subject:"\[ccp4bb\] Electron density"

Re: [ccp4bb] electron density close Histidine side chain

2020-07-21 Thread David Briggs

Hi Samer,

(1) Given that you say there is a relatively high concentration of Zn2+ ions in 
the crystallisation buffer, I suspect this might be your candidate.

(2) If the Zn2+ ion is correctly represented in the pdb file, your refinement 
program of choice will know what the target co-ordination distances should be, 
and should not give clash issues.

Good luck,

Dave


--

Dr David C. Briggs

Senior Laboratory Research Scientist

Signalling and Structural Biology Lab

The Francis Crick Institute

London, UK

==

Diamond User Committee MX representative

==

about.me/david_briggs


From: samer halabi 
Sent: 21 July 2020 11:08
To: ccp4bb@jiscmail.ac.uk ; David Briggs 

Subject: Re: [ccp4bb] electron density close Histidine side chain

Hello,
Thank you for your kind reply.
If the distances are still less than 2.2Å, would coot and Refmac still consider 
that as a clash. When I try to fit in Imidazole, even if the distance is more 
than 2.8Å, it is still considering it a clash.
Sorry, I should've mentioned how I purified the protein complex.
The protein is secreted in HighFive cells, to purify it  by its 6xHis tag, I 
used Ni sepharose excel beads, eluted with Imidazole and then further purified 
with size exclusion. To get rid of the tags and leucine zipper I used to mimic 
the transmembrane domain, I subjected the protein to V8 edndoproteinase in 0.1M 
Tris pH8.5 (cuts after an exposed Glutamate). Then purified again with Ni 
sepharose excel and size exclusion prior to crystallisation. It crystallised in 
0.2M Zinc acetate, 0.1M Imidazole pH 6.5, 10% PEG 8K. We used glycerol to fish 
the crystals out.
I have worked on three other crystals of the similar molecule, which 
crsytalized in different conditions, and this is the only one I see such blobs.

Thank you again.
Best regards,
Samer


On Monday, July 20, 2020, 06:25:09 PM GMT+1, David Briggs 
 wrote:


Hi Samer,

Did you use a His tag/Ni-NTA during purification? Sometimes Ni2+ ions leach off 
the Ni-NTA -  maybe the two "ears" are  accompanying waters?

Ni-His co-ordination distance is pretty short
(2-2.2Å - table 3 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872550/#!po=0.69<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC2872550%2F%23!po%3D0.69=02%7C01%7C%7Cdfc2bafb083e44e4f00e08d82d5e137e%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637309229367599545=u9oHbg6HzNOIeQFMUadyK4OIP1%2BaNFfLAdiPb7OAG8c%3D=0>)
 and might account for your bump when you model in a ligand.

Good luck!

Dave

--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs


From: CCP4 bulletin board  on behalf of Nils Marechal 
<4954a024d277-dmarc-requ...@jiscmail.ac.uk>
Sent: Monday, July 20, 2020 5:27:37 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] electron density close Histidine side chain

‌Dear Samer,

What king of cryo-protectant did you use ?

Such a bent density, with that size, looks like an ethylene-diol.

Best regards,

Nils Marechal

De : "samer halabi" <30c2162795b2-dmarc-requ...@jiscmail.ac.uk>
A : CCP4BB@JISCMAIL.AC.UK
Envoyé: lundi 20 Juillet 2020 18:17
Objet : [ccp4bb] electron density close Histidine side chain

Hello all,
I have few blobs in an MHC II structure I am working on, especially opposite to 
Histidine as in the accompanying screenshot, that I am confused about.

In the crystal conditions, I have Tris, Imidazole, Acetate, PEG and Glycerol.
Whatever ligand I am fitting in I am getting a clash (overlap -1.029), which 
makes me think whether there is a covalent bond forming between Histidine and 
other molecule. Perhaps by oxidation.

I would greatly appreciate if you can advice me about it, whether there is some 
kind of ligand I can try to fit and if this is something that occurs in some 
structures.
Thank you.
Best regards,
Samer



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The Francis Crick In

Re: [ccp4bb] electron density close Histidine side chain

2020-07-21 Thread samer halabi

 Hello,Thank you for your kind reply.In this case that could be either Zinc or 
Nickel. Sorry, I should've mentioned how I purified the protein complex.
The protein is secreted in HighFive cells, to purify it  by its 6xHis tag, I 
used Ni sepharose excel beads, eluted with Imidazole and then further purified 
with size exclusion. To get rid of the tags and leucine zipper I used to mimic 
the transmembrane domain, I subjected the protein to V8 edndoproteinase in 0.1M 
Tris pH8.5 (cuts after an exposed Glutamate). Then purified again with Ni 
sepharose excel and size exclusion prior to crystallisation. It crystallised in 
0.2M Zinc acetate, 0.1M Imidazole pH 6.5, 10% PEG 8K. We used glycerol to fish 
the crystals out.I have worked on three other crystals of the similar molecule, 
which crsytalized in different conditions, and this is the only one I see such 
blobs.
Thank you again.Best regards,Samer
On Monday, July 20, 2020, 08:02:04 PM GMT+1, Roger Rowlett 
 wrote:  
 
 Almost certainly a metal ion, possibly Ni(2+) if a Ni-NTA column was used for 
purification. Ni-N bond lengths are typically around 2.0 A. Additional density 
is probably coordinated water molecules, which should have similar Ni-O bond 
distances around 1.9 A. It is fairly common to find adventitious metal ions 
(zinc, copper, nickel) bound to His residues.
___
Roger S. Rowlett
Gordon & Dorothy Kline Professor, Emeritus
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

email: rrowl...@colgate.edu 

On Mon, Jul 20, 2020 at 12:17 PM samer halabi 
<30c2162795b2-dmarc-requ...@jiscmail.ac.uk> wrote:

Hello all,
I have few blobs in an MHC II structure I am working on, especially opposite to 
Histidine as in the accompanying screenshot, that I am confused about.

In the crystal conditions, I have Tris, Imidazole, Acetate, PEG and Glycerol.
Whatever ligand I am fitting in I am getting a clash (overlap -1.029), which 
makes me think whether there is a covalent bond forming between Histidine and 
other molecule. Perhaps by oxidation.

I would greatly appreciate if you can advice me about it, whether there is some 
kind of ligand I can try to fit and if this is something that occurs in some 
structures.
Thank you.
Best regards,
Samer

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Re: [ccp4bb] electron density close Histidine side chain

2020-07-21 Thread samer halabi

 Hello,Thank you for your kind reply.If the distances are still less than 2.2Å, 
would coot and Refmac still consider that as a clash. When I try to fit in 
Imidazole, even if the distance is more than 2.8Å, it is still considering it a 
clash.Sorry, I should've mentioned how I purified the protein complex.
The protein is secreted in HighFive cells, to purify it  by its 6xHis tag, I 
used Ni sepharose excel beads, eluted with Imidazole and then further purified 
with size exclusion. To get rid of the tags and leucine zipper I used to mimic 
the transmembrane domain, I subjected the protein to V8 edndoproteinase in 0.1M 
Tris pH8.5 (cuts after an exposed Glutamate). Then purified again with Ni 
sepharose excel and size exclusion prior to crystallisation. It crystallised in 
0.2M Zinc acetate, 0.1M Imidazole pH 6.5, 10% PEG 8K. We used glycerol to fish 
the crystals out.I have worked on three other crystals of the similar molecule, 
which crsytalized in different conditions, and this is the only one I see such 
blobs.
Thank you again.Best regards,Samer

On Monday, July 20, 2020, 06:25:09 PM GMT+1, David Briggs 
 wrote:  
 
 Hi Samer,

Did you use a His tag/Ni-NTA during purification? Sometimes Ni2+ ions leach off 
the Ni-NTA -  maybe the two "ears" are  accompanying waters?

Ni-His co-ordination distance is pretty short 
(2-2.2Å - table 3 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872550/#!po=0.69) and might 
account for your bump when you model in a ligand.

Good luck!

Dave

--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs
From: CCP4 bulletin board  on behalf of Nils Marechal 
<4954a024d277-dmarc-requ...@jiscmail.ac.uk>
Sent: Monday, July 20, 2020 5:27:37 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] electron density close Histidine side chain ‌Dear Samer,

What king of cryo-protectant did you use ?

Such a bent density, with that size, looks like an ethylene-diol.

Best regards,

Nils Marechal De : "samer halabi" 
<30c2162795b2-dmarc-requ...@jiscmail.ac.uk>
A : CCP4BB@JISCMAIL.AC.UK
Envoyé: lundi 20 Juillet 2020 18:17
Objet : [ccp4bb] electron density close Histidine side chain
 Hello all,
I have few blobs in an MHC II structure I am working on, especially opposite to 
Histidine as in the accompanying screenshot, that I am confused about.

In the crystal conditions, I have Tris, Imidazole, Acetate, PEG and Glycerol.
Whatever ligand I am fitting in I am getting a clash (overlap -1.029), which 
makes me think whether there is a covalent bond forming between Histidine and 
other molecule. Perhaps by oxidation.

I would greatly appreciate if you can advice me about it, whether there is some 
kind of ligand I can try to fit and if this is something that occurs in some 
structures.
Thank you.
Best regards,
Samer 
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Re: [ccp4bb] electron density close Histidine side chain

2020-07-21 Thread samer halabi

 Hello,Thank you for your kind reply.We used glycerol to fish out the 
crystals.Sorry for not including more info before, I thinkI should have 
mentioned how I purified the protein complex.
The protein is secreted in HighFive cells, to purify it  by its 6xHis tag, I 
used Ni sepharose excel beads, eluted with Imidazole and then further purified 
with size exclusion. To get rid of the tags and leucine zipper I used to mimic 
the transmembrane domain, I subjected the protein to V8 edndoproteinase in 0.1M 
Tris pH8.5 (cuts after an exposed Glutamate). Then purified again with Ni 
sepharose excel and size exclusion prior to crystallisation. It crystallised in 
0.2M Zinc acetate, 0.1M Imidazole pH 6.5, 10% PEG 8K.I have worked on three 
other crystals of the similar molecule, which crsytalized in different 
conditions, and this is the only one I see such blobs.Thank you gain.Best 
regards,Samer

On Monday, July 20, 2020, 05:39:23 PM GMT+1, Nils Marechal 
<4954a024d277-dmarc-requ...@jiscmail.ac.uk> wrote:  
 
 ‌Dear Samer,

What king of cryo-protectant did you use ?

Such a bent density, with that size, looks like an ethylene-diol.

Best regards,

Nils Marechal De : "samer halabi" 
<30c2162795b2-dmarc-requ...@jiscmail.ac.uk>
A : CCP4BB@JISCMAIL.AC.UK
Envoyé: lundi 20 Juillet 2020 18:17
Objet : [ccp4bb] electron density close Histidine side chain
 Hello all,
I have few blobs in an MHC II structure I am working on, especially opposite to 
Histidine as in the accompanying screenshot, that I am confused about.

In the crystal conditions, I have Tris, Imidazole, Acetate, PEG and Glycerol.
Whatever ligand I am fitting in I am getting a clash (overlap -1.029), which 
makes me think whether there is a covalent bond forming between Histidine and 
other molecule. Perhaps by oxidation.

I would greatly appreciate if you can advice me about it, whether there is some 
kind of ligand I can try to fit and if this is something that occurs in some 
structures.
Thank you.
Best regards,
Samer 
To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] electron density close Histidine side chain

2020-07-21 Thread samer halabi

 Hello,Thank you for your kind reply.Do I need to link them together in the 
structure? Is there a method for that?
>From the other replies I thought I should mention how I purified the protein 
>complex.The protein is secreted in HighFive cells, to purify it  by its 6xHis 
>tag, I used Ni sepharose excel beads, eluted with Imidazole and then further 
>purified with size exclusion. To get rid of the tags and leucine zipper I used 
>to mimic the transmembrane domain, I subjected the protein to V8 
>edndoproteinase in 0.1M Tris pH8.5 (cuts after an exposed Glutamate). Then 
>purified again with Ni sepharose excel and size exclusion prior to 
>crystallisation. It crystallised in 0.2M Zinc acetate, 0.1M Imidazole pH 6.5, 
>10% PEG 8K.I have worked on three other crystals of the similar molecule, 
>which crsytalized in different conditions, and this is the only one I see such 
>blobs.Thank you gain.Best regards,Samer
On Monday, July 20, 2020, 05:27:18 PM GMT+1, EchelonIV 
 wrote:  

 Hello,
what immediately comes into mind is phosphohistidine, especially since the 
density looks rather large, but the geometry seems a bit off for that but I 
cannot judge only from one angle. You could of course try to fit it in and see 
how it looks.
Cheers,Arne
On Mon, Jul 20, 2020 at 6:17 PM samer halabi 
<30c2162795b2-dmarc-requ...@jiscmail.ac.uk> wrote:

Hello all,
I have few blobs in an MHC II structure I am working on, especially opposite to 
Histidine as in the accompanying screenshot, that I am confused about.

