Re: [ccp4bb] Picture request: Evans & Sutherland Picture System 2 (PS2)

[Jon Cooper]

Someone has very kindly sent me a very good picture so the problem has now gone 
away, although I am happy to receive any other pictures out of nostalgic 
interest ;-0

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android


 Original Message 
On 18/09/2024 22:11, Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk> 
wrote:

>  Does anyone have a decent photograph (preferably in colour and in a 
> crystallographic context) of an E&S PS2 which I could use in an article, 
> acknowledging the source? There is a very good one on a museum website but 
> they haven't replied in a few days. I have googled quite a lot and, yes, 
> Donald Sutherland and Sony PlayStations feature prominently in the results so 
> far...
>  
>  Best wishes, Jon Cooper.
>  jon.b.coo...@protonmail.com
>  
>  Sent from Proton Mail Android
>  
>  
>  
>  To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] Picture request: Evans & Sutherland Picture System 2 (PS2)

[Jon Cooper]

Does anyone have a decent photograph (preferably in colour and in a 
crystallographic context) of an E&S PS2 which I could use in an article, 
acknowledging the source? There is a very good one on a museum website but they 
haven't replied in a few days. I have googled quite a lot and, yes, Donald 
Sutherland and Sony PlayStations feature prominently in the results so far...  

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android



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Re: [ccp4bb] Contact: Hexclude doesn't work?

[Jon Cooper]

Another thing could be if the atom type field is missing in the pdb file. It's 
the optional one on the far right.

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android

 Original Message 
On 30/08/2024 20:04, Dr. Kevin M Jude  wrote:

> I’m trying to run contact on a protonated pdb file and want to ignore 
> hydrogens, but when I use the HEXCLUDE keyword I still get hydrogen contacts. 
> Is it a bug, or am I doing it wrong? Pasting the top of the log file below.
>
> Thanks
>
> Kevin
>
> ###
>
> ###
>
> ###
>
> ### CCP4 8.0.017: CONTACT version 8.0.017 : ##
>
> ###
>
> User: kjude Run date: 30/ 8/2024 Run time: 12:02:24
>
> Please reference: Collaborative Computational Project, Number 4. 2011.
>
> "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 
> 235-242.
>
> as well as any specific reference in the program write-up.
>
> 
>
> ** PROGRAM CONTACT *
>
> Data line--- mode isub
>
> Data line--- limits 0 4.0
>
> Data line--- HEXCLUDE
>
> Data line--- from residue all chain A 1 to 60
>
> Data line--- to residue all chain B 1 to 60
>
> Data line--- end
>
> Atoms of all types will be used.
>
> Intersubunit contacts will be printed
>
> Atom-atom search will be done within the limits of 0.00 to 4.00 angstroms
>
> Logical name: XYZIN File name: 8da3.pdb1
>
> PDB file is being opened on unit 1 for INPUT.
>
> MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE
>
> RF RO
>
> 0.028 -0.000 -0.000 -0.000 35.546 0.000 0.000 -0.000
>
> -0.000 0.024 -0.000 0.000 0.000 42.449 0.000 0.000
>
> 0.000 -0.000 0.013 -0.000 0.000 0.000 74.288 -0.000
>
> -0.000 0.000 -0.000 1.000 -0.000 0.000 -0.000 1.000
>
> Xmin Xmax Ymin Ymax Zmin Zmax : 7.32 40.92 -8.96 33.26 29.29 77.18
>
> NX NY NZ boxes 8 11 10
>
> LIST OF CONTACTS :
>
> ==
>
> source atoms target atoms distance angle
>
> Asn 3A C ... Phe 32B CZ ... 3.74
>
> Asn 3A O ... Phe 32B CZ ... 3.71
>
> ... Phe 32B CE1 ... 3.77
>
> Asn 3A ND2 ... Trp 35B CZ3 ... 3.91
>
> ... Trp 35B CH2 ... 3.84
>
> Asn 3A HB2 ... Phe 32B CZ ... 3.96
>
> Asn 3A HB3 ... Phe 32B CZ ... 3.30
>
> ... Phe 32B CE1 ... 3.18
>
> ... Trp 35B CZ3 ... 3.86
>
> Asn 3A HD21 ... Trp 35B CH2 ... 3.85
>
> Asn 3A HD22 ... Asp 36B OD1 ... 3.80
>
> ... Trp 35B CZ3 ... 3.54
>
> ... Trp 35B CH2 ... 3.72
>
> Etc…
>
> --
>
> Kevin Jude, PhD
>
> Structural Biology Research Specialist, Garcia Lab
>
> Howard Hughes Medical Institute
>
> Stanford University School of Medicine
>
> Beckman B177, 279 Campus Drive, Stanford CA 94305
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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Re: [ccp4bb] Contact: Hexclude doesn't work?

[Jon Cooper]

Hello, you could run pdbset with the "exclude hydrogens" card or pdbcur with 
"delhydrogen". What contacts are you looking for e.g. crystallographic or 
intramolecular?

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android

 Original Message 
On 30/08/2024 20:04, Dr. Kevin M Jude  wrote:

> I’m trying to run contact on a protonated pdb file and want to ignore 
> hydrogens, but when I use the HEXCLUDE keyword I still get hydrogen contacts. 
> Is it a bug, or am I doing it wrong? Pasting the top of the log file below.
>
> Thanks
>
> Kevin
>
> ###
>
> ###
>
> ###
>
> ### CCP4 8.0.017: CONTACT version 8.0.017 : ##
>
> ###
>
> User: kjude Run date: 30/ 8/2024 Run time: 12:02:24
>
> Please reference: Collaborative Computational Project, Number 4. 2011.
>
> "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 
> 235-242.
>
> as well as any specific reference in the program write-up.
>
> 
>
> ** PROGRAM CONTACT *
>
> Data line--- mode isub
>
> Data line--- limits 0 4.0
>
> Data line--- HEXCLUDE
>
> Data line--- from residue all chain A 1 to 60
>
> Data line--- to residue all chain B 1 to 60
>
> Data line--- end
>
> Atoms of all types will be used.
>
> Intersubunit contacts will be printed
>
> Atom-atom search will be done within the limits of 0.00 to 4.00 angstroms
>
> Logical name: XYZIN File name: 8da3.pdb1
>
> PDB file is being opened on unit 1 for INPUT.
>
> MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE
>
> RF RO
>
> 0.028 -0.000 -0.000 -0.000 35.546 0.000 0.000 -0.000
>
> -0.000 0.024 -0.000 0.000 0.000 42.449 0.000 0.000
>
> 0.000 -0.000 0.013 -0.000 0.000 0.000 74.288 -0.000
>
> -0.000 0.000 -0.000 1.000 -0.000 0.000 -0.000 1.000
>
> Xmin Xmax Ymin Ymax Zmin Zmax : 7.32 40.92 -8.96 33.26 29.29 77.18
>
> NX NY NZ boxes 8 11 10
>
> LIST OF CONTACTS :
>
> ==
>
> source atoms target atoms distance angle
>
> Asn 3A C ... Phe 32B CZ ... 3.74
>
> Asn 3A O ... Phe 32B CZ ... 3.71
>
> ... Phe 32B CE1 ... 3.77
>
> Asn 3A ND2 ... Trp 35B CZ3 ... 3.91
>
> ... Trp 35B CH2 ... 3.84
>
> Asn 3A HB2 ... Phe 32B CZ ... 3.96
>
> Asn 3A HB3 ... Phe 32B CZ ... 3.30
>
> ... Phe 32B CE1 ... 3.18
>
> ... Trp 35B CZ3 ... 3.86
>
> Asn 3A HD21 ... Trp 35B CH2 ... 3.85
>
> Asn 3A HD22 ... Asp 36B OD1 ... 3.80
>
> ... Trp 35B CZ3 ... 3.54
>
> ... Trp 35B CH2 ... 3.72
>
> Etc…
>
> --
>
> Kevin Jude, PhD
>
> Structural Biology Research Specialist, Garcia Lab
>
> Howard Hughes Medical Institute
>
> Stanford University School of Medicine
>
> Beckman B177, 279 Campus Drive, Stanford CA 94305
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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Re: [ccp4bb] Mini map aide updates

[Jon Cooper]

A couple of updates to Mini Map Aide (https://minimapai.de), if anyone likes 
the idea of looking at maps on mobile phones, although I know many people look 
at their phones to get away from maps ;-

It can now draw symmetry-related molecules based on the space group symbol 
given in the CRYST1 card in the PDB file. At least one expert (Ian Tickle) was 
not very impressed with my method for generating the symmetry-mates, so do not 
expect the world's fastest performance! Still it should work for all of the 65 
enantio-morphic/genic space groups, except for R3 and R32 which are handled as 
H3 and H32. A few of the more common non-standard ones also work. It should 
handle about 99.89 % of the crystal structures in the PDB!

I also spotted recently that it was not displaying many (probably most) of the 
CCP4 maps which are downloadable from the EBI PDBe but that is now fixed, I 
think. At some stage they switched from storing maps which cover the deposited 
coordinates to storing the map for exactly one complete unit cell, which is 
quite elegant because the electron density values for a molecule that happens 
to be outside the cell can still be read on the fly quite easily.
Do let me know of any problems.

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent with [Proton Mail](https://proton.me/) secure email.

