley]

On 14/06/2017 14:09, Khoa Pham wrote:

Dear CCP4 members,

I am refining a structure with a resolution of ~ 2.9 A and the Rwork/Rfree are are 
0.34/0.37, respectively.
My question is that these Rwork/Rfree are acceptable for publication. 


If you have Phenix, try POLYGON. That will give you a good clue.

>If not, how can I

reduce them?



That is more complicated to answer.


Paul.

[ccp4bb] What are acceptable Rwork/Rfree for publication

[Khoa Pham]

Dear CCP4 members,

I am refining a structure with a resolution of ~ 2.9 A and the Rwork/Rfree are 
are 0.34/0.37, respectively.
My question is that these Rwork/Rfree are acceptable for publication. If not, 
how can I reduce them?

Thank you.

Khoa

The table of statics.
Space group

C121



Resolution (Å)

29.69-2.92

No of unique reflections

61569 (8747)

Rmerge (%)

20 (350)

Rpim (%)

11 (198)

I/*(I)

8.3 (0.5)

CC1/2

0.99 (0.33)

CCanomalous

N/A

Completeness (%)

98.5 (95.8)

Redundancy

4.2 (4.0)





Refinement



Resolution (Å)

29.69-2.92

No of reflections

58394 (4069)

Rwork/Rfree

0.3380/0.3689


R.m.s. deviations



   Bond lengths (Å)

0.0073

   Bond angles (o)

1.1062

[ccp4bb] Shape similarity of ligand binding sites

Dear ccp4bb,

I am trying to compare the shape of a ligand binding site in my protein with 
that of some homologues and mutants and was wondering how others go about this? 
 I specifically want to compare the shapes of the surface (similar to an sc 
analysis of an interface) rather than the positions of the atoms in the 
residues that make up the site.  I have come across PESDserv, but this doesn't 
do quite what I would like.  Any suggestions would be very welcome.

Best wishes,

Steve

Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717

This email and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorized recipient of the addressee, 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to this email.

Any views or opinions presented are solely those of the author and do not 
necessarily represent those of the Research Complex at Harwell.

There is no guarantee that this email or any attachments are free from viruses 
and we cannot accept liability for any damage which you may sustain as a result 
of software viruses which may be transmitted in or with the message.

We use an electronic filing system. Please send electronic versions of 
documents, unless paper is specifically requested.

This email may have a protective marking, for an explanation, please see:
http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm.

[ccp4bb] Cryo-EM symposium, 4-5 September 2017, Delft University of Technology

[Jolijn Leeuwenburgh]

Dear colleagues,

We are pleased to announce the International Cryo-EM Symposium that will take 
place from 4-5 September 2017 in Delft, the Netherlands.

With the aim to share the latest developments in 3D cryo-electron microscopy 
(EM) with scientists and students at the Delft University of Technology and in 
the Netherlands, we bring together the leaders in atomic scale single particle 
3D-EM and electron tomography of cells and tissue sections. We use this 
occasion to inaugurate the Cryo-EM laboratory that was recently established at 
the Department of Bionanoscience, featuring a JEOL 3200 FSC. The scientific 
program is divided into five sessions that summarize progress in biology and 
technical developments in cryo-EM. In addition, a workshop will take place 
after the symposium, where participants can learn about most recent technical 
advances in sample preparation, data acquisition and image processing. This 
workshop includes 
presentations from the best companies in the field and practical demonstrations 
for scientists interested in getting hands-on experience.
More information can be found at the symposium website:
www.tudelft.nl/cryoemsymposium

Due to limited capacity, early 
registration is 
encouraged.

We look forward to seeing you in Delft!
The organising committee
Professor Ariane Briegel (Leiden University), Professor Andreas Engel (Delft 
University of Technology)

Re: [ccp4bb] <4SSQ/LL> and resolution (in refmac logfile)

[Wei Ding]

Got it, thank you very much.