In the crystal conditions, I have Tris, Imidazole, Acetate, PEG and Glycerol.
Whatever ligand I am fitting in I am getting a clash (overlap -1.029), which 
makes me think whether there is a covalent bond forming between Histidine and 
other molecule. Perhaps by oxidation.

I would greatly appreciate if you can advice me about it, whether there is some 
kind of ligand I can try to fit and if this is something that occurs in some 
structures.
Thank you.
Best regards,
Samer

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-- 
--Arne RaasakkaPhD BiochemistryDepartment of Biomedicine, University of 
BergenNorway

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Re: [ccp4bb] electron density close Histidine side chain

2020-07-20 Thread Jon Cooper

Hello, do you have any negative difference density for the current position of 
the His side chain? If so, it may be in two confirmations. Just a thought.

Best wishes, Jon Cooper, E-mail: jon.b.coo...@protonmail.com

 Original Message 
On 20 Jul 2020, 17:16, samer halabi wrote:

> Hello all,
> I have few blobs in an MHC II structure I am working on, especially opposite 
> to Histidine as in the accompanying screenshot, that I am confused about.
>
> In the crystal conditions, I have Tris, Imidazole, Acetate, PEG and Glycerol.
> Whatever ligand I am fitting in I am getting a clash (overlap -1.029), which 
> makes me think whether there is a covalent bond forming between Histidine and 
> other molecule. Perhaps by oxidation.
>
> I would greatly appreciate if you can advice me about it, whether there is 
> some kind of ligand I can try to fit and if this is something that occurs in 
> some structures.
> Thank you.
> Best regards,
> Samer
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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Re: [ccp4bb] electron density close Histidine side chain

2020-07-20 Thread Roger Rowlett

Almost certainly a metal ion, possibly Ni(2+) if a Ni-NTA column was used
for purification. Ni-N bond lengths are typically around 2.0 A. Additional
density is probably coordinated water molecules, which should have similar
Ni-O bond distances around 1.9 A. It is fairly common to find adventitious
metal ions (zinc, copper, nickel) bound to His residues.

___
Roger S. Rowlett
Gordon & Dorothy Kline Professor, Emeritus
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

email: rrowl...@colgate.edu

On Mon, Jul 20, 2020 at 12:17 PM samer halabi <
30c2162795b2-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello all,
> I have few blobs in an MHC II structure I am working on, especially
> opposite to Histidine as in the accompanying screenshot, that I am confused
> about.
>
> In the crystal conditions, I have Tris, Imidazole, Acetate, PEG and
> Glycerol.
> Whatever ligand I am fitting in I am getting a clash (overlap -1.029),
> which makes me think whether there is a covalent bond forming between
> Histidine and other molecule. Perhaps by oxidation.
>
> I would greatly appreciate if you can advice me about it, whether there is
> some kind of ligand I can try to fit and if this is something that occurs
> in some structures.
> Thank you.
> Best regards,
> Samer
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] electron density close Histidine side chain

2020-07-20 Thread David Briggs

Hi Samer,

Did you use a His tag/Ni-NTA during purification? Sometimes Ni2+ ions leach off 
the Ni-NTA -  maybe the two "ears" are  accompanying waters?

Ni-His co-ordination distance is pretty short
(2-2.2Å - table 3 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872550/#!po=0.69) and might 
account for your bump when you model in a ligand.

Good luck!

Dave

--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs


From: CCP4 bulletin board  on behalf of Nils Marechal 
<4954a024d277-dmarc-requ...@jiscmail.ac.uk>
Sent: Monday, July 20, 2020 5:27:37 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] electron density close Histidine side chain

‌Dear Samer,

What king of cryo-protectant did you use ?

Such a bent density, with that size, looks like an ethylene-diol.

Best regards,

Nils Marechal

De : "samer halabi" <30c2162795b2-dmarc-requ...@jiscmail.ac.uk>
A : CCP4BB@JISCMAIL.AC.UK
Envoyé: lundi 20 Juillet 2020 18:17
Objet : [ccp4bb] electron density close Histidine side chain

Hello all,
I have few blobs in an MHC II structure I am working on, especially opposite to 
Histidine as in the accompanying screenshot, that I am confused about.

In the crystal conditions, I have Tris, Imidazole, Acetate, PEG and Glycerol.
Whatever ligand I am fitting in I am getting a clash (overlap -1.029), which 
makes me think whether there is a covalent bond forming between Histidine and 
other molecule. Perhaps by oxidation.

I would greatly appreciate if you can advice me about it, whether there is some 
kind of ligand I can try to fit and if this is something that occurs in some 
structures.
Thank you.
Best regards,
Samer



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Re: [ccp4bb] electron density close Histidine side chain

2020-07-20 Thread Nils Marechal

‌Dear 
Samer,

What king of cryo-protectant did you use ?

Such a bent density, with that size, looks like an ethylene-diol.

Best regards,

Nils Marechal


De : "samer 
halabi" 30c2162795b2-dmarc-requ...@jiscmail.ac.uk
A : CCP4BB@JISCMAIL.AC.UK
Envoyé: lundi 20 Juillet 2020 18:17
Objet : [ccp4bb] electron density close Histidine side chain




Helloall,
I have few blobs in 
an MHC II structure I am working on, especially opposite to Histidine as in the 
accompanying screenshot, that I am confused about.

In the crystal 
conditions, I have Tris, Imidazole, Acetate, PEG and Glycerol.
Whatever ligand I am 
fitting in I am getting a clash (overlap -1.029), which makes me think whether 
there is a covalent bond forming between Histidine and other molecule. Perhaps 
by oxidation.

I would greatly 
appreciate if you can advice me about it, whether there is some kind of ligand 
I can try to fit and if this is something that occurs in some 
structures.
Thankyou.
Bestregards,
Samer





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Re: [ccp4bb] electron density close Histidine side chain

2020-07-20 Thread Dale Tronrud

   If there is a covalent link, maybe sending a sample off to mass spec
would be a good idea.  That would remove some of the guesswork.

Dale Tronrud

On 7/20/2020 9:16 AM, samer halabi wrote:
> Hello all,
> I have few blobs in an MHC II structure I am working on, especially
> opposite to Histidine as in the accompanying screenshot, that I am
> confused about.
> 
> In the crystal conditions, I have Tris, Imidazole, Acetate, PEG and
> Glycerol.
> Whatever ligand I am fitting in I am getting a clash (overlap -1.029),
> which makes me think whether there is a covalent bond forming between
> Histidine and other molecule. Perhaps by oxidation.
> 
> I would greatly appreciate if you can advice me about it, whether there
> is some kind of ligand I can try to fit and if this is something that
> occurs in some structures.
> Thank you.
> Best regards,
> Samer
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 



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Re: [ccp4bb] electron density close Histidine side chain

2020-07-20 Thread EchelonIV

Hello,

what immediately comes into mind is phosphohistidine, especially since the
density looks rather large, but the geometry seems a bit off for that but I
cannot judge only from one angle. You could of course try to fit it in and
see how it looks.

Cheers,
Arne

On Mon, Jul 20, 2020 at 6:17 PM samer halabi <
30c2162795b2-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello all,
> I have few blobs in an MHC II structure I am working on, especially
> opposite to Histidine as in the accompanying screenshot, that I am confused
> about.
>
> In the crystal conditions, I have Tris, Imidazole, Acetate, PEG and
> Glycerol.
> Whatever ligand I am fitting in I am getting a clash (overlap -1.029),
> which makes me think whether there is a covalent bond forming between
> Histidine and other molecule. Perhaps by oxidation.
>
> I would greatly appreciate if you can advice me about it, whether there is
> some kind of ligand I can try to fit and if this is something that occurs
> in some structures.
> Thank you.
> Best regards,
> Samer
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>


-- 
--
Arne Raasakka
PhD Biochemistry
Department of Biomedicine, University of Bergen
Norway



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Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

2018-10-04 Thread John Berrisford

Hi

 

If you only want to view the EM volume for a PDB entry then you can do this 
directly from the PDB entry pages at PDBe. 

 

For example:

http://pdbe.org/6a5p

then click “3D visualisation” on the right hand side. 

 

It gets a compressed model and EM volume so will also work on your mobile phone…

 

John

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Zhijie Li
Sent: 10 September 2018 20:42
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for 
Cryo-EM structures.

 

Hi Kevin,

a)

If your goal is merely to display EM maps, then UCSF Chimera, COOT, pymol, etc. 
should all do. The EM maps are saved in the MRC format (.mrc or .mrcs). Despite 
a different extension and some minor differences in the headers, the MRC format 
is essentially the same format as our electron density maps (.ccp4 .map, etc.). 
Your favorite software for displaying crystallographic maps should work just 
fine. You will later find that owing to the fact that images are just 2D 
pixels, movies are series of 2D pixels,  maps are (saved as) 3D voxels, the 
single MRC/CCP4 format can hold many different types of data, including images, 
stacks of images, movies, maps, masks, etc..  That is why there is often also a 
.star file (similar to CIF files) that holds information on what is inside one 
or more MRC files. So be aware of what type of data you are opening. 

b)

To get an idea how cryo-EM single particle data processing works, the minimum 
you need would be RELION/EMAN2+UCSF Chimera (best for this job), which are all 
free to everyone. These will get you from the raw EM movies to the EM maps. 

If you have a computer with enough memory (16GB minimum, the more the better) 
and an Nvidia 1080TI card (~USD 800? a $150 1050TI can also get you started) 
you can already solve some EM structures! To do this, you need to get RELION 
and/or EMAN2 (ideally both):

https://www2.mrc-lmb.cam.ac.uk/relion/index.php?title=Download_%26_install

http://blake.bcm.edu/emanwiki/EMAN2/Install

The reason for the 1080TI card is that it allows the programs to use its 300+ 
GPU cores to accelerate computations. This capability is provided by Nvidia's 
CUDA library. You need to download the CUDA 8.0 library from Nvidia. CUDA 8.0 
needs to be installed before you compile RELION if you are going to compile it 
yourself (not quite necessary). 

At present, EMAN2 only uses GPU at the particle picking step so it is not 
essential to have a GPU card just for running EMAN2. But classifications and 
refinements will be very slow (days and weeks) without a GPU.

Ideally you should install everything in Linux, such as Ubuntu 16.04 mate. You 
will also need softwares such as Motioncor2, GCTF, CTFFind, for some jobs in 
the workflow. Certain settings need to be put as environmental variables in the 
Linux system. Please figure them out yourself. It will take days to succeed for 
first-timers.

 

You can start playing by following the tutorials of either RELION or EMAN2 with 
their own tutorial datasets. These datasets are not really raw data though: 
they are particle "stacks" that contain the particles picked from the raw 
micrographs. But starting from there would be the easiest way to learn the 
essentials. BTW, following the EMAN2 tutorial does not involve using a GPU at 
all. This might be true for the non-GPU version of RELION too. 

 

If you want to start from the very beginning, you can download the 396GB 
proteasome movie dataset from EMPIAR:

https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10025/

 

On youtube, Grant Jensen has a great series on cryoEM basics. I strongly 
suggest you to watch at least the part1, especially those having to do with 
CTF. 

https://www.youtube.com/watch?v=gDgFbAqdM_c 
<https://www.youtube.com/watch?v=gDgFbAqdM_c=PL8_xPU5epJdctoHdQjpfHmd_z9WvGxK8>
 =PL8_xPU5epJdctoHdQjpfHmd_z9WvGxK8-

Zhijie





On 10/09/2018 1:01 PM, Kevin Jin wrote:

Dear Herman and all ccp4ers, 

 

Many thanks for the helps and education from all of you. 

 

I am a fresh beginner in Cryo-EM,  and have no access to those resource, like 
Chimera, Phenix, Rosetta and papers, etc. For me, any answer will be valuable. 

 

Please forgive me for asking such a naive question.  I highly appreciate your 
comments and education.

 

Kevin

 

On Mon, Sep 10, 2018 at 5:28 AM mailto:herman.schreu...@sanofi.com> > wrote:

Hi Kevin, Pavel and others,

 

Since it seems that so far nobody answered the primary question: “Is there any 
sever available to create electron density maps for cryo-em structures?” So I 
will do it. The answer is very simple: They do not need to be created, they are 
available from the pdb!