On Sunday, 12 March 2023 at 00:11, Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> I am cautiously optimistic that there have been some improvements to my Mini 
> Map Aide (a basic map viewer mainly for mobile devices): http://minimapai.de
>
> - The browser does not accidentally 'go back' on scrolling upwards in the 
> graphics window.
> - Atom selection is now more accurate i.e. it almost works reliably, unlike 
> before.
> -
>
> Better memory management - it can go through several hundred residues without 
> crashing!
>
> -
>
> New virtual server!
>
> Best wishes, Jon Cooper.
> jon.b.coo...@protonmail.com
>
> Sent with [Proton Mail](https://proton.me/) secure email.
>
> --- Original Message ---
> On Wednesday, November 9th, 2022 at 00:30, Jon Cooper 
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> For info, or more likely amusement, the Mini Map Aide website which I put 
>> together a few months ago for looking at electron density maps, primarily on 
>> mobile devices:
>>
>> http://minimapai.de
>>
>> now allows tweaks to be made to individual amino acids and basic 
>> regularisation to be done, so there definitely is no excuse to shrink from 
>> building, or at least tweaking, models. It is still a bit harebrained and 
>> I'm not sure how the results of my geometry minimiser would stand up in any 
>> validation tests but, used cautiously, it seems to give better rmsd's than 
>> the 1974 lysozyme models ;-0
>>
>> Best wishes, Jon Cooper.
>> jon.b.coo...@protonmail.com
>>
>> Sent with [Proton Mail](https://proton.me/) secure email.
>>
>> ---
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> ---
>
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Re: [ccp4bb] CIF file Cannot Open by Coot

[Jon Cooper]

Can coot read the pdb file? If not it maybe because the space group is "nil". 
Try changing it to exactly "P 1"

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android

 Original Message 
On 19/08/2024 14:55, Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk> 
wrote:

> Hello, the cif file is exactly the same as before and it's not mmcif (as that 
> complaint mentions). I thought there might be some way of generating ligand 
> restraints with a pdb file, these days? Is prodrg still around? Probably not 
> - sorry for being a distraction ;-0 ;-0
>
> Best wishes, Jon Cooper.
> jon.b.coo...@protonmail.com
>
> Sent from Proton Mail Android
>
>  Original Message 
> On 19/08/2024 14:42, Hu, Wenhao  wrote:
>
>> Dear Jon,
>>
>> Thank you so much for all your effort! I really appreciate it. I’ve just 
>> tried to load the files, but unfortunately, it still won’t open and 
>> continues to show the error message I’ve attached here.
>>
>> Thanks again for your help.
>>
>> Best regards,
>>
>> Martin
>>
>> From: CCP4 bulletin board  on behalf of Jon Cooper 
>> <488a26d62010-dmarc-requ...@jiscmail.ac.uk>
>> Date: Monday, August 19, 2024 at 14:24
>> To: CCP4BB@JISCMAIL.AC.UK 
>> Subject: Re: [ccp4bb] CIF file Cannot Open by Coot
>>
>> ⚠ Caution: External sender
>>
>> I made your cif into a pdb (attached) which looks OK. Maybe worth trying 
>> with that.
>>
>> Best wishes, Jon Cooper.
>> jon.b.coo...@protonmail.com
>>
>> Sent from Proton Mail Android
>>
>>  Original Message 
>> On 19/08/2024 12:42, Martin Hu  wrote:
>>
>>> Dear All,
>>>
>>> Thank you all for your help. I’ve tried several approaches to input this 
>>> file, including changing the format to mmCIF, importing it as coordinates, 
>>> and checking the restraints in the file. However, I am still unable to 
>>> install the experimental ligand structure into the protein. It seems that 
>>> COOT or JLigand cannot read the restraints from the CIF file.
>>>
>>> I’m wondering if anyone has faced a similar problem before, and if there is 
>>> a way to input the experimental structure and save its restraints so that 
>>> it can be refined with the overall protein structure in Refmac?
>>>
>>> I’ve attached the original CIF file here for your reference (in .txt 
>>> format).
>>>
>>> Sincerely,
>>> Martin
>>>
>>> 
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> [https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cwenhao.hu.23%40UCL.AC.UK%7C4b5437b17d4c4905bbd908dcc05229e7%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C638596706623540130%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=l0Po7pO%2B5QxANPgjMOPRsZzuCyiu1Jx0xQ%2BVH4J08qQ%3D&reserved=0](https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1)
>>>
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Re: [ccp4bb] CIF file Cannot Open by Coot

[Jon Cooper]

Hello, the cif file is exactly the same as before and it's not mmcif (as that 
complaint mentions). I thought there might be some way of generating ligand 
restraints with a pdb file, these days? Is prodrg still around? Probably not - 
sorry for being a distraction ;-0 ;-0

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android

 Original Message 
On 19/08/2024 14:42, Hu, Wenhao  wrote:

> Dear Jon,
>
> Thank you so much for all your effort! I really appreciate it. I’ve just 
> tried to load the files, but unfortunately, it still won’t open and continues 
> to show the error message I’ve attached here.
>
> Thanks again for your help.
>
> Best regards,
>
> Martin
>
> From: CCP4 bulletin board  on behalf of Jon Cooper 
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk>
> Date: Monday, August 19, 2024 at 14:24
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: Re: [ccp4bb] CIF file Cannot Open by Coot
>
> ⚠ Caution: External sender
>
> I made your cif into a pdb (attached) which looks OK. Maybe worth trying with 
> that.
>
> Best wishes, Jon Cooper.
> jon.b.coo...@protonmail.com
>
> Sent from Proton Mail Android
>
>  Original Message 
> On 19/08/2024 12:42, Martin Hu  wrote:
>
>> Dear All,
>>
>> Thank you all for your help. I’ve tried several approaches to input this 
>> file, including changing the format to mmCIF, importing it as coordinates, 
>> and checking the restraints in the file. However, I am still unable to 
>> install the experimental ligand structure into the protein. It seems that 
>> COOT or JLigand cannot read the restraints from the CIF file.
>>
>> I’m wondering if anyone has faced a similar problem before, and if there is 
>> a way to input the experimental structure and save its restraints so that it 
>> can be refined with the overall protein structure in Refmac?
>>
>> I’ve attached the original CIF file here for your reference (in .txt format).
>>
>> Sincerely,
>> Martin
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> [https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cwenhao.hu.23%40UCL.AC.UK%7C4b5437b17d4c4905bbd908dcc05229e7%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C638596706623540130%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=l0Po7pO%2B5QxANPgjMOPRsZzuCyiu1Jx0xQ%2BVH4J08qQ%3D&reserved=0](https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1)
>>
>> This message was issued to members of 
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Re: [ccp4bb] Phenix real space refine getting lost ...

[Jon Cooper]

A 2 gigabyte map is a very big one. Maybe it needs resampling or cropping down 
to something in the megabyte range. 

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

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 Original Message 
On 07/08/2024 09:24, Klemens Wild  wrote:

>  Dear community
>  
>  small problem running phenix.real_space_refine on a high resolution map
>  via GUI (2.4 A, 2.05 GB) on a MacBook Pro 32 GB M1 ... Never encountered
>  this before, but always used smaller maps:
>  
>  Routine starts and job hangs upon extracting box (see attachment).
>  Separate job on map runs when I do wrapping (thought it might be this),
>  however, when I feed the GUI with this output, again nothing. Not sure
>  what the problem is (no log file indication or error message): some grid
>  things, unit cell issues, map too big?
>  
>  Some input would be helpful, as I am stuck ...
>  
>  Thx
>  
>  Klemens
>  
>  
>  
>  
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Re: [ccp4bb] Issue Aligning PanDDA Generated Map with PDB in PyMOL

[Jon Cooper]

It would be interesting (to me anyway) if you could run mapdump and post *just* 
the header info. 

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

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 Original Message 
On 22/07/2024 19:28, Aline Dias da Purificação 
<d5ed37c6eb7b-dmarc-requ...@jiscmail.ac.uk> wrote:

>  Hi everyone,
>  
>  I’m having trouble aligning a map generated by PanDDA (event map) with its 
> corresponding PDB file in PyMOL. The map is in `native.ccp4` format and it 
> loads correctly in Coot, aligning perfectly with the PDB. However, when I 
> load the same files in PyMOL, the map appears misaligned with the structure.
>  
>  
>  
>  ### What I've Tried:
>  1. **Loading in Coot:** The map and PDB align correctly in Coot.
>  2. **Using `phenix.map_box`:**
> ```bash
> phenix.map_box map_file=Entry-A12A-event_1_1-BDC_0.24_map.native.ccp4 
> pdb_file=Entry-A12A.pdb
> ```
> This generates a new map, but it still appears misaligned in PyMOL.
>  
>  
>  Has anyone faced similar issues with PanDDA maps in PyMOL? Any suggestions 
> for ensuring the map aligns correctly in PyMOL?
>  
>  Any help or suggestions would be greatly appreciated, as I need charming 
> figures for publication.
>  
>  Thank you a lot!
>  
>  
>  
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Re: [ccp4bb] how to create a figure of a blob

[Jon Cooper]

I am afraid I don't have knowledge of pymol options but can't one make a 
separate pdb file with a dummy atom at the desired position so that the map is 
centred there and then turn that molecule/atom off for the rendering step with 
the main molecule left on. Probably I completely misunderstood. CueMol does 
this, too.

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

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 Original Message 
On 18/07/2024 15:33, Andrea Smith  wrote:

> Hi,
>
> I have a “green blob” in my map and I want to create a picture of it. What is 
> the best option to do this?
>
> Normally, to make figures of maps, I use pymol's "display ccp4 maps", but 
> pymol shows maps around “site”. So if I don't fit anything into my blob, I 
> can't create a “site” and display the map.
>
> Is printscreen from Coot my only option?
>
> Thank you for suggestions,
>
> Andrea
>
> ---
>
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Re: [ccp4bb] Lattice expansion

[Jon Cooper]

Hello, with a=b in both cases, I am sure you have considered tetragonal. I 
remember convincing myself something was F222 when it actually was I422.