--

Wei Ding
P.O.Box 603
The Institute of Physics,Chinese Academy of Sciences
Beijing,China
100190
Tel: +86-10-82649083
E-mail: ding...@iphy.ac.cn



At 2017-06-14 16:54:23, "Phil Evans"  wrote:
>4(sin theta/lambda)^2 = 1/d^2
>
>> On 14 Jun 2017, at 09:30, Wei Ding  wrote:
>> 
>> Dear all,
>> what is the relationship between  <4SSQ/LL> and resolution?
>> In refmac logfile, there is a table:
>>  <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  
>> FSCwork CorrFoFcFree CorrFoFcWork$$
>>  $$
>>   0.0065130   0.894171   0.872301   0.882  0.734  0.8235  0.8078 
>>  0.4204  0.5580
>>   0.0178288   0.879174   0.856462   0.871  0.724  0.8470  0.7811 
>>  0.6633  0.6237
>>   0.0292394   0.882179   0.814573   0.860  0.748  0.8308  0.7431 
>>  0.7682  0.5245
>> 
>> but when I open this logfile by logview, this table become a graph, and 
>> those values are convert to Resolution[A]:  4.47, 3.16 
>> So what is the transform formula between 4SSQ/LL and Resolution?
>> Thank you for your time.
>> 
>> 
>> --
>> Wei Ding
>> P.O.Box 603
>> The Institute of Physics,Chinese Academy of Sciences
>> Beijing,China
>> 100190
>> Tel: +86-10-82649083
>> E-mail: ding...@iphy.ac.cn
>> 
>> 
>>  
>> 
>> 
>>  

Re: [ccp4bb] <4SSQ/LL> and resolution (in refmac logfile)

[Phil Evans]

4(sin theta/lambda)^2 = 1/d^2

> On 14 Jun 2017, at 09:30, Wei Ding  wrote:
> 
> Dear all,
> what is the relationship between  <4SSQ/LL> and resolution?
> In refmac logfile, there is a table:
>  <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  
> FSCwork CorrFoFcFree CorrFoFcWork$$
>  $$
>   0.0065130   0.894171   0.872301   0.882  0.734  0.8235  0.8078  
> 0.4204  0.5580
>   0.0178288   0.879174   0.856462   0.871  0.724  0.8470  0.7811  
> 0.6633  0.6237
>   0.0292394   0.882179   0.814573   0.860  0.748  0.8308  0.7431  
> 0.7682  0.5245
> 
> but when I open this logfile by logview, this table become a graph, and those 
> values are convert to Resolution[A]:  4.47, 3.16 
> So what is the transform formula between 4SSQ/LL and Resolution?
> Thank you for your time.
> 
> 
> --
> Wei Ding
> P.O.Box 603
> The Institute of Physics,Chinese Academy of Sciences
> Beijing,China
> 100190
> Tel: +86-10-82649083
> E-mail: ding...@iphy.ac.cn
> 
> 
>  
> 
> 
>  

[ccp4bb] <4SSQ/LL> and resolution (in refmac logfile)

[Wei Ding]

Dear all,
what is the relationship between  <4SSQ/LL> and resolution?
In refmac logfile, there is a table:
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork 
CorrFoFcFree CorrFoFcWork$$
 $$
  0.0065130   0.894171   0.872301   0.882  0.734  0.8235  0.8078  
0.4204  0.5580
  0.0178288   0.879174   0.856462   0.871  0.724  0.8470  0.7811  
0.6633  0.6237
  0.0292394   0.882179   0.814573   0.860  0.748  0.8308  0.7431  
0.7682  0.5245

but when I open this logfile by logview, this table become a graph, and those 
values are convert to Resolution[A]:  4.47, 3.16 
So what is the transform formula between 4SSQ/LL and Resolution?
Thank you for your time.




--

Wei Ding
P.O.Box 603
The Institute of Physics,Chinese Academy of Sciences
Beijing,China
100190
Tel: +86-10-82649083
E-mail: ding...@iphy.ac.cn