 

To give an example: On the RCSB pdb web-site, I searched for entry 5vai. Then 
under the button “Download Files” I selected “Download EM Map” and downloaded 
emd_8653.map.gz. As the name suggests, this file needs to be unzipped, but this 
is tri

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

2018-09-10 Thread Zhijie Li

 if the authors did not deposit their EM-map, you cannot
download it, but the same is true for X-ray structure factors.

Happy viewing!

Herman

*Von:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>] *Im Auftrag von *Ian Tickle
*Gesendet:* Montag, 10. September 2018 12:58
*An:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Betreff:* [EXTERNAL] Re: [ccp4bb] Electron density maps for
Cryo-EM structures.

Hi Marin

I was about to comment on that too but then I realised that Pavel
is referring to the map _contours_  (which is what most people
using a map visualisation program like Coot actually see).  So the
contoured map does represent an iso-potential surface.  I'm sure
Pavel is aware that the original cryo-EM maps are 3-dimensional
objects.

Cheers

-- Ian

On Mon, 10 Sep 2018 at 10:49, Marin van Heel
<057a89ab08a1-dmarc-requ...@jiscmail.ac.uk
<mailto:057a89ab08a1-dmarc-requ...@jiscmail.ac.uk>> wrote:


Unfortunately,

The problem here lies primarily in the answer given,  not so
much in the question asked by a newcomer:

"1) In cryo-EM maps are not electron density maps but surfaces
representing electric potential. "

The answer appears to reflect the widespread misunderstanding
that EM images (and hence cryo-EM maps)  only show the
surfaces not the internal density of the complexes we study.
In my Imperial College/Leiden University lecture notes, I have
always used the below slide to illustrate this point.

Cheers,

Marin





On 10/09/2018 01:38, Pavel Afonine wrote:

Hi,

Is there any sever available to create electron
density maps for cryo-em structures?

The questions are nonsensical. Here is why:

1) In cryo-EM maps are not electron density maps but
surfaces representing electric potential.

2) Creating such a map is essentially carrying on from
cryo-EM experiment and obtaining the 3D reconstruction.

Are you really sure about what you are asking for?

Or, we should create the maps from mmCIF.

mmCIF is a file format. It may contain representations of
rabbits, boysenberries or some diffraction data. So.. how
you think it may be related to cryo-EM, in your particular
case?

I am particularly interested in those cryo-em
structures with high resolution, like 2.6~2.8A.

Sure, all are excited about high-res cryo-EM!!!

Please give me an education.

Sure. One of available universities can do this.

Cheers,

Pavel




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-- 


==

  


     Prof Dr Ir Marin van Heel

  


     Laboratório Nacional de Nanotecnologia - LNNano

     CNPEM/LNNano, Campinas, Brazil

  


     Skype:  Marin.van.Heel

     email:  marin.vanheel(A_T)gmail.com

<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmail.com=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=oyq4_tjHvYKRzK3yN_rOpIQo6sflk9725vR5aINqpHg=dS2VEfbgNj0-C_rK4Gz-4eXTJsZj7sQEp5cuMvr1i5g=>

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     and:    mvh.office(A_T)gmail.com
<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmail.com=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=oyq4_tjHvYKRzK3yN_rOpIQo6sflk9725vR5aINqpHg=dS2VEfbgNj0-C_rK4Gz-4eXTJsZj7sQEp5cuMvr1i5g=>   

  


--

     Emeritus Professor of Cryo-EM Data Processing

     Leiden University

--

     Emeritus Professor of Structural Biology

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

2018-09-10 Thread Kevin Jin

Dear Garib,

Thank you! I will definitely check the website immediately.

Sorry, I forgot to mention that I have been a user for CCP4 since 1998.
CCP4 is a great tool and reliable for crystallography, love it!

Cheers,

Kevin


On Mon, Sep 10, 2018 at 10:09 AM Garib Murshudov 
wrote:

> Dear Kevin,
>
> You can have access to all these resources (And ccpem, ccp4). They are
> free for non-commercial users.
>
> (You can also have access to any papers you want via https://sci-hub.tw/
> <http://scihub.tw>, it is also free but …)
>
> If you want to see some of the maps then you can go to emdb at
> https://www.ebi.ac.uk/pdbe/emdb/, they have many cryoEM maps and tools to
> visualise them.
>
> If you want to generate maps from coordinates then refmac  from ccp4 and
> ccpem has an option to generate 3D electrostatic potential from
> coordinates. I can send a script for that.
>
> Regards
> Garib
>
> P.S. In spite of some unusual answers you should not be afraid asking
> questions on ccp4 bb. This bulletin board is exactly for this type of
> questions.
>
>
> On 10 Sep 2018, at 18:01, Kevin Jin  wrote:
>
> Dear Herman and all ccp4ers,
>
> Many thanks for the helps and education from all of you.
>
> I am a fresh beginner in Cryo-EM,  and have no access to those resource,
> like Chimera, Phenix, Rosetta and papers, etc. For me, any answer will be
> valuable.
>
> Please forgive me for asking such a naive question.  I highly appreciate
> your comments and education.
>
> Kevin
>
> On Mon, Sep 10, 2018 at 5:28 AM  wrote:
>
>> Hi Kevin, Pavel and others,
>>
>>
>>
>> Since it seems that so far nobody answered the primary question: “Is
>> there any sever available to create electron density maps for cryo-em
>> structures?” So I will do it. The answer is very simple: They do not need
>> to be created, they are available from the pdb!
>>
>>
>>
>> To give an example: On the RCSB pdb web-site, I searched for entry 5vai.
>> Then under the button “Download Files” I selected “Download EM Map” and
>> downloaded emd_8653.map.gz. As the name suggests, this file needs to be
>> unzipped, but this is trivial.
>>
>>
>>
>> Then in Coot in the “File” pull-down menu, I select “Open Map” to load
>> the map.
>>
>> Next, you may not see anything since to contour level might be too high
>> (when I load the map, the contour level is around 6 rmsd) so you have to
>> scroll down the contour level to see anything. As Marin and Ian pointed
>> out, the maps are very similar to regular electron density maps, probably
>> with the exception that the EM “electron density” maps are influenced by
>> the local charge density. However in coot they behave 100% identical and
>> you can scroll up and down the contour level as you like.
>>
>>
>>
>> Of course, if the authors did not deposit their EM-map, you cannot
>> download it, but the same is true for X-ray structure factors.
>>
>>
>>
>> Happy viewing!
>>
>>
>>
>> Herman
>>
>>
>>
>>
>>
>>
>>
>> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag
>> von *Ian Tickle
>> *Gesendet:* Montag, 10. September 2018 12:58
>> *An:* CCP4BB@JISCMAIL.AC.UK
>> *Betreff:* [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM
>> structures.
>>
>>
>>
>>
>>
>> Hi Marin
>>
>>
>>
>> I was about to comment on that too but then I realised that Pavel is
>> referring to the map _contours_  (which is what most people using a map
>> visualisation program like Coot actually see).  So the contoured map does
>> represent an iso-potential surface.  I'm sure Pavel is aware that the
>> original cryo-EM maps are 3-dimensional objects.
>>
>>
>>
>> Cheers
>>
>>
>>
>> -- Ian
>>
>>
>>
>> On Mon, 10 Sep 2018 at 10:49, Marin van Heel <
>> 057a89ab08a1-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>
>> Unfortunately,
>>
>> The problem here lies primarily in the answer given,  not so much in the
>> question asked by a newcomer:
>>
>> "1) In cryo-EM maps are not electron density maps but surfaces
>> representing electric potential. "
>>
>> The answer appears to reflect the widespread misunderstanding that EM
>> images (and hence cryo-EM maps)  only show the surfaces not the internal
>> density of the complexes we study.
>> In my Imperial College/Leiden University  lecture notes, I have always
>> used the below slide to il

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

2018-09-10 Thread Garib Murshudov

Dear Kevin,

You can have access to all these resources (And ccpem, ccp4). They are free for 
non-commercial users. 

(You can also have access to any papers you want via https://sci-hub.tw/ 
<http://scihub.tw/>, it is also free but …)

If you want to see some of the maps then you can go to emdb at 
https://www.ebi.ac.uk/pdbe/emdb/ <https://www.ebi.ac.uk/pdbe/emdb/>, they have 
many cryoEM maps and tools to visualise them.

If you want to generate maps from coordinates then refmac  from ccp4 and ccpem 
has an option to generate 3D electrostatic potential from coordinates. I can 
send a script for that.

Regards
Garib

P.S. In spite of some unusual answers you should not be afraid asking questions 
on ccp4 bb. This bulletin board is exactly for this type of questions.


> On 10 Sep 2018, at 18:01, Kevin Jin  wrote:
> 
> Dear Herman and all ccp4ers,
> 
> Many thanks for the helps and education from all of you. 
> 
> I am a fresh beginner in Cryo-EM,  and have no access to those resource, like 
> Chimera, Phenix, Rosetta and papers, etc. For me, any answer will be 
> valuable. 
> 
> Please forgive me for asking such a naive question.  I highly appreciate your 
> comments and education.
> 
> Kevin
> 
> On Mon, Sep 10, 2018 at 5:28 AM  <mailto:herman.schreu...@sanofi.com>> wrote:
> Hi Kevin, Pavel and others,
> 
>  
> 
> Since it seems that so far nobody answered the primary question: “Is there 
> any sever available to create electron density maps for cryo-em structures?” 
> So I will do it. The answer is very simple: They do not need to be created, 
> they are available from the pdb!
> 
>  
> 
> To give an example: On the RCSB pdb web-site, I searched for entry 5vai. Then 
> under the button “Download Files” I selected “Download EM Map” and downloaded 
> emd_8653.map.gz. As the name suggests, this file needs to be unzipped, but 
> this is trivial.
> 
>  
> 
> Then in Coot in the “File” pull-down menu, I select “Open Map” to load the 
> map.
> 
> Next, you may not see anything since to contour level might be too high (when 
> I load the map, the contour level is around 6 rmsd) so you have to scroll 
> down the contour level to see anything. As Marin and Ian pointed out, the 
> maps are very similar to regular electron density maps, probably with the 
> exception that the EM “electron density” maps are influenced by the local 
> charge density. However in coot they behave 100% identical and you can scroll 
> up and down the contour level as you like.
> 
>  
> 
> Of course, if the authors did not deposit their EM-map, you cannot download 
> it, but the same is true for X-ray structure factors.
> 
>  
> 
> Happy viewing!
> 
>  
> 
> Herman
> 
>  
> 
>  
> 
>  
> 
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK 
> <mailto:CCP4BB@JISCMAIL.AC.UK>] Im Auftrag von Ian Tickle
> Gesendet: Montag, 10. September 2018 12:58
> An: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
> Betreff: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.
> 
>  
> 
>  
> 
> Hi Marin
> 
>  
> 
> I was about to comment on that too but then I realised that Pavel is 
> referring to the map _contours_  (which is what most people using a map 
> visualisation program like Coot actually see).  So the contoured map does 
> represent an iso-potential surface.  I'm sure Pavel is aware that the 
> original cryo-EM maps are 3-dimensional objects.
> 
>  
> 
> Cheers
> 
>  
> 
> -- Ian
> 
>  
> 
> On Mon, 10 Sep 2018 at 10:49, Marin van Heel 
> <057a89ab08a1-dmarc-requ...@jiscmail.ac.uk 
> <mailto:057a89ab08a1-dmarc-requ...@jiscmail.ac.uk>> wrote:
> 
> 
> Unfortunately,
> 
> The problem here lies primarily in the answer given,  not so much in the 
> question asked by a newcomer:
> 
> "1) In cryo-EM maps are not electron density maps but surfaces representing 
> electric potential. "
> 
> The answer appears to reflect the widespread misunderstanding that EM images 
> (and hence cryo-EM maps)  only show the surfaces not the internal density of 
> the complexes we study.
> In my Imperial College/Leiden University  lecture notes, I have always used 
> the below slide to illustrate this point.
> 
> Cheers,
> 
> Marin
> 
> 
> 
> 
> 
> On 10/09/2018 01:38, Pavel Afonine wrote:
> 
> Hi,
> 
>  
> 
> Is there any sever available to create electron density maps for cryo-em 
> structures?
> 
>  
> 
> The questions are nonsensical. Here is why:
> 
>  
> 
> 1) In cryo-EM maps are not electron density maps but surfaces representing 
> electric potential.
> 
>

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

2018-09-10 Thread Kevin Jin

Dear Herman and all ccp4ers,

Many thanks for the helps and education from all of you.