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

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 Original Message 
On 08/07/2024 12:07, Nichols, Charlie  wrote:

> Hi,
>
> I am trying to recapitulate a published crystallisation system. The published 
> crystal form is P212121 approx cell dimensions 80, 80, 120 // 90, 90, 90 with 
> one trimer in the ASU
>
> We did not get any crystals in the published conditions but have found a new 
> condition giving data to a much higher resolution than the published one but 
> there is a problem…
>
> New crystal form is F222 with approx cell dimensions 40, 40, 120 // 90, 90, 
> 90 – this cell is too small to fit one monomer let alone one trimer.
>
> The prep is remarkably clean and there is a high volume of crystals in the 
> drop so unlikely to be a contaminant. I have tried molrep with individual 
> domains in case there has been degradation during crystallisation but this 
> does not look at all promising.
>
> I am wondering, given the almost exact halving of the a/b cell dimensions and 
> almost exact equivalence of the c cell dimension, whether this is a 
> particularly egregious form of twinning where the twin is three 2-fold screw 
> axes to cause an apparent reduction in the unit cell.
>
> Is there a way to expand the data from the current 40, 40, 120 // 90, 90, 90 
> unit cell to the larger ‘super-cell’ 80, 80, 120 // 90, 90, 90 with four 
> copies of the data to then attempt either molep or just twin refinement with 
> the original published model?
>
> Any comments / help appreciated – NB: I can’t share the actual data or even 
> the target as they are confidential client data…
>
> Thanks, take care,
>
> Charlie Nichols
>
> ---
>
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Re: [ccp4bb] Imosflm help twinned crystal data

[Jon Cooper]

That's one you made earlier ;-0

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

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 Original Message 
On 04/07/2024 20:13, CCP4BB wrote:

> Hi
>
> The best advice I can give if you're new to iMosflm is to work through this 
> tutorial, and feel free to ask questions.
>
> https://www.mrc-lmb.cam.ac.uk/mosflm/imosflm/ver740/documentation/tutorial.html
>
> Note that I don't work on the project any more so I have to concentrate on 
> the day job - but I can help if you're willing to be a little patient...
>
> Harry
> --
> Dr Harry Powell
>
> On 4 Jul 2024, at 18:42, Marco 
> <d0eb7bee83ae-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hi all I am trying to use imosflm in ccp4i2 to re-process my diffraction 
>> data, since the autoprocessed data from XDS at the synchotron is not giving 
>> me a solution. I think the crystal has decent resolution around 2.5-2.6A. I 
>> think the crystal might be twinned however and thus might be making 
>> structural solution difficult for a beginner crystallographer like me. 
>> However an expert in my lab was able to solve the structure with the data 
>> and told me to use imosflm to reprocess the data. They want me to figure 
>> this out on my own with that hint. Is there any tips or resources you can 
>> recommend to help me process my twinned data?
>>
>> Thank you
>>
>> Happy 4th of July!
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
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> ---
>
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Re: [ccp4bb] Imosflm help twinned crystal data

[Jon Cooper]

Oh dear, that sounds like Blue Peter science. I regret though that I haven't 
used mosflm in earnest for a while myself. I do hope someone can be more 
helpful. 

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

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 Original Message 
On 04/07/2024 18:42, Marco <d0eb7bee83ae-dmarc-requ...@jiscmail.ac.uk> 
wrote:

>  Hi all I am trying to use imosflm in ccp4i2 to re-process my diffraction 
> data, since the autoprocessed data from XDS at the synchotron is not giving 
> me a solution. I think the crystal has decent resolution around 2.5-2.6A. I 
> think the crystal might be twinned however and thus might be making 
> structural solution difficult for a beginner crystallographer like me. 
> However an expert in my lab was able to solve the structure with the data and 
> told me to use imosflm to reprocess the data. They want me to figure this out 
> on my own with that hint. Is there any tips or resources you can recommend to 
> help me process my twinned data?
>  
>  Thank you
>  
>  Happy 4th of July!
>  
>  
>  
>  To unsubscribe from the CCP4BB list, click the following link:
>  https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>  
>  This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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>



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Re: [ccp4bb] Comparing datasets with different resolution/quality

[Jon Cooper]

Comparing maps sounds just like the sort of thing the Uppsala suite did. Maybe 
you can find an old binary for mapman or mapman2(?) or compile it from Martin 
Winn's github page. The closest I can find is EDSTATS which I think is in the 
old ccp4 gui.

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

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 Original Message 
On 14/06/2024 20:58, Matt Mcleod  wrote:

> I should clarify. I am mostly concerned about the electron density map.
>
> I want to make sure that I can most closely compare the maps from two 
> different quality structures, rather than the datasets themselves via CC1/2 
> or other metrics. This is more so for interpreting structural changes.
>
> For example, if there is sparse density for some particular thing indicating 
> partial occupancy, how can I compare those two maps. So for low-resolution 
> datasets, maybe there is less density but is that because of data quality or 
> because in that dataset there is a lower occupancy through some meaningful 
> structural change (compared to higher resolution/better data)?
>
> On Fri, 14 Jun 2024 at 14:16, Matt McLeod  wrote:
>
>> Hi all,
>>
>> I am wondering what the best practice is to compare datasets that are of the 
>> same protein but different quality, for instance 2 vs. 3 A.
>>
>> I know that truncating the structures to the same resolution bin is alright, 
>> but the data quality in the lower resolution bins are also not the same. Is 
>> there a way to "inject" noise into the data such that the bins are more 
>> similar?
>>
>> These datasets cannot be recollected at higher resolution since they are 
>> collected at increasingly high pressure, and the resolution change is 
>> anticorrelated with the pressure; no way to get around crystal stability.
>>
>> Any suggestions are appreciated,
>> Matt
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
>> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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>
> --
>
> Matthew Jordan McLeod, PhD
> Post-Doctoral Fellow - Cornell University
>
> ---
>
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Re: [ccp4bb] Ligand identification in X-ray density

[Jon Cooper]

Or, it could be MPD ;-?

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

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 Original Message 
On 05/06/2024 17:54, Jeroen Mesters wrote:

> Thank you for this intriguing information!
>
> At the same time, this also implies that not all entities that have been 
> modelled as MPD are actually MDP but could also be a betain, right!?…..
>
> Best,
>
> Jeroen
>
> __
> Dr. math. et dis. nat. Jeroen R. Mesters
> Biological Safety Officer (BBS)
> Deputy, Lecturer, Program Coordinator Infection Biology
> Visiting Professorship in Biophysics South Bohemian University
> University of Lübeck
> Center for Structural and Cell Biology in Medicine
> Institute of Biochemistry
> Ratzeburger Allee 160
> 23562 Lübeck
>
> https://orcid.org/-0001-8532-6699
>
>> Am 05.06.2024 um 18:41 schrieb Zachary A. Wood :
>>
>> Hello Everyone,
>>
>> It does look like trimethylglycine (betaine), but another view might help. 
>> If it is, it is also made in ecoli and PEOPLE. It is a pretty common 
>> metabolite in the microbial and animal kingdom…useful for balancing osmotic 
>> stress and stabilizing protein structure (it is a strong kosmotrope).
>>
>> Best regards,
>>
>> Z
>>
>> ***
>> Zachary A. Wood, Ph.D. (He/Him)
>> Professor and Graduate Coordinator
>>
>> Josiah Meigs Distinguished Teaching Professor
>>
>> Associate Director of SER-CAT
>> Department of Biochemistry & Molecular Biology
>> University of Georgia
>> Life Sciences Building, Rm A426B
>> 120 Green Street
>> Athens, GA 30602-7229
>> Office: 706-583-0304
>> Lab: 706-583-0303
>> FAX: 706-542-1738
>> ***
>>
>> From:CCP4 bulletin board  on behalf of Jeroen Mesters 
>> <cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>
>> Date:Wednesday, June 5, 2024 at 12:29 PM
>> To:CCP4BB@JISCMAIL.AC.UK
>> Subject:Re: [ccp4bb] Ligand identification in X-ray density
>>
>> You don't often get email 
>> fromcf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk.[Learn why this is 
>> important](https://aka.ms/LearnAboutSenderIdentification)
>>
>> [EXTERNAL SENDER - PROCEED CAUTIOUSLY]
>>
>> Hi,
>>
>> proteins my pick up ligands from the „source" from which they were 
>> isolated…. Looks to me like trimethylglycine, an amino-acid derivative found 
>> in plants…
>>
>> Regards,
>>
>> Jeroen
>>
>> __
>>
>> https://orcid.org/-0001-8532-6699
>>
>>> Am 05.06.2024 um 17:44 schrieb Khadijah Ameen Khan 
>>> :
>>>
>>> Dear All,
>>>
>>> I am a first-year PhD student in a structural biology lab. I am building a 
>>> model in 1.5 ang X-ray diffraction data. I would appreciate your 
>>> suggestions for fitting a ligand in an unknown X-ray density (attached 
>>> image) in the protein binding pocket. The details for protein purification 
>>> and crystallization buffers are below:
>>>
>>> Purification: NaCl, Tris-HCl pH 8.5, Glycerol
>>>
>>> Crystallization: Carboxylic acid mix (Sodium formate, Ammonium acetate, 
>>> Sodium citrate, Potassium Sodium Tartrate and Sodium Oxamate),Tris, Bicine 
>>> buffer, Precipitant (PEG3350, MPD)
>>>
>>> I have tried fitting all the buffer and crystallization components but none 
>>> of these components are giving the right solution (Either the difference 
>>> map gets red with increased B-factor or it remains green).
>>>
>>> I would really appreciate your input on this. I have attached an image 
>>> showing the density.
>>>
>>> Thank you.
>>
>> ---
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
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Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

[Jon Cooper]

Another factor might be that ccpem uses a different axis order to gemmi and 
ccp4 ;-0

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

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 Original Message 
On 05/06/2024 12:51, Guillaume Gaullier  wrote:

> With a cryoEM map, it's easier to do the rigid-body fitting of step 2 in real 
> space (this is trivial to do interactively in ChimeraX) rather than by MR.
>
> ---
>
> From: CCP4 bulletin board  on behalf of Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
> Sent: Wednesday, June 5, 2024 1:39:56 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for 
> Difference Map
>
> Hmm - rather tricky! I would do an MR search with the crystal model v the EM 
> density,
> Steps would be:
> 1) convert EM density to "structure factors". - there are tools which do this 
> ..
> 1a) You need to go back to ccp4i - program sfall to read map to generate SFs 
> from map - then cad or sftools to add a fake SigF column
> 2) Solve MR search with the model v these "structure factors" using them as 
> Fobs
> 3) Calculate the structure factors from the MR positiooned model and get the 
> difference map..
>
> On Wed, 5 Jun 2024 at 11:46, Martin Malý  wrote:
>
>> Dear Devbrat,
>>
>> I am now playing with a similar problem but I don't have a simple solution 
>> for you as I'm also quite stuck. You can check these software tools which 
>> involve some scripting in Python (NumPy, SciPy) and C++:
>>
>> EMDA (for cryoEM maps, included in CCP-EM)
>> https://gitlab.com/ccpem/emda
>> https://doi.org/10.1016/j.jsb.2021.107826
>>
>> Gemmi (mainly for crystallography, included in CCP4)
>> https://gemmi.readthedocs.io/en/latest/grid.html
>>
>> Maybe there are also some relevant features in CCTBX (included in CCP4 and 
>> Phenix).
>>
>> Cheers,
>> Martin
>>
>> On 05/06/2024 07:00, Devbrat Kumar wrote:
>>
>>> Hello Everyone,
>>>
>>> Greetings!
>>>
>>> I have a query regarding the resampling of cryoEM density to match crystal 
>>> density to obtain a density difference map. Specifically, I am trying to 
>>> determine if it is feasible to resample a cryoEM map with an XRD density 
>>> map. However, each time I attempt this, the resampling output provides an 
>>> arbitrary ASU resample map, resulting in a significant loss of major 
>>> density.
>>>
>>> I have been using Coot and Chimera for this process but have not achieved 
>>> the desired outcome. Please guide me or suggest how to move forward with 
>>> this. My goal is to create an accurate final density difference map.
>>>
>>> Thank you in advance for your help.
>>>
>>> Warm Regards-
>>> Devbrat Kumar
>>>
>>> ---
>>>
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Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

[Jon Cooper]

It would be interesting to know if this will affect the the electron density 
maps which are downloadable from the EBI:

www.ebi.ac.uk/pdbe

They don't currently serve the older dsn6 format, only ccp4, I think.

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android


 Original Message 
On 31/05/2024 16:36, Ezra Peisach 
<d150cd71a251-dmarc-requ...@jiscmail.ac.uk> wrote:

>  In fall of 2024, electron density map coefficients will be available in
>  the public PDB archive for all X-ray structures. These map coefficients
>  will be the same as used in wwPDB Validation Reports.
>  
>  The new map coefficients files will replace the electron density maps
>  and combined map coefficient files calculated and distributed by RCSB
>  PDB and used by the NGLviewer at RCSB.org. These data (served by
>  EDMAPS.rcsb.org) are calculated using publicly-available coordinate
>  files and structure factor files and offered in DSN6 formatted map files
>  and MTZ formatted map coefficient files. RCSB PDB plans to shutdown the
>  NGL viewer by July 2024
>  (https://www.rcsb.org/news/feature/65b42d3fc76ca3abcc925d15) and will no
>  longer need the data served by EDMAPS.rcsb.org.
>  
>  RCSB PDB will be phasing out EDMAPS.rcsb.org:
>  
>    *  June 28, 2024: DSN6-formatted map files will no longer be
>  provided. EDMAPS.rcsb.org will only serve MTZ files with map coefficients.
>    *  Fall 2024: Electron density map coefficients will be available
>  in the public PDB archive for all X-ray structures. At this point,
>  EDMAPS.rcsb.org will be shut down, including access to MTZ files with
>  map coefficients from this service.
>  
>  To help users with this transition, RCSB PDB will be holding a Virtual
>  Office Hour on Thursday June 13, 2024 from 1:00pm-2:00pm Eastern,
>  10:00am-11am Pacific. Please register online for this event at
>  https://go.rutgers.edu/psx4pr63.
>  
>  Questions about this transition or the Virtual Office Hour can be sent
>  to i...@rcsb.org.
>  
>  
>  
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Re: [ccp4bb] Translational non-crystallographic symmetry giving low R-factors

[Jon Cooper]

There's nothing wrong with translational NCS. It is what it is ;-0

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

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 Original Message 
On 29 May 2024, 15:49, Kay Diederichs wrote:

> Hi Catherine, I think you meant to write "giving high R-factors". To add to 
> what Esko and Eleanor wrote: There is nothing wrong with your data or 
> spacegroup or refinement; it is just that the tNCS produces two sets of 
> reflections: half or your reflections are statistically "normal" (as if no 
> tNCS were there), and the other half is quite weak (their intensities would 
> be zero if the translation were 0,-0.5,0.5 which is not far from 
> 0.072,-0.498,0.5). As a result, one half of your reflections has a relatively 
> good agreement of Fcalc and Fobs; the other half agrees relatively worse 
> because a) they have less weight in refinement, b) their measurement error is 
> relatively higher than that of the strong reflections. The R-factor 
> calculation knows nothing about this, it just uses all reflections and so you 
> get something like an average R-factor which is of course higher than that of 
> the strong half. I'd say just document this in the paper you write about the 
> structure. It would be useful/interesting for such cases to have a program 
> that calculates R-values separately for the two classes of reflections (it 
> should be possible to do this with a script that employs CCP4 sftools, I 
> think). HTH, Kay On Wed, 29 May 2024 13:48:46 +, Catherine Back  wrote: 
> >Hi, > >I have collected data for a protein which solved easily to 1.6 � 
> using MR. However, during data analysis and refinement it clearly has 
> translational NCS. According to Xtriage on Phenix: >Frac. coord.: 0.072, 
> -0.498, 0.5 >Distance to origin: 68.798 >Height relative to origin: 51.479% 
> >p-value (height): 5.577e-05 > >Wilson value and L-test suggests no twinning. 
> > >It solved using Molrep in ccp4i2. P2 21 21. All stats look good, but even 
> after refinement (not fully and completely finalised yet) R= 0.24 and 
> Rfree=0.27. Also, it appears the 2 molecules in the AU have swapped a helix 
> with their respective symmetry partners. I'm pretty sure I now have the 
> correct space group, and tried various others with much less success. > > > 
> 1. >Will these Rfactors be 'good'/low enough to publish for a dataset at 
> 1.6�? > 2. >Should I be doing anything else during structure solving to 
> alleviate the effects of tNCS? (I did try using Phaser to solve the 
> structure, but the stats were much worse and even though 'tNCS is present 
> correction factors were not applied'. I'm not sure why. > >Many thanks, >Cat 
> > > >Dr Catherine R. Back (she/her) > >Senior Post-doctoral Research 
> Associate > >School of Biochemistry > >University of Bristol > >UK > > > > 
> > > 
> >To unsubscribe from the CCP4BB list, click the following link: 
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Re: [ccp4bb] AW: [ccp4bb] a dinosaur asks ... PDB format query

[Jon Cooper]

You could probably get it to delete everything except CA's too.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 15 May 2024, 13:22, Jon Cooper wrote:

> It sounds as though you need the power of the script. You can (from memory) 
> run pdbcur to drop the aniso lines and hydrogen atoms, which helps.
>
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>
> Sent from Proton Mail mobile
>
>  Original Message 
> On 15 May 2024, 13:11, Hughes, Jonathan wrote:
>
>> hello CCP4 people, rather off-topic: is there a purpose-written windows 
>> editor for PDF files? with interleaved anisotropy lines, missing column 
>> delimiters etc., simply extracting the B-factors for Ca atoms is hard work 
>> using a standard character editor. would anyone think of working with DNA 
>> without proper tools? best jon -- Prof. Dr. Jon Hughes Department of Physics 
>> Free University of Berlin & Institute for Plant Physiology Justus Liebig 
>> University Giessen Germany 
>>  To 
>> unsubscribe from the CCP4BB list, click the following link: 
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Re: [ccp4bb] AW: [ccp4bb] a dinosaur asks ... PDB format query

[Jon Cooper]

It sounds as though you need the power of the script. You can (from memory) run 
pdbcur to drop the aniso lines and hydrogen atoms, which helps.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 15 May 2024, 13:11, Hughes, Jonathan wrote:

> hello CCP4 people, rather off-topic: is there a purpose-written windows 
> editor for PDF files? with interleaved anisotropy lines, missing column 
> delimiters etc., simply extracting the B-factors for Ca atoms is hard work 
> using a standard character editor. would anyone think of working with DNA 
> without proper tools? best jon -- Prof. Dr. Jon Hughes Department of Physics 
> Free University of Berlin & Institute for Plant Physiology Justus Liebig 
> University Giessen Germany 
>  To 
> unsubscribe from the CCP4BB list, click the following link: 
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message 
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Re: [ccp4bb] What could these crystals be?