I am a fresh beginner in Cryo-EM,  and have no access to those resource,
like Chimera, Phenix, Rosetta and papers, etc. For me, any answer will be
valuable.

Please forgive me for asking such a naive question.  I highly appreciate
your comments and education.

Kevin

On Mon, Sep 10, 2018 at 5:28 AM  wrote:

> Hi Kevin, Pavel and others,
>
>
>
> Since it seems that so far nobody answered the primary question: “Is there
> any sever available to create electron density maps for cryo-em
> structures?” So I will do it. The answer is very simple: They do not need
> to be created, they are available from the pdb!
>
>
>
> To give an example: On the RCSB pdb web-site, I searched for entry 5vai.
> Then under the button “Download Files” I selected “Download EM Map” and
> downloaded emd_8653.map.gz. As the name suggests, this file needs to be
> unzipped, but this is trivial.
>
>
>
> Then in Coot in the “File” pull-down menu, I select “Open Map” to load the
> map.
>
> Next, you may not see anything since to contour level might be too high
> (when I load the map, the contour level is around 6 rmsd) so you have to
> scroll down the contour level to see anything. As Marin and Ian pointed
> out, the maps are very similar to regular electron density maps, probably
> with the exception that the EM “electron density” maps are influenced by
> the local charge density. However in coot they behave 100% identical and
> you can scroll up and down the contour level as you like.
>
>
>
> Of course, if the authors did not deposit their EM-map, you cannot
> download it, but the same is true for X-ray structure factors.
>
>
>
> Happy viewing!
>
>
>
> Herman
>
>
>
>
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *Ian Tickle
> *Gesendet:* Montag, 10. September 2018 12:58
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM
> structures.
>
>
>
>
>
> Hi Marin
>
>
>
> I was about to comment on that too but then I realised that Pavel is
> referring to the map _contours_  (which is what most people using a map
> visualisation program like Coot actually see).  So the contoured map does
> represent an iso-potential surface.  I'm sure Pavel is aware that the
> original cryo-EM maps are 3-dimensional objects.
>
>
>
> Cheers
>
>
>
> -- Ian
>
>
>
> On Mon, 10 Sep 2018 at 10:49, Marin van Heel <
> 057a89ab08a1-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>
> Unfortunately,
>
> The problem here lies primarily in the answer given,  not so much in the
> question asked by a newcomer:
>
> "1) In cryo-EM maps are not electron density maps but surfaces
> representing electric potential. "
>
> The answer appears to reflect the widespread misunderstanding that EM
> images (and hence cryo-EM maps)  only show the surfaces not the internal
> density of the complexes we study.
> In my Imperial College/Leiden University  lecture notes, I have always
> used the below slide to illustrate this point.
>
> Cheers,
>
> Marin
>
>
>
>
>
> On 10/09/2018 01:38, Pavel Afonine wrote:
>
> Hi,
>
>
>
> Is there any sever available to create electron density maps for cryo-em
> structures?
>
>
>
> The questions are nonsensical. Here is why:
>
>
>
> 1) In cryo-EM maps are not electron density maps but surfaces representing
> electric potential.
>
>
>
> 2) Creating such a map is essentially carrying on from cryo-EM experiment
> and obtaining the 3D reconstruction.
>
>
>
> Are you really sure about what you are asking for?
>
>
>
> Or, we should create the maps from mmCIF.
>
>
>
> mmCIF is a file format. It may contain representations of rabbits,
> boysenberries or some diffraction data. So.. how you think it may be
> related to cryo-EM, in your particular case?
>
>
>
> I am particularly interested in those cryo-em structures with high
> resolution, like 2.6~2.8A.
>
>
>
> Sure, all are excited about high-res cryo-EM!!!
>
>
>
> Please give me an education.
>
>
>
> Sure. One of available universities can do this.
>
>
>
> Cheers,
>
> Pavel
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8

Re: [ccp4bb] Electron density maps for Cryo-EM structures.

2018-09-10 Thread Natesh Ramanathan

Dear Kevin,

 Are you referring to "generating a  map"  from the model (PDB
coordinates) generated from tracing the chain in the ab-initio EM map?

Best wishes,
Natesh

On Mon, 10 Sep 2018 at 09:58, Kevin Jin  wrote:

>  Dear All,
>
> Is there any sever available to create electron density maps for cryo-em
> structures? Or, we should create the maps from mmCIF. I am particularly
> interested in those cryo-em structures with high resolution, like 2.6~2.8A.
>
> Please give me an education.
>
> Thanks,
>
> Kevin
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>


-- 
--
"Live Simply and do Serious Things .. "
- Dorothy Mary Crowfoot Hodgkin OM, FRS

"In Science truth always wins"
- Max Ferdinand Perutz OM FRS
--
Dr. Ramanathan Natesh
Assistant Professor,
School of Biology,
Indian Institute of Science Education and Research Thiruvananthapuram
(IISER-TVM),
Maruthamala P.O., Vithura,
Thiruvananthapuram,  695551, Kerala, India

nat...@iisertvm.ac.in
http://www.researcherid.com/rid/C-4488-2008
ORCID: http://orcid.org/-0002-1145-5962
https://publons.com/author/1520837/ramanathan-natesh#profile
http://faculty.iisertvm.ac.in/natesh

Office Ph. 0091- 471-2778087



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[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

2018-09-10 Thread Herman . Schreuder

Hi Kevin, Pavel and others,

Since it seems that so far nobody answered the primary question: “Is there any
sever available to create electron density maps for cryo-em structures?” So I
will do it. The answer is very simple: They do not need to be created, they are
available from the pdb!

To give an example: On the RCSB pdb web-site, I searched for entry 5vai. Then
under the button “Download Files” I selected “Download EM Map” and downloaded
emd_8653.map.gz. As the name suggests, this file needs to be unzipped, but this
is trivial.

Then in Coot in the “File” pull-down menu, I select “Open Map” to load the map.
Next, you may not see anything since to contour level might be too high (when I
load the map, the contour level is around 6 rmsd) so you have to scroll down
the contour level to see anything. As Marin and Ian pointed out, the maps are
very similar to regular electron density maps, probably with the exception that
the EM “electron density” maps are influenced by the local charge density.
However in coot they behave 100% identical and you can scroll up and down the
contour level as you like.

Of course, if the authors did not deposit their EM-map, you cannot download it,
but the same is true for X-ray structure factors.

Happy viewing!

Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Ian
Tickle
Gesendet: Montag, 10. September 2018 12:58
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

Hi Marin

I was about to comment on that too but then I realised that Pavel is referring
to the map _contours_ (which is what most people using a map visualisation
program like Coot actually see). So the contoured map does represent an
iso-potential surface. I'm sure Pavel is aware that the original cryo-EM maps
are 3-dimensional objects.

Cheers

-- Ian

On Mon, 10 Sep 2018 at 10:49, Marin van Heel
<057a89ab08a1-dmarc-requ...@jiscmail.ac.uk<mailto:057a89ab08a1-dmarc-requ...@jiscmail.ac.uk>>
wrote:

Unfortunately,

The problem here lies primarily in the answer given, not so much in the
question asked by a newcomer:

"1) In cryo-EM maps are not electron density maps but surfaces representing
electric potential. "

The answer appears to reflect the widespread misunderstanding that EM images
(and hence cryo-EM maps) only show the surfaces not the internal density of
the complexes we study.
In my Imperial College/Leiden University lecture notes, I have always used the
below slide to illustrate this point.

Cheers,

Marin

[cid:part1.5DA80E33.F02E5B7D@googlemail.com]

On 10/09/2018 01:38, Pavel Afonine wrote:
Hi,

Is there any sever available to create electron density maps for cryo-em
structures?

The questions are nonsensical. Here is why:

1) In cryo-EM maps are not electron density maps but surfaces representing
electric potential.

2) Creating such a map is essentially carrying on from cryo-EM experiment and
obtaining the 3D reconstruction.

Are you really sure about what you are asking for?

Or, we should create the maps from mmCIF.

mmCIF is a file format. It may contain representations of rabbits,
boysenberries or some diffraction data. So.. how you think it may be related to
cryo-EM, in your particular case?

I am particularly interested in those cryo-em structures with high resolution,
like 2.6~2.8A.

Sure, all are excited about high-res cryo-EM!!!

Please give me an education.

Sure. One of available universities can do this.

Cheers,
Pavel

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=oyq4_tjHvYKRzK3yN_rOpIQo6sflk9725vR5aINqpHg=A66BPdK7455wfEqkW7nlTOFIrLwyiZ0P6iRXbkPPZFs=>

Prof Dr Ir Marin van Heel

Laboratório Nacional de Nanotecnologia - LNNano

CNPEM/LNNano, Campinas, Brazil

Skype: Marin.van.Heel

email:
marin.vanheel(A_T)gmail.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmail.com=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=oyq4_tjHvYKRzK3yN_rOpIQo6sflk9725vR5aINqpHg=dS2VEfbgNj0-C_rK4Gz-4eXTJsZj7sQEp5cuMvr1i5g=>

marin.vanheel(A_T)lnnano.cnpem.br<https://urldefense.proofpoint.com/v2/url?u=http-3A__lnnano.cnpem.br=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=oyq4_tjHvYKRzK3yN_rOpIQo6sflk9725vR5aINqpHg=yJ2hAZdRJw5ICBpLLolSUKM1Dp8cAemaHi6pNIR5Ua4=>

and:
mvh.office(A_T)gmail.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmail.com=DwMFaQ=Dbf

[ccp4bb] AW: [ccp4bb] Electron density maps for Cryo-EM structures.

2018-09-10 Thread Hughes, Jon

yes, but irrespective of how much one knows or thinks one knows, one should
avoid being gratuitously offensive.
cheers
jon

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Ian
Tickle
Gesendet: Montag, 10. September 2018 12:58
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Electron density maps for Cryo-EM structures.

Hi Marin

Cheers

-- Ian

On Mon, 10 Sep 2018 at 10:49, Marin van Heel
<057a89ab08a1-dmarc-requ...@jiscmail.ac.uk<mailto:057a89ab08a1-dmarc-requ...@jiscmail.ac.uk>>
wrote:

Unfortunately,

The problem here lies primarily in the answer given, not so much in the
question asked by a newcomer:

"1) In cryo-EM maps are not electron density maps but surfaces representing
electric potential. "

Cheers,

Marin

[cid:part1.5DA80E33.F02E5B7D@googlemail.com]

On 10/09/2018 01:38, Pavel Afonine wrote:
Hi,

Is there any sever available to create electron density maps for cryo-em
structures?

The questions are nonsensical. Here is why:

1) In cryo-EM maps are not electron density maps but surfaces representing
electric potential.

2) Creating such a map is essentially carrying on from cryo-EM experiment and
obtaining the 3D reconstruction.

Are you really sure about what you are asking for?

Or, we should create the maps from mmCIF.

mmCIF is a file format. It may contain representations of rabbits,
boysenberries or some diffraction data. So.. how you think it may be related to
cryo-EM, in your particular case?

I am particularly interested in those cryo-em structures with high resolution,
like 2.6~2.8A.

Sure, all are excited about high-res cryo-EM!!!

Please give me an education.

Sure. One of available universities can do this.

Cheers,
Pavel

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Prof Dr Ir Marin van Heel

Laboratório Nacional de Nanotecnologia - LNNano

CNPEM/LNNano, Campinas, Brazil

Skype: Marin.van.Heel

email: marin.vanheel(A_T)gmail.com<http://gmail.com>

marin.vanheel(A_T)lnnano.cnpem.br<http://lnnano.cnpem.br>

and:mvh.office(A_T)gmail.com<http://gmail.com>

Emeritus Professor of Cryo-EM Data Processing

Leiden University

Emeritus Professor of Structural Biology

Imperial College London

Faculty of Natural Sciences

email: m.vanheel(A_T)imperial.ac.uk<http://imperial.ac.uk>

I receive many emails per day and, although I try,

there is no guarantee that I will actually read each incoming email.

To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Electron density maps for Cryo-EM structures.

2018-09-09 Thread Kevin Jin

Great, thanks!