[Jon Cooper]

Hello, what is in the purification buffer?

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 13 May 2024, 15:15, 张慧欣 wrote:

> Hi all
> We have been trying with no success to crystalize a protein. Recently we got 
> these strange shape "crystals". They are hard and flat . Any ideas as to what 
> could cause this? The crystallization conditions is:0.06M Divalents 0.1M 
> BICINE 0.1M Tris pH8.5 20% Ethylene glycol 10% PEG8000
>
> ---
>
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Re: [ccp4bb] replacement for Scientific Linux

[Jon Cooper]

Hello Harry

Any of the top 50 on distrowatch.com will basically be fine and the next 20 or 
so on the list will probably be fine. Then you start getting into the twilight 
zone. I am sure that will help greatly to narrow down your choice ;-0

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

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 Original Message 
On 26 Apr 2024, 16:46, Harry Powell wrote:

> Hi folks For many years I’ve been using Scientific Linux as my OS of choice 
> (when not using my Mac) - but it’s been discontinued. SL was based on RHEL, 
> and had useful things like a less-buggy Fortran/C/C++ compiler than that 
> released by RH. What do people here recommend as a replacement? Harry 
>  To 
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Re: [ccp4bb] Voidoo cavity volume tool: cavity.lib file

[Jon Cooper]

I can see the file here:

https://github.com/martynwinn/Uppsala-Software-Factory/tree/master/voidoo

Hope that will help.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

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 Original Message 
On 10 Apr 2024, 12:05, Ankur Kumar Singh wrote:

> Dear All,
>
> I want to use voidoo cavity volume tool (Uppsala software facility) to 
> determine cavity volume around a specific set of residues (G.J. Kleywegt & 
> T.A. Jones (1994)). Unfortunately, I don't have the cavity.lib file that is 
> required for this tool. I tried downloading the files from the FTP link 
> provided on the USF server, but that didn't work. Please let me know if 
> anyone has this file.
>
> I appreciate any help you can provide.
>
> Thank you
> -
> Regards,
> Ankur K Singh
> Graduate Student
> Indian Institute of Science, Bangalore
> India, 560012
>
> ---
>
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Re: [ccp4bb] MTZ to ccp4/MRC map

[Jon Cooper]

Gemmi is probably easiest.

gemmi sf2map -s3 --mapmask=my.pdb my.mtz my.map

Vary s (sampling) according to taste ;-0

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

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 Original Message 
On 6 Apr 2024, 12:00, Cryo EM wrote:

> Hi all,
>
> I was wondering what would be the best way to convert a MTZ file to MRC or 
> CCP4 map?
> I have a corresponding PDB file with me.
>
> Thanks
>
> ---
>
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Re: [ccp4bb] Rwork and Rfree the same?

[Jon Cooper]

What type of Rfree flags do you have? The CCP4 flags will be a random integer 
between 0 and 19, with 0 being used for the free set. Reminding myself: "Phenix 
uses the CNS/XPLOR convention for R-free flags, where 1 marks the test set and 
0 the "working" set." Shelx is different, too, but that probably doesn't matter 
here. Anyway, I think if you have a phenix Rfree set, 95% of the reflections 
will have flags of zero (the phenix working set) and CCP4 would regard these as 
the test set and only use the phenix Rfree set (5% of the data) for the working 
set. Don't ask how I know, but you can get Rfree values lower than Rwork at 
this point. Combine this with low completeness and perhaps that is what is 
happening.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

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 Original Message 
On 28 Feb 2024, 16:21, Justin Cruite wrote:

> Thanks everyone,
>
> I agree, 18.4% Rwork and Rfree is too good to be true for a 3.4 Å dataset. 
> The data was processed using autoProc and the staranisano mtz was used for 
> MR. The completeness is only 38%. It could be that the Rfree and Rwork 
> reflection sets are small because of this? What is the best way to check the 
> number of reflections used for Rwork and Rfree? Is this dataset usable at all?
>
> Thanks!
>
> Justin
>
> On Wed, Feb 28, 2024 at 10:21 AM nicfoos  wrote:
>
>> Hello Justin,
>>
>> There is something weird in your results. You mention Rwork/Rfree of
>> 0.1837.
>> This means a pretty good refinement and also is very unusual to be
>> obtain for a resolution of 3.37.
>> Additionally you should not have Rfree = Rwork.
>> I suspect something wrong with you Rfree reflections sets. What size is
>> it ? Is your dataset complet ?
>> How did you cut the res. ?
>>
>> I hope this may help you.
>>
>> Nicolas
>>
>> On 2024-02-28 16:10, Justin Cruite wrote:
>>> Hi everyone,
>>>
>>> What does it mean if your Rwork and Rfree are exactly the same?
>>>
>>> I solved a 3.37 Å structure with Phaser-MR and immediately ran 10
>>> cycles of refinement with wxc = 0.1. Everything else at default. The
>>> Rwork and Rfree are both 0.1837. Is this bad?
>>>
>>> Thank you!
>>>
>>> Justin
>>>
>>> -
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> ---
>
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Re: [ccp4bb] [off topic] Recovering pET expression plasmid from BL21 strain

[Jon Cooper]

This should all go fine. You can maxi- or mini-prep the plasmid DNA from the 
expression strain and transform it back into a cloning strain for sequencing, 
etc.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

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 Original Message 
On 19 Feb 2024, 00:49, Javier Gonzalez wrote:

> Dear all,
> I'm sure this issue comes up very often, but for the first time in our lab we 
> need to recover a pET-type expression plasmid from a BL21-like E. coli strain 
> (NEB's T7 Express).
> I know a RecA+ strain is not suitable for plasmid production, but the basic 
> plan is to grow and mini-prep the cells to recover the plasmid and later 
> transform another E coli strain (Top10) to make frozen stocks and for plasmid 
> production.
> Is this a regular practice or is there any known protocol we should follow?
> Any advice will be greatly appreciated.
>
> Best wishes,
> Javier
>
> --
>
> Dr. Javier M. González
> Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET)
> Universidad Nacional de Santiago del Estero (UNSE)
> RN9, Km 1125. Villa El Zanjón. (G4206XCP)
> Santiago del Estero. Argentina
>
> Tel: +54-(0385)-4238352
> [Email](mailto:bio...@gmail.com) [Twitter](https://twitter.com/_biojmg)
>
> ---
>
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Re: [ccp4bb] Interface Configuration and Mapslicer Question

[Jon Cooper]

Thank you for clarifying that. It may not be much consolation but I thought it 
might be useful to know that there are no problems with running mapslicer from 
the command line on linux but my font could be better ;-0

https://u.cubeupload.com/jbcooper/mapslicer.png

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

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On Sunday, 18 February 2024 at 19:03, Bernhard Rupp  
wrote:

> Thanks, Jon. Finding the peaks is not the problem; the *.ha file contains 
> those, as do the pdf. map sections.
>
> It is that I don’t know how to properly fix that Interface Configuration file 
> to have the PS distiller and mapslicer display the output.
>
> This problem occurs on 2 independent CCP4i installations on different Windows 
> 10/11 computers
>
> Thx, BR
>
> From: CCP4 bulletin board  On Behalf Of Jon Cooper
> Sent: Sunday, February 18, 2024 09:39
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Interface Configuration and Mapslicer Question
>
> You could search for peaks of decreasing height by stepping back through 
> through alphabet with your text searches. Of course, peakmax will do a good 
> job of finding them anyway.
>
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>
> Sent from Proton Mail mobile
>
>  Original Message 
> On 18 Feb 2024, 17:35, Jon Cooper < 
> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> I think we used to use mapsig for printing map sections with single 
>> characters to show peak height. You could set it so that low or no density 
>> was just a dot and higher values were 0...9 ... A... Z ... * #, etc. up to 
>> the maximum or maybe it was another one of Ian's programs. It made peak 
>> searching with a text editor pretty easy just by searching for the 
>> characters corressponding to the high values. I don't know if that's any use.
>>
>> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>>
>> Sent from Proton Mail mobile
>>
>>  Original Message 
>> On 18 Feb 2024, 03:29, Bernhard Rupp < hofkristall...@gmail.com> wrote:
>>
>>> Der CCP4 Experts & Developers,
>>>
>>> I am exercising in CCP4i (Windows, 8.0.017) some old-fashioned native 
>>> Patterson maps for NCS analysis, using ‘patterson’ of FFT which produces 
>>> the *.map (dump) file and 3 Harker *.plt files.
>>>
>>> Unfortunately, epic fail on the display of the results.
>>>
>>> The ghostview (cf. image) I cannot install (some dll error) and it also 
>>> seems deprecated.
>>>
>>> As a workaround I use pltdev to generate a *.ps file and distil it into a 
>>> pdf and then display. Works, but ghostly 20th century
>>>
>>> ...or I display the map directly in Coot and eyeball the 
>>> peakssurprisingly neat and educational.
>>>
>>> Q1: Do we have a direct way in the GUI to convert/display these CCP4 plt 
>>> files?
>>>
>>> I failed adding as PSviewer "C:\Program Files (x86)\Adobe\Acrobat 
>>> DC\Acrobat\acrodist.exe" in the interface configuration (problem maybe the 
>>> blanks).
>>>
>>> But the entry in the Interface Configuration (config.def) seems sensibly 
>>> quoted:
>>>
>>> PS_PREVIEW_NAME,4 _text acrodist.exe
>>>
>>> PS_PREVIEW_COM,4 _text "C:\Program Files (x86)\Adobe\Acrobat 
>>> DC\Acrobat\acrodist.exe"
>>>
>>> Q2: how do I properly enter the path to the distiller in the interface 
>>> configuration?
>>>
>>> Mapslicer is also uncooperative (cf. img).
>>>
>>> The Interface Configuration entry informs me that “ccp4mapwish [file join 
>>> [GetEnvPath CCP4I_TOP] bin mapslicer.tcl]”.
>>>
>>> Q3: How should I fix this (I swear I did not wish with the installation)?
>>>
>>> In search of a more modern approach to this map analysis I also tried 
>>> CCP4i2 and Phenix, but there was no task like
>>>
>>> “Make a native Patterson and show me the *&%# map” to be found.
>>>
>>> Q4: would this be a useful task to provide?
>>>
>>> (a selfrotation task exists in ccp4i2 via molrep, and there, PS viewing 
>>> works just fine).
>>>
>>> Cheers, BR
>>>
>>> --
>>>
>>> Bernhard Rupp, Psilosopher
>>>
>>> https://psilosophy.org/
>>>
>>> https://www.hofkristallamt.org/
>>>
>>> b...@hofkristallamt.