On Sun, Sep 9, 2018 at 9:49 PM Pavel Afonine  wrote:

> P.S.: all questions are welcome of course, no labeling. It's just some of
> them are so orthogonal to common sense that answers my be such as well.
> Best,
> Pavel
>
> On Sun, Sep 9, 2018 at 9:38 PM Pavel Afonine  wrote:
>
>> Hi,
>>
>> Is there any sever available to create electron density maps for cryo-em
>>> structures?
>>>
>>
>> The questions are nonsensical. Here is why:
>>
>> 1) In cryo-EM maps are not electron density maps but surfaces
>> representing electric potential.
>>
>> 2) Creating such a map is essentially carrying on from cryo-EM experiment
>> and obtaining the 3D reconstruction.
>>
>> Are you really sure about what you are asking for?
>>
>>
>>> Or, we should create the maps from mmCIF.
>>>
>>
>> mmCIF is a file format. It may contain representations of rabbits,
>> boysenberries or some diffraction data. So.. how you think it may be
>> related to cryo-EM, in your particular case?
>>
>>
>>> I am particularly interested in those cryo-em structures with high
>>> resolution, like 2.6~2.8A.
>>>
>>
>> Sure, all are excited about high-res cryo-EM!!!
>>
>>
>>> Please give me an education.
>>>
>>
>> Sure. One of available universities can do this.
>>
>> Cheers,
>> Pavel
>>
>>

-- 
Kevin Jin

Sharing knowledge each other is always very joyful..

Website: http://www.jinkai.org/



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Re: [ccp4bb] Electron density maps for Cryo-EM structures.

2018-09-09 Thread Pavel Afonine

P.S.: all questions are welcome of course, no labeling. It's just some of
them are so orthogonal to common sense that answers my be such as well.
Best,
Pavel

On Sun, Sep 9, 2018 at 9:38 PM Pavel Afonine  wrote:

> Hi,
>
> Is there any sever available to create electron density maps for cryo-em
>> structures?
>>
>
> The questions are nonsensical. Here is why:
>
> 1) In cryo-EM maps are not electron density maps but surfaces representing
> electric potential.
>
> 2) Creating such a map is essentially carrying on from cryo-EM experiment
> and obtaining the 3D reconstruction.
>
> Are you really sure about what you are asking for?
>
>
>> Or, we should create the maps from mmCIF.
>>
>
> mmCIF is a file format. It may contain representations of rabbits,
> boysenberries or some diffraction data. So.. how you think it may be
> related to cryo-EM, in your particular case?
>
>
>> I am particularly interested in those cryo-em structures with high
>> resolution, like 2.6~2.8A.
>>
>
> Sure, all are excited about high-res cryo-EM!!!
>
>
>> Please give me an education.
>>
>
> Sure. One of available universities can do this.
>
> Cheers,
> Pavel
>
>



To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Electron density maps for Cryo-EM structures.

2018-09-09 Thread Pavel Afonine

Hi,

Is there any sever available to create electron density maps for cryo-em
> structures?
>

The questions are nonsensical. Here is why:

1) In cryo-EM maps are not electron density maps but surfaces representing
electric potential.

2) Creating such a map is essentially carrying on from cryo-EM experiment
and obtaining the 3D reconstruction.

Are you really sure about what you are asking for?


> Or, we should create the maps from mmCIF.
>

mmCIF is a file format. It may contain representations of rabbits,
boysenberries or some diffraction data. So.. how you think it may be
related to cryo-EM, in your particular case?


> I am particularly interested in those cryo-em structures with high
> resolution, like 2.6~2.8A.
>

Sure, all are excited about high-res cryo-EM!!!


> Please give me an education.
>

Sure. One of available universities can do this.

Cheers,
Pavel



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Electron density maps for Cryo-EM structures.

2018-09-09 Thread Kevin Jin

 Dear All,

Is there any sever available to create electron density maps for cryo-em
structures? Or, we should create the maps from mmCIF. I am particularly
interested in those cryo-em structures with high resolution, like 2.6~2.8A.

Please give me an education.

Thanks,

Kevin



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Re: [ccp4bb] Electron density

2018-05-13 Thread Keller, Jacob

I know you mentioned trying buffer components, but it does look a lot like TRIS 
to me, maybe a different conformation than you’re modelling?

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
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its deletion, so that we can ensure such a mistake does not occur in the future.

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Daniel 
Garcia
Sent: Sunday, May 13, 2018 8:40 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Electron density

Dear all,

I am currently refining a structure and found a intriguing electron density at 
the protein surface (pictures attached, the Fo-Fc map is contoured at >3.5 
sigma). My first candidates were molecules from my protein prep or 
crystallisation buffer, but none of them seem to fit well. I can observe that 
the ligand is nearby the side chains of a tyrosine, a lysine, a threonine and a 
glutamate residue, and it is close to the carbonyl oxygens of the protein 
backbone of a nearby loop. The shape of this density is not pyramidal, but it 
is not planar either.

Do you have any suggestions to solve this density based on your own experience? 
My crystallisation buffer contains tartrate, ammonium sulphate, and CHES, and 
my protein is in Tris buffer containing DTT and sodium chloride.

Best regards,

--
Mario

Re: [ccp4bb] Electron density

2018-05-13 Thread Daniel Garcia

Thanks for your quick responses. I used ethylene glycol as cryoprotectant.
Indeed I had 1% DMSO as part of the crystallisation condition (I forgot to
include that), but DMSO is too small to fit this density and DMSO has a
trigonal pyramidal structure, which differs a bit to what I have in my
structure.

On Mon, May 14, 2018 at 11:12 AM, Ethan Merritt 
wrote:

> On Monday, 14 May 2018 10:39:32 Daniel Garcia wrote:
> > Dear all,
> >
> > I am currently refining a structure and found a intriguing electron
> density
> > at the protein surface (pictures attached, the Fo-Fc map is contoured at
> > >3.5 sigma). My first candidates were molecules from my protein prep or
> > crystallisation buffer, but none of them seem to fit well. I can observe
> > that the ligand is nearby the side chains of a tyrosine, a lysine, a
> > threonine and a glutamate residue, and it is close to the carbonyl
> oxygens
> > of the protein backbone of a nearby loop. The shape of this density is
> not
> > pyramidal, but it is not planar either.
> >
> > Do you have any suggestions to solve this density based on your own
> > experience? My crystallisation buffer contains tartrate, ammonium
> sulphate,
> > and CHES, and my protein is in Tris buffer containing DTT and sodium
> > chloride.
>
> DMSO?
>
>
> >
> > Best regards,
> >
> >
>
> --
> Ethan A Merritt, Dept of Biochemistry
> Biomolecular Structure Center,  K-428 Health Sciences Bldg
> MS 357742,   University of Washington, Seattle 98195-7742
>



-- 
Mario Daniel García

Re: [ccp4bb] Electron density

2018-05-13 Thread Ethan Merritt

On Monday, 14 May 2018 10:39:32 Daniel Garcia wrote:
> Dear all,
> 
> I am currently refining a structure and found a intriguing electron density
> at the protein surface (pictures attached, the Fo-Fc map is contoured at
> >3.5 sigma). My first candidates were molecules from my protein prep or
> crystallisation buffer, but none of them seem to fit well. I can observe
> that the ligand is nearby the side chains of a tyrosine, a lysine, a
> threonine and a glutamate residue, and it is close to the carbonyl oxygens
> of the protein backbone of a nearby loop. The shape of this density is not
> pyramidal, but it is not planar either.
> 
> Do you have any suggestions to solve this density based on your own
> experience? My crystallisation buffer contains tartrate, ammonium sulphate,
> and CHES, and my protein is in Tris buffer containing DTT and sodium
> chloride.

DMSO?


> 
> Best regards,
> 
> 

-- 
Ethan A Merritt, Dept of Biochemistry
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] Electron density

2018-05-13 Thread Joel Tyndall

Did you happen to use glycerol as a cryoprotectant?

From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Daniel Garcia
Sent: Monday, 14 May 2018 12:40 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Electron density

Dear all,

I am currently refining a structure and found a intriguing electron density at 
the protein surface (pictures attached, the Fo-Fc map is contoured at >3.5 
sigma). My first candidates were molecules from my protein prep or 
crystallisation buffer, but none of them seem to fit well. I can observe that 
the ligand is nearby the side chains of a tyrosine, a lysine, a threonine and a 
glutamate residue, and it is close to the carbonyl oxygens of the protein 
backbone of a nearby loop. The shape of this density is not pyramidal, but it 
is not planar either.

Do you have any suggestions to solve this density based on your own experience? 
My crystallisation buffer contains tartrate, ammonium sulphate, and CHES, and 
my protein is in Tris buffer containing DTT and sodium chloride.

Best regards,

--
Mario

Re: [ccp4bb] Electron density map for publications

2017-12-18 Thread raj kumar

Thanks sir

On Tue, Dec 19, 2017 at 11:05 AM, Bernhard Rupp <hofkristall...@gmail.com>
wrote:

> *Unbiased positive omit* difference density, not just any fo-fc.
>
> Br
>
> On Dec 18, 2017 9:22 PM, "chenzhonghao...@163.com" <
> chenzhonghao...@163.com> wrote:
>
> Dear Raj,
>
>   Usually,   fo-fc is the best way to show.
>
>
> best,
>
>
> --
> chenzhonghao...@163.com
>
>
> *From:* raj kumar <rajk13...@gmail.com>
> *Date:* 2017-12-19 13:07
> *To:* CCP4BB <CCP4BB@JISCMAIL.AC.UK>
> *Subject:* [ccp4bb] Electron density map for publications
> Hi
> Which electron density map (fo-fc  or 2fo-fc) should I use for
> representing the density of the bound ligand?
> Thanks
> Raj
>
>
>

Re: [ccp4bb] Electron density map for publications

2017-12-18 Thread Bernhard Rupp

*Unbiased positive omit* difference density, not just any fo-fc.

Br

On Dec 18, 2017 9:22 PM, "chenzhonghao...@163.com" <chenzhonghao...@163.com>
wrote:

Dear Raj,

  Usually,   fo-fc is the best way to show.


best,


--
chenzhonghao...@163.com


*From:* raj kumar <rajk13...@gmail.com>
*Date:* 2017-12-19 13:07
*To:* CCP4BB <CCP4BB@JISCMAIL.AC.UK>
*Subject:* [ccp4bb] Electron density map for publications
Hi
Which electron density map (fo-fc  or 2fo-fc) should I use for representing
the density of the bound ligand?
Thanks
Raj

Re: [ccp4bb] Electron density map for publications

2017-12-18 Thread chenzhonghao...@163.com

Dear Raj,

  Usually,   fo-fc is the best way to show.


best,




chenzhonghao...@163.com
 
From: raj kumar
Date: 2017-12-19 13:07
To: CCP4BB
Subject: [ccp4bb] Electron density map for publications
Hi
Which electron density map (fo-fc  or 2fo-fc) should I use for representing the 
density of the bound ligand?
Thanks
Raj

Re: [ccp4bb] Electron density map for publications

2017-12-18 Thread Bernhard Rupp

http://journals.iucr.org/d/issues/2013/02/00/index.html

 

Best, BR

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of raj kumar
Sent: Monday, December 18, 2017 8:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Electron density map for publications

 

Hi

Which electron density map (fo-fc  or 2fo-fc) should I use for representing the 
density of the bound ligand?

Thanks

Raj

[ccp4bb] Electron density map for publications

2017-12-18 Thread raj kumar

Hi
Which electron density map (fo-fc  or 2fo-fc) should I use for representing
the density of the bound ligand?
Thanks
Raj

Re: [ccp4bb] Electron density in PDBe

2017-11-30 Thread Phoebe A. Rice

I agree that density looks dubious, the B-factor distribution among DNA atoms 
is odd (sudden shifts from blue to red) and the little wwPDB bar charts are on 
the red side.  

But what about the density for the protein?  
The structure is of a hexameric helicase with with dsDNA going through the 
hole, so the space group being nearly-R3 or R32 doesn't shock me: one would 
expect the DNA to subtly break the symmetry. 

Could it simply be very poorly ordered DNA going making a pseudo-continuous 
helix going through the crystal? Or maybe the symmetry isn't broken, and DNA 
backbone is in 3 different rotational states even if there's rough density for 
the planes of the bases?

++

Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago

pr...@uchicago.edu
https://voices.uchicago.edu/phoebericelab/



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Anastassis 
Perrakis [a.perra...@nki.nl]
Sent: Thursday, November 30, 2017 12:56 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Electron density in PDBe

Interesting structure:

a=b=c=α=β=γ=107 in P1
Estimated twinning fraction 0.439 for k,l,h and 0.439 for l,h,k

In other words R32? ;-)

The PDB-REDO map has some interesting features, one strand has bases density at 
.0 sigma, the other not, see attched.

The NCS averaging they used is kind of interesting. It reads correct if I read 
through, but if something is done wrong, I am guessing it might result in 
erronous features.

As a side note, the refereeing in eLife is interesting. The reviewing editor is 
Stephen Bell; an excellent scientist, but not a crystallographer. Referees 
opted to stay anonymous - but one could speculate they are not 
crystallogrpahers either, as they did not raise any crystallographic questions. 
The validation summary, well, it could have raised some red flags … sorry, it 
did raise red flags, or to be exact red bold boxes. Evidently, nobody looked at 
them.

Have fun -

A.



[cid:B25D7E2E-FD64-40A6-9DBD-60DEF50D9249@home]
[cid:5B0AA6A0-834B-46C7-AE56-8C6DFFB2F62D@home]
A.



On 30 Nov 2017, at 19:01, Wim Burmeister 
<wim.burmeis...@ibs.fr<mailto:wim.burmeis...@ibs.fr>> wrote:

Dear all,
I am doing some analysis on pdb entry 5tct.
I realized that the electron density on the PDBe site (obtained from EDS) shows 
much more model bias than the one obtained from the pdb file and the cif 
reflection data file using ccp4i (import + refmac5 with 0 cycle positional 
refinement). Using the mtz file from pdb-redo a similar map is obtained.
When I read the publication 5kleywegt et al, 2004) on EDS, I understood that 
essentially the same approach is used (refmac with 0 cycle refinement followed 
by fft map calculation).
Does anybody have an idea where the discrepancy comes from ?
I join a jpg with the electron density of the 3 approaches. The contour level 
is about 3 sigma.
Best,
Wim

ps: I expect that the electron density of the DNA is not really present as the 
entry has a number of flaws.
--

Wim Burmeister
Professeur
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs

CS 20192
38044 Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr<mailto:wim.burmeis...@ibs.fr>
Tel:+33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
website<http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/>

[ccp4bb] Electron density of penicillin (Re: [ccp4bb] Google Gets it Right)

2014-05-12 Thread Tomas Malinauskas

Dear Gregg et al.,

On Mon, May 12, 2014 at 4:28 PM, Gregg Crichlow gregg.crich...@gmail.comwrote:

 Actually, it was noticing penG that made me mouse over it myself. After
 spending many years completing a thesis on beta-lactamases, I was very
 surprised - and excited - to see that on something as main-stream as
 Google. But then when I paid attention more closely, I saw that they even
 have a good representation of the electron density in three orthogonal
 planes surrounding the molecule!  Dr. James Knox (my thesis advisor) just
 informed me that the density maps are on exhibit at the British Museum of
 Science.


The electron density map of penicillin is deposited at the Museum of the
History of Science in Oxford too, a photo I took few years ago is here:

https://drive.google.com/file/d/0B4TVGcERcQ7veGZXS1lEMXBqck0/edit?usp=sharing

Best wishes,
Tomas

Re: [ccp4bb] Electron density server

2013-10-26 Thread Gerard DVD Kleywegt


The server has been rebooted and appears to be working again.

--Gerard




On Fri, 25 Oct 2013, Rojan Shrestha wrote:


Hello,



Is EDS (electron density server) dead? In the absence of EDS, how can be mtz
file directly downloaded?



Regards,



Rojan





Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

[ccp4bb] Electron density server

2013-10-25 Thread Rojan Shrestha

Hello,

 

Is EDS (electron density server) dead? In the absence of EDS, how can be mtz
file directly downloaded?

 

Regards,

 

Rojan

Re: [ccp4bb] Electron density server

2013-10-25 Thread Clement Angkawidjaja


Dear Rojan,

Get the mmCIF, then use CIF2MTZ from CCP4.

Cheers,
Clement

On 10/25/13 3:07 PM, Rojan Shrestha wrote:


Hello,

Is EDS (electron density server) dead? In the absence of EDS, how can 
be mtz file directly downloaded?


Regards,

Rojan

Re: [ccp4bb] electron density assignment

2013-02-04 Thread David Schuller

Generate an anomalous map and look for peaks. Many metals would generate 
anomalous.



On 02/04/13 07:39, Gang Dong wrote:


Dear all,

Here are some hexmeric densities we observed in our 1.6-A resolution 
2Fo-Fc map. They are located in between two dimers. Although 7 waters 
would fit nicely in the densities, we are not sure whether they might 
be something else (metals?). Any suggestions are welcome. Thanks! Gang



...

--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

Re: [ccp4bb] electron density assignment

2013-02-04 Thread Joern Krausze


Hi,

I observed a very similar hexagonal arrangement of electron density blobs
in one of my structures recentely and asked the CCP4bb community to help
me explain it. Unfortunately, noone could come up with some satisfactory
explanation, so I gave up on interpreting this rogue density. What was
certain beyond doubt is that it was somehow caused by the presence of
cobalt ions. Do you, by chance, also have cobalt or similar ions present
in your crystallization condition?

Regards,
Joern

**
Address:

Joern Krausze
Molecular Structural Biology
Helmholtz Centre for Infection Research
Inhoffenstrasse 7
38124 Braunschweig
Germany

Email:  joern.krau...@helmholtz-hzi.de
Phone:  +49 (0)531 6181 7023 (office)
+49 (0)531 6181 7020 (lab)
**

On Mon, 4 Feb 2013, Gang Dong wrote:



Dear all,



Here are some “hexmeric” densities we observed in our 1.6-A resolution 2Fo-Fc 
map. They are located in between two dimers. Although 7 waters would fit nicely 
in the densities,
we are not sure whether they might be something else (metals?). Any suggestions 
are welcome. Thanks! Gang



[IMAGE]

__

Gang Dong, PhD

Junior Group Leader

Max F. Perutz Laboratories (MFPL)

Dr. Bohrgasse 9/3

A-1030 Vienna, Austria



Phone: +43-1-4277-61625

FAX: +43-1-4277-9616

http://www.mfpl.ac.at/mfpl-group/group/dong.html











Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 
Braunschweig | www.helmholtz-hzi.de

Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, 
Bundesministerium für Bildung und Forschung
Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches Ministerium 
für Wissenschaft und Kultur
Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf Richter, MBA
Gesellschaft mit beschränkter Haftung (GmbH)
Sitz der Gesellschaft: Braunschweig
Handelsregister: Amtsgericht Braunschweig, HRB 477

Re: [ccp4bb] electron density assignment

2013-02-04 Thread Dr. Anthony Addlagatta

***
This message has been scanned by the InterScan for CSC SSM by IICT security 
policy and found to be free of known security risks.
***


Dear Gang,

By chance, P222 is your space group?

It seems to be three perpendicular two-fold axes are passing through your 
central atom
which makes them all fall in the same plane. From the density it looks more 
like a water
in the center but anomalous density map should help.

Good luck.

Anthony  

-
Dr. Anthony Addlagatta
Center for Chemical Biology 
Indian Institute of Chemical Technology [IICT]
Tarnaka, Hyderabad
AP-500 607, INDIA
Tel:91-40-27191812
Web: https://sites.google.com/site/chembioliict/home/dr-anthony-addlagatta-1

-- Original Message ---
From: Gang Dong gang.d...@univie.ac.at
To: CCP4BB@JISCMAIL.AC.UK
Sent: Mon, 4 Feb 2013 13:39:39 +0100
Subject: [ccp4bb] electron density assignment

 ***
 This message has been scanned by the InterScan for CSC SSM at IICT and found 
 to be
free of known security risks.
 ***
 
 Dear all,
 
 Here are some hexmeric densities we observed in our 1.6-A resolution
 2Fo-Fc map. They are located in between two dimers. Although 7 waters would
 fit nicely in the densities, we are not sure whether they might be something
 else (metals?). Any suggestions are welcome. Thanks! Gang
 
 __
 
 Gang Dong, PhD
 
 Junior Group Leader
 
 Max F. Perutz Laboratories (MFPL)
 
 Dr. Bohrgasse 9/3
 
 A-1030 Vienna, Austria
 
 Phone: +43-1-4277-61625
 
 FAX: +43-1-4277-9616
 
 http://www.mfpl.ac.at/mfpl-group/group/dong.html
--- End of Original Message ---

This Mail Scanned by ClamAV and Spammassassin

[ccp4bb] electron density peak volume

2012-07-06 Thread Andrew Pannifer

Hi,
Is there a way to ask peakmax to output the volume of each electron density 
peak that it detects (or is there a reasonably straightforward way to do this 
via an alternative command line runnable approach?)
Cheers,
Alan

Re: [ccp4bb] electron density peak volume

2012-07-06 Thread Tim Gruene

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Alan,

do you think the notion of 'volume of a peak' makes sense? You are
probably asking for the number of connected pixels around a local
maximum above a certain threshold - again, not sure whether this is a
useful concept and I am not aware of a program doing this calculation.

Regards,
Tim

On 07/06/12 15:40, Andrew Pannifer wrote:
 Hi, Is there a way to ask peakmax to output the volume of each
 electron density peak that it detects (or is there a reasonably
 straightforward way to do this via an alternative command line
 runnable approach?) Cheers, Alan
 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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Jo3h/z4RMXcWFJI9MzMku5A=
=/8p9
-END PGP SIGNATURE-

Re: [ccp4bb] electron density peak volume

2012-07-06 Thread Pavel Afonine

Hi Tim,

a possible way of thinking about this is:

say you have N (=nx*ny*nz) nodes of the grid on which you sampled the map,
and the unit cell volume is Vcell, and you are looking at a blob identified
at some level. Then the volume of this blob can be defined as Vblob =
np*Vcell/N, where np is the number of grid nodes inside the blob.

Pavel

On Fri, Jul 6, 2012 at 7:30 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:

 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1

 Dear Alan,

 do you think the notion of 'volume of a peak' makes sense? You are
 probably asking for the number of connected pixels around a local
 maximum above a certain threshold - again, not sure whether this is a
 useful concept and I am not aware of a program doing this calculation.

 Regards,
 Tim

 On 07/06/12 15:40, Andrew Pannifer wrote:
  Hi, Is there a way to ask peakmax to output the volume of each
  electron density peak that it detects (or is there a reasonably
  straightforward way to do this via an alternative command line
  runnable approach?) Cheers, Alan
 

 - --
 - --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen

 GPG Key ID = A46BEE1A

 -BEGIN PGP SIGNATURE-
 Version: GnuPG v1.4.12 (GNU/Linux)
 Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

 iD8DBQFP9vaLUxlJ7aRr7hoRAi4uAJ4vO3QwPeg4zDIduTKhGgMN1tytXgCguCUr
 Jo3h/z4RMXcWFJI9MzMku5A=
 =/8p9
 -END PGP SIGNATURE-

Re: [ccp4bb] electron density peak volume

2012-07-06 Thread Tim Gruene

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi Pavel,

that's probably how I'd program it, too. Still I am not aware of an
existing (command line) program which does that, and I am not sure of
its benefit from a users point of view. I can imagine that many
programs internally make use of the 'blob' volume for various purposes.

Cheers,
Tim

On 07/06/12 17:01, Pavel Afonine wrote:
 Hi Tim,
 
 a possible way of thinking about this is:
 
 say you have N (=nx*ny*nz) nodes of the grid on which you sampled
 the map, and the unit cell volume is Vcell, and you are looking at
 a blob identified at some level. Then the volume of this blob can
 be defined as Vblob = np*Vcell/N, where np is the number of grid
 nodes inside the blob.
 
 Pavel
 
 On Fri, Jul 6, 2012 at 7:30 AM, Tim Gruene
 t...@shelx.uni-ac.gwdg.de wrote:
 
 Dear Alan,
 
 do you think the notion of 'volume of a peak' makes sense? You are 
 probably asking for the number of connected pixels around a local 
 maximum above a certain threshold - again, not sure whether this is
 a useful concept and I am not aware of a program doing this
 calculation.
 
 Regards, Tim
 
 On 07/06/12 15:40, Andrew Pannifer wrote:
 Hi, Is there a way to ask peakmax to output the volume of
 each electron density peak that it detects (or is there a
 reasonably straightforward way to do this via an alternative
 command line runnable approach?) Cheers, Alan
 
 
 
 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFP9v+qUxlJ7aRr7hoRAmEGAKDlWqKmeL3Woq3RG2kLdH+KMjue6ACgruAg
8Jy2MOq1OigufOsO+ud/uJQ=
=tBk4
-END PGP SIGNATURE-

Re: [ccp4bb] electron density peak volume

2012-07-06 Thread Ed Pozharski


On 07/06/2012 09:40 AM, Andrew Pannifer wrote:


Hi,

Is there a way to ask peakmax to output the volume of each electron 
density peak that it detects (or is there a reasonably straightforward 
way to do this via an alternative command line runnable approach?)


Cheers,

Alan



There might be a way to do it using some of the brilliant USF tools.  A 
somewhat convoluted workaround would be to cut the piece of the map 
surrounding the peak, then converting it to mask using MAPMAN with 
cutoff of your choosing.  You can then use MAMA's island_erase method to 
identify the main blob of density and count the nodes to get the volume.