Re: [ccp4bb] Interface Configuration and Mapslicer Question

[Jon Cooper]

You could search for peaks of decreasing height by stepping back through 
through alphabet with your text searches. Of course, peakmax will do a good job 
of finding them anyway.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 18 Feb 2024, 17:35, Jon Cooper wrote:

> I think we used to use mapsig for printing map sections with single 
> characters to show peak height. You could set it so that low or no density 
> was just a dot and higher values were 0...9 ... A... Z ... * #, etc. up to 
> the maximum or maybe it was another one of Ian's programs. It made peak 
> searching with a text editor pretty easy just by searching for the characters 
> corressponding to the high values. I don't know if that's any use.
>
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>
> Sent from Proton Mail mobile
>
>  Original Message 
> On 18 Feb 2024, 03:29, Bernhard Rupp wrote:
>
>> Der CCP4 Experts & Developers,
>>
>> I am exercising in CCP4i (Windows, 8.0.017) some old-fashioned native 
>> Patterson maps for NCS analysis, using ‘patterson’ of FFT which produces the 
>> *.map (dump) file and 3 Harker *.plt files.
>>
>> Unfortunately, epic fail on the display of the results.
>>
>> The ghostview (cf. image) I cannot install (some dll error) and it also 
>> seems deprecated.
>>
>> As a workaround I use pltdev to generate a *.ps file and distil it into a 
>> pdf and then display. Works, but ghostly 20th century
>>
>> ...or I display the map directly in Coot and eyeball the 
>> peakssurprisingly neat and educational.
>>
>> Q1: Do we have a direct way in the GUI to convert/display these CCP4 plt 
>> files?
>>
>> I failed adding as PSviewer "C:\Program Files (x86)\Adobe\Acrobat 
>> DC\Acrobat\acrodist.exe" in the interface configuration (problem maybe the 
>> blanks).
>>
>> But the entry in the Interface Configuration (config.def) seems sensibly 
>> quoted:
>>
>> PS_PREVIEW_NAME,4 _text acrodist.exe
>>
>> PS_PREVIEW_COM,4 _text "C:\Program Files (x86)\Adobe\Acrobat 
>> DC\Acrobat\acrodist.exe"
>>
>> Q2: how do I properly enter the path to the distiller in the interface 
>> configuration?
>>
>> Mapslicer is also uncooperative (cf. img).
>>
>> The Interface Configuration entry informs me that “ccp4mapwish [file join 
>> [GetEnvPath CCP4I_TOP] bin mapslicer.tcl]”.
>>
>> Q3: How should I fix this (I swear I did not wish with the installation)?
>>
>> In search of a more modern approach to this map analysis I also tried CCP4i2 
>> and Phenix, but there was no task like
>>
>> “Make a native Patterson and show me the *&%# map” to be found.
>>
>> Q4: would this be a useful task to provide?
>>
>> (a selfrotation task exists in ccp4i2 via molrep, and there, PS viewing 
>> works just fine).
>>
>> Cheers, BR
>>
>> --
>>
>> Bernhard Rupp, Psilosopher
>>
>> https://psilosophy.org/
>>
>> https://www.hofkristallamt.org/
>>
>> b...@hofkristallamt.org
>>
>> +1 925 209 7429
>>
>> +43 676 571 0536
>>
>> --
>>
>> All models are wrong but some are useful.
>>
>> --
>>
>> ---
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>> ---
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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Re: [ccp4bb] Interface Configuration and Mapslicer Question

[Jon Cooper]

I think we used to use mapsig for printing map sections with single characters 
to show peak height. You could set it so that low or no density was just a dot 
and higher values were 0...9 ... A... Z ... * #, etc. up to the maximum or 
maybe it was another one of Ian's programs. It made peak searching with a text 
editor pretty easy just by searching for the characters corressponding to the 
high values. I don't know if that's any use.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 18 Feb 2024, 03:29, Bernhard Rupp wrote:

> Der CCP4 Experts & Developers,
>
> I am exercising in CCP4i (Windows, 8.0.017) some old-fashioned native 
> Patterson maps for NCS analysis, using ‘patterson’ of FFT which produces the 
> *.map (dump) file and 3 Harker *.plt files.
>
> Unfortunately, epic fail on the display of the results.
>
> The ghostview (cf. image) I cannot install (some dll error) and it also seems 
> deprecated.
>
> As a workaround I use pltdev to generate a *.ps file and distil it into a pdf 
> and then display. Works, but ghostly 20th century
>
> ...or I display the map directly in Coot and eyeball the 
> peakssurprisingly neat and educational.
>
> Q1: Do we have a direct way in the GUI to convert/display these CCP4 plt 
> files?
>
> I failed adding as PSviewer "C:\Program Files (x86)\Adobe\Acrobat 
> DC\Acrobat\acrodist.exe" in the interface configuration (problem maybe the 
> blanks).
>
> But the entry in the Interface Configuration (config.def) seems sensibly 
> quoted:
>
> PS_PREVIEW_NAME,4 _text acrodist.exe
>
> PS_PREVIEW_COM,4 _text "C:\Program Files (x86)\Adobe\Acrobat 
> DC\Acrobat\acrodist.exe"
>
> Q2: how do I properly enter the path to the distiller in the interface 
> configuration?
>
> Mapslicer is also uncooperative (cf. img).
>
> The Interface Configuration entry informs me that “ccp4mapwish [file join 
> [GetEnvPath CCP4I_TOP] bin mapslicer.tcl]”.
>
> Q3: How should I fix this (I swear I did not wish with the installation)?
>
> In search of a more modern approach to this map analysis I also tried CCP4i2 
> and Phenix, but there was no task like
>
> “Make a native Patterson and show me the *&%# map” to be found.
>
> Q4: would this be a useful task to provide?
>
> (a selfrotation task exists in ccp4i2 via molrep, and there, PS viewing works 
> just fine).
>
> Cheers, BR
>
> --
>
> Bernhard Rupp, Psilosopher
>
> https://psilosophy.org/
>
> https://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> All models are wrong but some are useful.
>
> --
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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Re: [ccp4bb] mtz/cif file for depostion

[Jon Cooper]

From your refmac refinement job in i2, this should give you the combined mtz?

[test.jpg]

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent with [Proton Mail](https://proton.me/) secure email.

On Friday, 9 February 2024 at 17:54, Palm, Gottfried 
<b793af054fc6-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear all,
> I have problems preparing my experimental data (XRD) for deposition. I have 
> two mtz files, which work well for refmac5, with an FREER column in one file 
> and Iplus, SIGIplus, Iminus, SIGIminus columns in the second file. I merged 
> them into one mtz file with cad (in ccp4i).
> The validation server doesn't take two separate mtz files, but complains 
> about missing data in the merged file. I guess because FREER ended up in 
> "Columns common to all datasets" and the other columns in "Dataset #1: 
> 356211/DEFAULT/NATIVE".
> Can I somehow move the FREER column to Dataset #1?
> With "Merge experimental data objects to MTZ Export 'old' style MTZ file" in 
> ccp4i2, the problem is the same.
> I also tried converting to cif many ways, but failed.
> I have used OneDep at EBI.
>
> Best Regards
> Gottfried
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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Re: [ccp4bb] mtz/cif file for depostion

[Jon Cooper]

Hello, there's a way to export all the columns in one file, rather than trying 
to deposit two mini-mtz's. The problem is remembering how when I'm away from 
the computer. It's one of the export options that you find when digging around 
a bit. Maybe it needs a right-click on one of the icons - bit hard for mac 
users, I know ;-0

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 9 Feb 2024, 17:54, Palm, Gottfried wrote:

> Dear all,
> I have problems preparing my experimental data (XRD) for deposition. I have 
> two mtz files, which work well for refmac5, with an FREER column in one file 
> and Iplus, SIGIplus, Iminus, SIGIminus columns in the second file. I merged 
> them into one mtz file with cad (in ccp4i).
> The validation server doesn't take two separate mtz files, but complains 
> about missing data in the merged file. I guess because FREER ended up in 
> "Columns common to all datasets" and the other columns in "Dataset #1: 
> 356211/DEFAULT/NATIVE".
> Can I somehow move the FREER column to Dataset #1?
> With "Merge experimental data objects to MTZ Export 'old' style MTZ file" in 
> ccp4i2, the problem is the same.
> I also tried converting to cif many ways, but failed.
> I have used OneDep at EBI.
>
> Best Regards
> Gottfried
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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Re: [ccp4bb] Crystallizing a tough target