You may want to look into MAPMAN peek command too.  It allows both 
getting the interpolated density value at the peak position and integral 
density over volume surrounding it.  If you make certain assumptions 
about the peak shape (gaussian?) you can deduce the peak volume from 
these two numbers.


Cheers,

Ed.


--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs

Re: [ccp4bb] Electron density improvement with resolution graphic

2009-12-05 Thread Tim Gruene

You may also have a look at James Holton's page 
http://ucxray.berkeley.edu/~jamesh/movies/ and take a screenshot of one of 
his movies.

Tim

--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A


On Fri, 4 Dec 2009, Brad Bennett wrote:


Hi all-
I recall seeing a long time ago a figure which showed the progressive
improvement of electron density as one increases resolution, say from 6
to 3.5 to 2A. I believe I've seen two versions- one a larger scale pic
showing the ability to model side chains of alpha helices at higher
resolutions and the other a simpler graphic of a tyrosine aromatic ring
showing the electron density hole in the middle of the ring once near
atomic resolution maps are obtained. Does anyone have, in their teaching
notes or a textbook or presentation, a graphic which displays this? I
need it for a talk this weekend and Google searches have come up blank.
If all else fails, I can generate it myself...(lazy sigh)

Thanks in advance-
Brad

[ccp4bb] Electron density improvement with resolution graphic

2009-12-04 Thread Brad Bennett

Hi all-
I recall seeing a long time ago a figure which showed the progressive
improvement of electron density as one increases resolution, say from 6 to
3.5 to 2A. I believe I've seen two versions- one a larger scale pic showing
the ability to model side chains of alpha helices at higher resolutions and
the other a simpler graphic of a tyrosine aromatic ring showing the electron
density hole in the middle of the ring once near atomic resolution maps are
obtained. Does anyone have, in their teaching notes or a textbook or
presentation, a graphic which displays this? I need it for a talk this
weekend and Google searches have come up blank. If all else fails, I can
generate it myself...(lazy sigh)

Thanks in advance-
Brad

Re: [ccp4bb] Electron density improvement with resolution graphic

2009-12-04 Thread Jim Fairman

You can find one here on the Cambridge X-ray crystallography course website:
 http://www-structmed.cimr.cam.ac.uk/Course/Fitting/fittingtalk.html

On Fri, Dec 4, 2009 at 8:25 PM, Brad Bennett bradbennet...@gmail.comwrote:

 Hi all-
 I recall seeing a long time ago a figure which showed the progressive
 improvement of electron density as one increases resolution, say from 6 to
 3.5 to 2A. I believe I've seen two versions- one a larger scale pic showing
 the ability to model side chains of alpha helices at higher resolutions and
 the other a simpler graphic of a tyrosine aromatic ring showing the electron
 density hole in the middle of the ring once near atomic resolution maps are
 obtained. Does anyone have, in their teaching notes or a textbook or
 presentation, a graphic which displays this? I need it for a talk this
 weekend and Google searches have come up blank. If all else fails, I can
 generate it myself...(lazy sigh)

 Thanks in advance-
 Brad




-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
Cell: 1-865-748-8672
Lab: 1-301-594-9230
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] Electron density improvement with resolution graphic

2009-12-04 Thread Jonathan Winger

James Holton has a great little movie showing how electron density  
changes with decreasing resolution:  http://ucxray.berkeley.edu/~jamesh/movies/resolution.mpeg


Jon

On Dec 4, 2009, at 5:37 PM, Jim Fairman wrote:

You can find one here on the Cambridge X-ray crystallography course  
website:  http://www-structmed.cimr.cam.ac.uk/Course/Fitting/fittingtalk.html


On Fri, Dec 4, 2009 at 8:25 PM, Brad Bennett  
bradbennet...@gmail.com wrote:

Hi all-
I recall seeing a long time ago a figure which showed the  
progressive improvement of electron density as one increases  
resolution, say from 6 to 3.5 to 2A. I believe I've seen two  
versions- one a larger scale pic showing the ability to model side  
chains of alpha helices at higher resolutions and the other a  
simpler graphic of a tyrosine aromatic ring showing the electron  
density hole in the middle of the ring once near atomic resolution  
maps are obtained. Does anyone have, in their teaching notes or a  
textbook or presentation, a graphic which displays this? I need it  
for a talk this weekend and Google searches have come up blank. If  
all else fails, I can generate it myself...(lazy sigh)


Thanks in advance-
Brad



--
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
Cell: 1-865-748-8672
Lab: 1-301-594-9230
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] Electron density improvement with resolution graphic

2009-12-04 Thread Bernhard Rupp

This could be useful:

 

http://www.ruppweb.org/Xray/resolution.html

 

BR

 

From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Brad
Bennett
Sent: Friday, December 04, 2009 5:26 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Electron density improvement with resolution graphic

 

Hi all-
I recall seeing a long time ago a figure which showed the progressive
improvement of electron density as one increases resolution, say from 6 to
3.5 to 2A. I believe I've seen two versions- one a larger scale pic showing
the ability to model side chains of alpha helices at higher resolutions and
the other a simpler graphic of a tyrosine aromatic ring showing the electron
density hole in the middle of the ring once near atomic resolution maps are
obtained. Does anyone have, in their teaching notes or a textbook or
presentation, a graphic which displays this? I need it for a talk this
weekend and Google searches have come up blank. If all else fails, I can
generate it myself...(lazy sigh)

Thanks in advance-
Brad

[ccp4bb] electron density slabs

2009-09-08 Thread hayato Jumonji

Dear all, I've phased 3 wavelength SeMet dataset with SHELX and the
resulting mtz on Coot  shows ~5.4 A apart slabs in water channel. I've
captured part of the electron density at 0.4sigma. The slabs appear through
out the electron density and parallel to AB plane (space group P21212). Most
of the electron density in the protein region looks good. But about 30% of
the protein region is affected by this regular noise and appeared choppy.
Although the protein region is still choppy, I do not see the slabs on
another dataset. Could anyone suggest where I am getting this noise and how
to avoid it ? Thanks in advance.
attachment: SS.jpg

[ccp4bb] Fwd: [ccp4bb] electron density slabs

2009-09-08 Thread Poul Nissen

This could be due to biscuit contamination of your protein - did you eat cake before setting up your crystallisation drops?Alternatively it could be a Fourier ripple - a very strong 5.4 Å resolution 00l reflection which is not correctPoulBegin forwarded message:From: hayato Jumonji hay.jumo...@gmail.comDate: 8. sep 2009 11.37.07 GMT+02:00To: CCP4BB@JISCMAIL.AC.UKSubject: [ccp4bb] electron density slabsReply-To: hayato Jumonji hay.jumo...@gmail.com Dear all, I've phased 3 wavelength SeMet dataset withSHELX and the resulting mtz on Coot shows ~5.4 A apart slabs in water channel. I've captured part of the electron density at 0.4sigma. The slabs appear through out the electron density and parallel to AB plane (space group P21212). Most of the electron density in the protein region looks good. But about 30% of the protein region is affected by this regular noise and appeared choppy. Although the protein region is still choppy, I do not see the slabs on another dataset. Could anyone suggest where I am getting this noise and how to avoid it ? Thanks in advance.

Re: [ccp4bb] electron density slabs

2009-09-08 Thread Eleanor Dodson


Slabs are almost always due to  rogue huge reflection(s).

If you run mtzdump on the refmac_output.mtz you will find the maximum 
value and average value of each column.


If you run
fft hklin refmac_output.mtz
LABI F1=FWT PHI=PHWT then the log file gives you the indices of the 
largest reflection.

(search for largest in the log file..)

If that term is  than the mean there might well be something wrong - 
you will have to track back through the data processing to find out what..
If you have used scala the input mtz will have listed all measurements 
of that reflection.


(You can use mtzdump  with keyword START h k l to see what its value is..)

Eleanor






hayato Jumonji wrote:

Dear all, I've phased 3 wavelength SeMet dataset with SHELX and the
resulting mtz on Coot  shows ~5.4 A apart slabs in water channel. I've
captured part of the electron density at 0.4sigma. The slabs appear through
out the electron density and parallel to AB plane (space group P21212). Most
of the electron density in the protein region looks good. But about 30% of
the protein region is affected by this regular noise and appeared choppy.
Although the protein region is still choppy, I do not see the slabs on
another dataset. Could anyone suggest where I am getting this noise and how
to avoid it ? Thanks in advance.

Re: [ccp4bb] electron density map

2009-08-21 Thread Anastassis Perrakis


hi -

my two cents:

1. I am puzzled to see only positive and no negative density in the  
picture
2. I would contour difference maps at 3.5 in general for significant  
features

3. why is the 2fofc 'heavily biased' ? Its a 2mFo-DFc map presumably,
and lots have been said about these maps not being so biased these days
of maximum likelihood. With an Rfree of 27% and 80% similarity (!not  
homology, please!)
model to start with, even at 3.0 A I cant agree I expect maps to be  
'heavily biased'.
Sorry James, but I find these maps essential, and not essentially  
useless.
4. if you want to really look for wrong direction, registry trouble,  
pep flips,
you are much better of looking at validation reports for that regions  
and less at the density.
If these residues look nice in e.g. Ramachandran plots, I would guess  
the green density

might at the end be a 'technicality'.

What I would do is apply first some small random shift (0.5 A) to all  
atoms,
go back to Refmac, start with a new TLD tensors from 0 and reset B  
factors,

refine, make sure my RMSZ scores for distances and angles is 0.5-1.0,
look at maps again and make sure I see both red and green peaks at 3.5,
run a validation test with molprobity or whatcheck, and then look for  
and correct mistakes.



best,

Tassos

PS Since there were a few posting like that lately, with pictures  
attached, could we please
follow the suggested ccp4bb etiquette and not post attachments of  
pictures,

but make them available online for whoever is really interested only?



On Aug 21, 2009, at 7:28, James Stroud wrote:


I agree with Artem. I also don't think you have a register problem.
All of the residues show typical 2fofc density for their types,
especially considering the 3A data. The disappearing act of the asp
carboxyl is typical of solvent exposed aspartates. Assuming the
register is correct, you have a carbonyl flip somewhere throwing off
the whole segment. The phe is telltale. The 2 dimensionality and
limited region of the picture makes a full diagnosis difficult.

Also, the 2fofc is heavily biased. Don't trust it when it tells you
where things are. I find 2fofcs essentially useless. Your milage may
vary.

James


On Aug 20, 2009, at 5:24 PM, Mike England wrote:


Hi all,

I will appreciate the comments on the 2Fo-Fc (1.5 sigma) and Fo-Fc
(3.0 sigma) (at coot) maps as shown in attached picture .

I am working at 3.0 A resolution (MR phasing with more than 80%
homology) and current Rfree  is 0.27 and  FOM of 0.8.

How to interpret the positive density (green) in Fo-Fc map which
overlaps with the C-alpha tube? The side-chains of the polypeptide
around this regions seems to be properly fitting and registry of the
sequence seems to be OK.

Is this due to some kind of model bias?

Thanks in advance.

Mike
Picture 1.png


P please don't print this e-mail unless you really need to
Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

Re: [ccp4bb] electron density map

2009-08-21 Thread Ed Pozharski

Tassos is absolutely right.  While it's unlikely that many subscribers
of the ccp4bb today suffer the indecency of checking their mailbox over
4kbps flaky modem connection (also known as wishful staring at the
progress bar), it still seems pointless to distribute hundreds of
megabytes into mailboxes of several hundreds (thousands?) of
subscribers.

One great option is Google's Picasa - easy to set up, cross-platform,
completely free and you can add mysterious links to your messages, e.g.

http://picasaweb.google.com/lh/photo/30MIQ8CfqZkXVzM6W3t1cA?feat=directlink

or go completely undercover with TinyURL

http://tinyurl.com/lvfd3w


Or should I have attached 80kb file instead because paperclip button is
easier to reach?

 
 PS Since there were a few posting like that lately, with pictures
 attached, could we please
 follow the suggested ccp4bb etiquette and not post attachments of
 pictures,
 but make them available online for whoever is really interested only?

Re: [ccp4bb] electron density map

2009-08-20 Thread Artem Evdokimov

Hi,

 

Hard to say w/o moving the thing around, but it could be: pep flips, or even
(less likely) wrong chain direction. Incidentally, some of thr the side
chains 'just don't look right to me' - interpret that one as you wish but
e.g. the leucine in the middle seems particularly wrong (try auto-find best
conformer in Coot, I bet the opposite conformer is picked as the best).The
very bottom-most residue's carbonyl doesn't seem to be in the density
either.

 

Suggestions:

 

1.  Delete the top and bottom-most residues and execute real space
refinement a few times - drag the carbonyls around manually and see what
happens
2.  Replace all residues with glycine, do the real space refinement, and
then a few rounds of Refmac - see what comes up and rebuild sidechains.

 

Artem

 

Nothing is built on stone; all is built on sand, but we must build as if
the sand were stone 

 Jorge Luis Borges

 

  _  

From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Mike
England
Sent: Thursday, August 20, 2009 7:24 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] electron density map

 

Hi all,

 

I will appreciate the comments on the 2Fo-Fc (1.5 sigma) and Fo-Fc (3.0
sigma) (at coot) maps as shown in attached picture .

 

I am working at 3.0 A resolution (MR phasing with more than 80% homology)
and current Rfree  is 0.27 and  FOM of 0.8.

 

How to interpret the positive density (green) in Fo-Fc map which overlaps
with the C-alpha tube? The side-chains of the polypeptide around this
regions seems to be properly fitting and registry of the sequence seems to
be OK.

 

Is this due to some kind of model bias? 

 

Thanks in advance.

 

Mike

Re: [ccp4bb] electron density map

2009-08-20 Thread James Stroud

I agree with Artem. I also don't think you have a register problem.  
All of the residues show typical 2fofc density for their types,  
especially considering the 3A data. The disappearing act of the asp  
carboxyl is typical of solvent exposed aspartates. Assuming the  
register is correct, you have a carbonyl flip somewhere throwing off  
the whole segment. The phe is telltale. The 2 dimensionality and  
limited region of the picture makes a full diagnosis difficult.


Also, the 2fofc is heavily biased. Don't trust it when it tells you  
where things are. I find 2fofcs essentially useless. Your milage may  
vary.


James


On Aug 20, 2009, at 5:24 PM, Mike England wrote:


Hi all,

I will appreciate the comments on the 2Fo-Fc (1.5 sigma) and Fo-Fc  
(3.0 sigma) (at coot) maps as shown in attached picture .


I am working at 3.0 A resolution (MR phasing with more than 80%  
homology) and current Rfree  is 0.27 and  FOM of 0.8.


How to interpret the positive density (green) in Fo-Fc map which  
overlaps with the C-alpha tube? The side-chains of the polypeptide  
around this regions seems to be properly fitting and registry of the  
sequence seems to be OK.


Is this due to some kind of model bias?

Thanks in advance.

Mike
Picture 1.png

Re: [ccp4bb] Electron Density Maps

2009-08-10 Thread Folmer Fredslund

Dear Pascal,

2009/8/10 Pascal Egea pas...@msg.ucsf.edu:
 Dear All,
 I am currently carrying the refinement of a structure and comparing the
 results obtained in Refmac, Phenix and CNS.
 While Phenix and Refmac write maps and their corresponding coefficients in
 mtz format allowing display of 2Fo-Fc and Fo-Fc maps in COOT, the
 corresponding Fo-Fc map as written by CNS does not show positive and
 negatives peaks. There is density but it does not look like why I would
 expect for a Fo-Fc map. Why is that?

Is your map read as an Fo-Fc map? I guess not...

I believe there is a way to tell COOT that you want to load you CNS
map as a difference map.
This section
http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_6.html#SEC160
of the user manual might explain better.


Hope this helps,
Folmer Fredslund

Re: [ccp4bb] Electron Density Maps

2009-08-10 Thread Kevin Cowtan

If you want to display CNS maps in Coot and have them on the right 
scale, then you need to do one of two things. Either:


1. Don't use the map file, use the reflection file containing the map 
coefficients, or


2. Change the setting in CNS which controls the extent of the output 
map. Instead of outputting a map covering a single molecule, you need to 
output a map covering a whole asymmetric unit (or if you prefer a whole 
unit cell).


The Xplor maps output by CNS are output in O mode, not Coot mode, by 
default. This is due to a fundamental difference in understanding what a 
map is between programs which work crystal space (e.g. Coot, Quanta, 
XtalView) and those which don't.


Kevin


Pascal Egea wrote:

Dear All,

I am currently carrying the refinement of a structure and comparing the 
results obtained in Refmac, Phenix and CNS.


While Phenix and Refmac write maps and their corresponding coefficients 
in mtz format allowing display of 2Fo-Fc and Fo-Fc maps in COOT, the 
corresponding Fo-Fc map as written by CNS does not show positive and 
negatives peaks. There is density but it does not look like why I would 
expect for a Fo-Fc map. Why is that? 

I am also surprised by the differences between maps and their contouring 
levels between Refmac/Phenix and CNS. Is the way to scale ED maps 
different between those programs? Can differences in the way to perform 
bulk solvent correction account for those differences?


Thanks in advance for your suggestions.


Pascal Egea

Re: [ccp4bb] Electron density function for ligands in real space?

2007-10-29 Thread Eleanor Dodson


If you put the coordinates into COOT it will give you a validation score.
If you use the CCP$i map correlation procedures it will also give you a 
CC for the density match.


The input in each case is the reflection file with appropriate amplitude 
and phase terms.


What you use depends on what phases are available.
Experimental phases - use FP PHI and FOM
Output of REFMAC refinement - maybe FWT and PHWT after you have excluded 
the ligand from the refinement calculation?



Eleanor
Ask if you need more detailed ideas..


Qing Zhang wrote:

Hello,

I'm new in x-ray crystallography and trying to compute real-space 
electron density for ligands. The goal is to evaluate match of ligands 
with density peaks (like computing local R values in real space). What 
would be the best electron density function that considers ligand 
atomic numbers/radii, density map resolution, and some local protein 
information (to estimate B values of ligand atoms)?


Thank you in advance.

Qing Zhang

[ccp4bb] Electron density function for ligands in real space?

2007-10-26 Thread Qing Zhang


Hello,

I'm new in x-ray crystallography and trying to compute real-space 
electron density for ligands. The goal is to evaluate match of ligands 
with density peaks (like computing local R values in real space). What 
would be the best electron density function that considers ligand atomic 
numbers/radii, density map resolution, and some local protein 
information (to estimate B values of ligand atoms)?


Thank you in advance.

Qing Zhang


begin:vcard
fn:Qing Zhang, Ph.D.
n:Zhang;Qing
org:The Scripps Research Institute;Department of Molecular Biology
adr:mail MB-5;;10550 North Torrey Pines Road;La Jolla;CA;92037;U.S.A.
email;internet:[EMAIL PROTECTED]
title:Research Associate
tel;work:858-784-2333
tel;fax:858-784-2860
tel;cell:917-509-3182
url:http://www.scripps.edu/~qzhang
version:2.1
end:vcard

Re: [ccp4bb] electron density maps in Coot vs O / Pymol

2007-02-14 Thread William Scott

I use this to get the same maps:

http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/mapcover
http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/mapcoverdiff

I used zsh but I think it should work with current versions of bash.

mac minista wrote:
 Dear all,

   I have noticed that going from refmac 5 (script) to generate fo-fc and
 2fo-fc maps in O / Pymol once and Coot in the other, the outcome is not
 exactly the same electron density maps-I mean some differences are seen.
  I have used the following columns in Coot (latest version): FOFCWT,
 PHFOFCWT and 2FOFCWT, PH2FOFCWT.  The .o map file was generated using
 FFT, MAPMASK and MAPMAN.
   I want to know why I am not getting identical maps, and if there is a
 solution to avoid this problem then I would really appreciate your help.

   With regards
   Mac


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Re: [ccp4bb] electron density maps in Coot vs O / Pymol

2007-02-14 Thread Paul Emsley

On Wed, 2007-02-14 at 07:59 -0800, mac minista wrote:
 Dear all,
  
 I have noticed that going from refmac 5 (script) to generate fo-fc and
 2fo-fc maps in O / Pymol once and Coot in the other, the outcome is
 not exactly the same electron density maps-I mean some differences are
 seen.  I have used the following columns in Coot (latest version):
 FOFCWT, PHFOFCWT and 2FOFCWT, PH2FOFCWT.  The .o map file was
 generated using FFT, MAPMASK and MAPMAN.
 I want to know why I am not getting identical maps, and if there is a
 solution to avoid this problem then I would really appreciate your
 help.

Well, the devil is in the detail.
a MAPMAN map in O vs a REFMAC MTZ in Coot.  Somewhat apples and oranges.
Stating the obvious: the griding and contour level may well be
different.  The contouring algorithms certainly are.

How about a Coot/Refmac + Mapman map in O 
or a 
MAPMAN map in Coot?  
Then the differences will be more clear?

What do you get if you overlapmap
ADD 1 -1 
and look at differences there?

Re: [ccp4bb] electron density maps in Coot vs O / Pymol

2007-02-14 Thread Peter Adrian Meyer

Hi Mac,

   I have noticed that going from refmac 5 (script) to generate fo-fc and
 2fo-fc maps in O / Pymol once and Coot in the other, the outcome is not
exactly the same electron density maps-I mean some differences are seen.
  I have used the following columns in Coot (latest version): FOFCWT,
 PHFOFCWT and 2FOFCWT, PH2FOFCWT.  The .o map file was generated using
FFT, MAPMASK and MAPMAN.
   I want to know why I am not getting identical maps, and if there is a
 solution to avoid this problem then I would really appreciate your help.

There could be any number of reasons; which is more likely would depend on
the level of differences between the maps.  In (rough) level of
significance, the ones I can think of are:

1. inputs - are your scripts using the same columns as coot (if I'm
understanding correctly that coot is calculating the maps on the fly for
you)?

2. FFT specific stuff - are both maps being calculated using the same
gridpoints and FFT algorithm?

3. contouring issues - the graphics programs may be using different
contouring algorithms; if you're contouring by sigma/rms deviation, then
this can be affected by the size of the region used for rms determination
(are the maps the same size?).  Map normalization may also be an issue.

4. Computational noise - I've been able to get non-identical maps just
by changing the variable precision (identical input files) used by the
programs.  The differences are minimal, but observable.  I'm assuming that
you're using a single system for both maps, otherwise there could be
additional issues (although these should also be relatively minor).

One thing that shouldn't make a difference - O can directly read ccp4
formatted maps, so using FFT with xyzlim asu and reading in O with qmap or
fmap should let you skip over the mapmask/mapman steps.

As far as your specific case, run down the list of things that could have
an effect (there may be other issues that I'm forgetting), and eventually
you should find where the differences are.

Good luck,

Pete

Pete Meyer
Fu Lab
BMCB grad student
Cornell University

Re: [ccp4bb] electron density maps in Coot vs O / Pymol

2007-02-14 Thread Soisson, Stephen Michael

I am guessing it is a difference in normalization, but I would love to hear a 
definitive answer from someone.

Steve

-Original Message-
From: CCP4 bulletin board on behalf of mac minista
Sent: Wed 2/14/2007 10:59 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] electron density maps in Coot vs O / Pymol

Dear all,

I have noticed that going from refmac 5 (script) to generate fo-fc and 2fo-fc 
maps in O / Pymol once and Coot in the other, the outcome is not exactly the 
same electron density maps-I mean some differences are seen.  I have used the 
following columns in Coot (latest version): FOFCWT, PHFOFCWT and 2FOFCWT, 
PH2FOFCWT.  The .o map file was generated using FFT, MAPMASK and MAPMAN.
I want to know why I am not getting identical maps, and if there is a solution 
to avoid this problem then I would really appreciate your help.

With regards
Mac

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Re: [ccp4bb] electron density maps in Coot vs O / Pymol

2007-02-14 Thread mac minista

Hi, 

thank you for your suggestions, the difference I am
seeing in the maps is mainly with the Fo-Fc maps i.e.
what appears in coot does not always appear in
O/Pymol. Here are the scripts for FFT and MAPMASK:

FFT

#!/bin/sh

set -e

fft hklin  model.mtz  mapout fofc_f.map eof
title fofc map
labin F1=FOFCWT PHI=PHFOFCWT
end
eof

#
fft hklin  model.mtz  mapout 2fofc_f.map eof
title 2fofc map
labin F1=2FOFCWT PHI=PH2FOFCWT
end
eof

MAPMASK

#!/bin/sh

set -e

# Run mapmask after fft to extend the map
mapmask mapin fofc_f.map  mapout fofc_fext.map \
xyzin  model.pdb eof
border 2.0
eof
#
mapmask mapin 2fofc_f.map  mapout 2fofc_fext.map \
xyzin model.pdb eof
border 2.0
eof

I will try and get some figures.
 

Regards
Mac


 

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