[Jon Cooper]

Limited proteolytic might help, too.

https://www.nature.com/articles/nmeth1118

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 5 Feb 2024, 10:27, kavyashreem wrote:

> Dear All,
>
> Has anyone worked on a protein which is highly soluble even at 80mg/ml?
>
> We have one such candidate, which does not precipitate even at 80mg/ml 
> instead forms phase separated globules in crystallization plate, which 
> eventually hardens over a period of 1 to 1.5 months (which is florescent 
> under UV microscope.)
>
> We tried screening at different pH, but failed to get any hits.
>
> Since we got few conditions in which the phase separated globules solidified, 
> we focused on them and expanded with 120mg/ml protein, still there were not 
> visible precipitates except for the phase separation. This has been a 
> challenging target so far. We have tried with different constructs, which 
> unfortunately are not soluble!
>
> Does POMs help in such cases? Or do you have any other suggestion.
>
> Thank you
>
> Regards
>
> Kavya
>
> CONFIDENTIAL: This email and any files transmitted with it are confidential 
> and intended solely for the use of the individual or group to whom they are 
> addressed. If you have received this email in error, please notify the sender 
> immediately and delete this e-mail from your system. It is NOT AUTHORISED to 
> copy, forward, or in any way reveal the contents of this message to anyone.
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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Re: [ccp4bb] Data reprocessing

[Jon Cooper]

I have one or two in my garage ;-0

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 27 Jan 2024, 19:46, Randy John Read wrote:

> Hi, The current policy of the PDB is that you can deposit a re-refinement of 
> a structure deposited by someone else only if you publish a new paper about 
> it, so that there is a citation associated with the structure. Of course, 
> echoing Eleanor, if you find an issue with someone else’s structure the most 
> collegiate thing to do is to inform the authors and attempt to work with them 
> to fix up the problem. Best wishes, Randy > On 27 Jan 2024, at 07:00, Eleanor 
> Dodson wrote: > > Did you make the original deposition ? If so the pdb 
> accepts re-depositions... > > If it was done by someone else I guess the 
> courteous thing is to notify them and maybe talk to the pdb- redo team? > 
> Cheers Eleanor > > On Sat, 27 Jan 2024 at 01:53, Lucas Souza  wrote: > Dear 
> all, > > After auditing and reprocessing a deposited structure with clear 
> processing mistakes (missing/wrong residues and ligands with evident density) 
> prior to some analysis that are going to be published, what should be done? 
> Re-deposit the structure with a "reprocess" flag? Reopen the PDB deposition 
> and update the files? Or simply state in the publication that the data was 
> reprocessed? > > I'm curious if there's a consensus on handling situations of 
> this nature. > > Cheers, > Lucas > 
>  > > 
> To unsubscribe from the CCP4BB list, click the following link: > 
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This 
> message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
> hosted by www.jiscmail.ac.uk, terms & conditions are available at 
> https://www.jiscmail.ac.uk/policyandsecurity/ > > To unsubscribe from the 
> CCP4BB list, click the following link: > 
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 - Randy 
> J. Read Department of Haematology, University of Cambridge Cambridge 
> Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building 
> Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. 
> www-structmed.cimr.cam.ac.uk 
>  To 
> unsubscribe from the CCP4BB list, click the following link: 
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message 
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Re: [ccp4bb] Query on density fitting to phosphate

[Jon Cooper]

Hello, happy Boxing day.

Re: "The inappropriate identification of an ion as PO4(-3) will significantly 
degrade the quality of any electrostatic potential one calculates from the 
model."

A couple of comments. I always deleted solvents and counter-ions, etc, when 
doing this sort of thing, given all the uncertainties about their ionisation 
state. Not being clever enough to do electrostatic calculations properly 
(evidently), let alone write an FFT refinement program ;-0, I thought that was 
the best way to look at the charge on the protein itself. I agree it is very 
honourable to make an informed decision about a ligand's protonation state and 
to deposit one's preferred model, but there are an awful lot of other hydrogens 
that are not considered in a typical X-ray structure analysis ;-0 Maybe this is 
where neutron and electron diffraction can/will be able to help.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 25 Dec 2023, 09:52, Dale Tronrud wrote:

> Hi, I wanted to correct a statement by Prof. Peat about the ionic state of 
> phosphate in solution. Phosphate has four states differing by the number of 
> attached hydrogen atoms. The number of hydrogen atoms depends on the pH, or 
> maybe it is the other way around since phosphate is used as a buffer. I've 
> attached a plot of the fraction of each species as a function of pH 
> (Citation: "By Clarolux - Own work, CC BY-SA 4.0, 
> https://commons.wikimedia.org/w/index.php?curid=90586171";). There you can see 
> that for all pH's usually seen in mother liquors the solution is almost 
> completely either HPO4(-2) and H2PO4(-1). A binding site may, of course, 
> prefer a species that is present in low concentration but such a protein will 
> be fighting entropy to fill its pocket. Unless your mother liquor has an 
> extreme pH you should expect that the phosphate species you are seeing in 
> your crystal has either one or two hydrogen atoms attached. Their presence 
> will affect both the nature of the hydrogen bonding of the protein to the 
> phosphate and will change the length of the P-O bonds (with the P-O-H bond 
> being about 0.05 A longer than the P=O bond). The two lengths will only be 
> distinguishable given very high resolution diffraction data but there are 
> examples in the PDB where the differences are clear. You can determine the 
> presence of an hydrogen atom at much lower resolution if the hydrogen bond is 
> made with an obligate hydrogen bond acceptor. The inappropriate 
> identification of an ion as PO4(-3) will significantly degrade the quality of 
> any electrostatic potential one calculates from the model. I did a 
> quick-and-dirty search of the PDB for the various species of phosphates in 
> PDB entries. While I found 5979 models with PO4(-3) (ID: PO4) I only found 42 
> with HPO4(-2) (ID: PI) and 27 with H2PO4(-1) (ID: 2HP). I didn't find any 
> H3PO4 and could not find an ID code for that molecule. (This search was done 
> quite a while ago.) I believe depositors are mostly assuming the ID PO4 
> indicates any protonation of a phosphate ion but that is not correct. I am 
> unaware of any ID that is defined as a phosphate ion with unknown protonation 
> state. To conform to the wwPDB standards a depositor must do their best, 
> using the limited data available to them, to choose one species of phosphate 
> when they identify the presence of one, but almost certainly that choice 
> should not be PO4. As usual, just causing trouble, Dale E. Tronrud On 
> 12/17/2023 1:05 PM, Tom Peat wrote: > Dear Arpita, > > The hydrogens on 
> phosphate, just like sodium and potassium, will come > off the oxygens in 
> water. > To be more explicit, you don't have mono- or di-hydrogen phosphate 
> in > water (except transiently), you just have phosphate, depending somewhat 
> > on the pH of course. At 2.5 Angstrom resolution, there is no way to > 'see' 
> hydrogens with X-rays. > Depending on the wavelength you used for your data 
> collection, you could > try doing an anomalous map and see if you have any 
> anomalous signal at > this position, which may help in identifying what the 
> density is. > Best of luck, tom > > 
>  > 
> *From:* CCP4 bulletin board  on behalf of Arpita > Goswami  > *Sent:* Sunday, 
> December 17, 2023 9:46 PM > *To:* CCP4BB@JISCMAIL.AC.UK  > *Subject:* 
> [ccp4bb] Query on density fitting to phosphate > > You don't often get email 
> from bt.arp...@gmail.com. Learn why this is > important  > > > Dear All, > > 
> Hope you all are doing well. > > The density in the image (in lin

Re: [ccp4bb] what is isomorphous?

[Jon Cooper]

Hello Harry,

I think this is the paper you mean:
https://scripts.iucr.org/cgi-bin/paper?S0365110X56002552

They gave depressingly low estimates of how much the cell dimensions could 
change in order for isomorphous replacement to still work. In reality, unit 
cells can shrink and swell, but the fractional atomic coordinates remain 
relatively unchanged (right?) so bigger unit cell differences still allow the 
method to work.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 21 Dec 2023, 09:07, Harry Powell wrote:

> Hi Didn’t Francis Crick have something to say about this in the early 1950s? 
> I’m sure it was published but off the top of my mind I can’t think where (one 
> of the more “established” members of this community will be able to give 
> chapter and verse)! If you want to read something a little more detailed than 
> people have mentioned here, there’s a “Methods in Enzymology” chapter by 
> Charlie Carter (?) et al from the early part of this century on the subject - 
> again, I can’t remember exactly who or when. Have a good break (which reminds 
> me to register for the CCP4 Study Weekend)! Harry > On 21 Dec 2023, at 08:04, 
> Tim Gruene  wrote: > > Hi Doeke, > > you can take the coordinates of B and do 
> a rigid body refinement > against the data from A. If this map is sufficient 
> to reproduce model A > (including model building and more refinement cycles), 
> then B is > isomorphous to A. You can do this the other way round, and the 
> result > may not be the same - hence, the mathematical definition of 
> isomorphous > is not identical to the practical use of 'isomorphous' 
> structures when > it comes to phasing. You can repeat this for each side of 
> the triangle > (each in two directions) in order to label the semantic 
> triangle. > > Merry Christmas, more peace on earth and sanity for the 
> elections in > 2024! > > Tim > > On Wed, 20 Dec 2023 20:15:17 + "Hekstra, 
> Doeke Romke" >  wrote: > >> Dear colleagues, >> >> Something to muse over 
> during the holidays: >> >> Let's say we have three crystal forms of the same 
> protein, for >> example crystallized with different ligands. Crystal forms A 
> and B >> have the same crystal packing, except that one unit cell dimension 
> >> differs by, for example, 3%. Crystal form C has a different crystal >> 
> packing arrangement altogether. What is the right nomenclature to >> describe 
> the relationship between these crystal forms? >> >> If A and B are 
> sufficiently different that their phases are >> essentially uncorrelated, 
> what do we call them? Near-isomorphous? >> Non-isomorphous? Do we need a 
> different term to distinguish them from >> C or do we call all three datasets 
> non-isomorphous? >> >> Thanks for helping us resolve our semantic tangle. >> 
> >> Happy holidays! >> Doeke >> >> = >> >> Doeke Hekstra >> Assistant 
> Professor of Molecular & Cellular Biology, and of Applied >> Physics (SEAS), 
> Director of Undergraduate Studies, Chemical and >> Physical Biology Center 
> for Systems Biology, Harvard University >> 52 Oxford Street, NW311 >> 
> Cambridge, MA 02138 >> Office: 617-496-4740 >> Admin: 617-495-5651 (Lin Song) 
> >> >> >> >> 
>  >> 
> >> To unsubscribe from the CCP4BB list, click the following link: >> 
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> This 
> message was issued to members of www.jiscmail.ac.uk/CCP4BB, a >> mailing list 
> hosted by www.jiscmail.ac.uk, terms & conditions are >> available at 
> https://www.jiscmail.ac.uk/policyandsecurity/ > > > > -- > -- > Tim Gruene > 
> Head of the Centre for X-ray Structure Analysis > Faculty of Chemistry > 
> University of Vienna > > Phone: +43-1-4277-70202 > > GPG Key ID = A46BEE1A > 
> >  > 
> > To unsubscribe from the CCP4BB list, click the following link: > 
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Re: [ccp4bb] what is isomorphous?

[Jon Cooper]

My apologies my second paragraph was badly wrong. What Ian Tickle said in 2008 
(and to save him writing it all again ;-) is:

"In general crystallographic usage 'isomorphous' refers to the similarity of 
crystal structures,
i.e. same arrangement of atoms in the a.u. and the same symmetry. So strictly 
speaking, isomorphous crystals may have different cell parameters, so that NaCl 
and KCl are isomorphous (both being cubic with the same atomic arrangment), but 
the cell parameter of KCl is significantly greater than that of NaCl because 
the K ion is bigger. In MX 'isomorphous' usually implies both that the crystal 
form and structure are very similar
and that the cell parameters are equal. It's perfectly possible that two 
crystals of completely different structures in the same space group 
accidentally have the same cell parameters, but clearly they would not be 
isomorphous, since the primary criterion is that the structures are similar. So 
it's not true to say by either definition that crystals are isomorphous if they 
have the same cell and symmetry, nor is it true that under this definition of 
isomorphism chemical similarity is a pre-requisite."

"Rather the primary criterion of isomorphism is that the components that the 
structures have in common are not just similar but essentially identical (so 
the structures may have additional components that are not in common), and 
equality of symmetry and lattice parameters follow from this."
On Wednesday, 20 December 2023 at 22:21, Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Unless you have a degree in maths, the IUCr's "Little Dictionary of 
> Crystallography" by A. Authier and G. Chapuis (2014) defies comprehension on 
> this matter (it's all to do with set / group theory, I think, and there are 
> many more morphisms covered in about 6 pages: homo, epi, mono, endo, auto).
>
> Having discussed this with Ian Tickle, about 10 or 12 years ago, the formal 
> (?) definition of isomorphous simply means that the unit cells of two or more 
> crystals are the same, but the structure/molecule/compound/mineral, etc, does 
> not even have to be the same. A sensible definition for dumb biologists might 
> be to say that A and B are isomorphous, but C isn't.
>
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>
> Sent from Proton Mail mobile
>
>  Original Message 
> On 20 Dec 2023, 20:15, Hekstra, Doeke Romke < doeke_heks...@harvard.edu> 
> wrote:
>
>> Dear colleagues,
>>
>> Something to muse over during the holidays:
>>
>> Let’s say we have three crystal forms of the same protein, for example 
>> crystallized with different ligands. Crystal forms A and B have the same 
>> crystal packing, except that one unit cell dimension differs by, for 
>> example, 3%. Crystal form C has a different crystal packing arrangement 
>> altogether. What is the right nomenclature to describe the relationship 
>> between these crystal forms?
>>
>> If A and B are sufficiently different that their phases are essentially 
>> uncorrelated, what do we call them? Near-isomorphous? Non-isomorphous?
>>
>> Do we need a different term to distinguish them from C or do we call all 
>> three datasets non-isomorphous?
>>
>> Thanks for helping us resolve our semantic tangle.
>>
>> Happy holidays!
>>
>> Doeke
>>
>> =
>>
>> Doeke Hekstra
>>
>> Assistant Professor of Molecular & Cellular Biology, and of Applied Physics 
>> (SEAS),
>>
>> Director of Undergraduate Studies, Chemical and Physical Biology
>>
>> Center for Systems Biology, Harvard University
>>
>> 52 Oxford Street, NW311
>>
>> Cambridge, MA 02138
>>
>> Office: 617-496-4740
>>
>> Admin: 617-495-5651 (Lin Song)
>>
>> ---
>>
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Re: [ccp4bb] what is isomorphous?

[Jon Cooper]

Unless you have a degree in maths, the IUCr's "Little Dictionary of 
Crystallography" by A. Authier and G. Chapuis (2014) defies comprehension on 
this matter (it's all to do with set / group theory, I think, and there are 
many more morphisms covered in about 6 pages: homo, epi, mono, endo, auto).

Having discussed this with Ian Tickle, about 10 or 12 years ago, the formal (?) 
definition of isomorphous simply means that the unit cells of two or more 
crystals are the same, but the structure/molecule/compound/mineral, etc, does 
not even have to be the same. A sensible definition for dumb biologists might 
be to say that A and B are isomorphous, but C isn't.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 20 Dec 2023, 20:15, Hekstra, Doeke Romke wrote:

> Dear colleagues,
>
> Something to muse over during the holidays:
>
> Let’s say we have three crystal forms of the same protein, for example 
> crystallized with different ligands. Crystal forms A and B have the same 
> crystal packing, except that one unit cell dimension differs by, for example, 
> 3%. Crystal form C has a different crystal packing arrangement altogether. 
> What is the right nomenclature to describe the relationship between these 
> crystal forms?
>
> If A and B are sufficiently different that their phases are essentially 
> uncorrelated, what do we call them? Near-isomorphous? Non-isomorphous?
>
> Do we need a different term to distinguish them from C or do we call all 
> three datasets non-isomorphous?
>
> Thanks for helping us resolve our semantic tangle.
>
> Happy holidays!
>
> Doeke
>
> =
>
> Doeke Hekstra
>
> Assistant Professor of Molecular & Cellular Biology, and of Applied Physics 
> (SEAS),
>
> Director of Undergraduate Studies, Chemical and Physical Biology
>
> Center for Systems Biology, Harvard University
>
> 52 Oxford Street, NW311
>
> Cambridge, MA 02138
>
> Office: 617-496-4740
>
> Admin: 617-495-5651 (Lin Song)
>
> ---
>
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Re: [ccp4bb] extra Fo-Fc density in two Cysteines

[Jon Cooper]

Hello, you seem to have positive difference density for the Cys sulphur/sulfur 
atom. It would be worth checking it's occupancy.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 18 Dec 2023, 17:03, Liliana Margent wrote:

> Hi there, We’ve been having an issue in trying to clear regions of Fo-Fc 
> density from a few cysteines during the refinement process. We were wondering 
> if anyone had seen something similar so they could offer some insight on the 
> likely chemistry at hand, and a potential refinement solution. Attached are 
> two images of the observed extra density at two cysteines, 505 and 518. We 
> have modeled acetylated cysteine, s-hydroxycysteine, and s-mercaptocysteine 
> but it does not solve the density. The protein in question is a Protein 
> Tyrosine Phosphatase known as STEP (PTPN5), with data collected to a 
> resolution of 1.79 Å. The crystals were grown in bis-tris pH 6.65, 200mM 
> Li2SO4, ~30% PEG3350. Of note, prior to data collection the crystal was 
> conserved at room temp for long time where it dried, and was subsequently 
> rehydrated with mother liquor. Thank you so much.
>
> ---
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Re: [ccp4bb] Query on density fitting to phosphate

[Jon Cooper]

Hello, it doesn't look like a phosphate very much, to be honest, and being so 
close to the carboxylate suggests it isn't. Is there any chance that it is an 
alternative conformation of the Arg side chain? If you model it as water, is 
there residual positive difference density?

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

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 Original Message 
On 17 Dec 2023, 10:46, Arpita Goswami wrote:

> Dear All,
>
> Hope you all are doing well.
>
> The density in the image (in link below) is fitted with PO4 ion, although the 
> crystallization condition has both mono and dihydrogen phosphate which is not 
> fitting without hydrogen. But the resolution is 2.5 A, so hydrogen may not be 
> put in, or is there any way to do so? Otherwise placing water is the final 
> option.
>
> https://i.postimg.cc/4N7q2K0p/Screenshot-from-2023-12-17-16-07-07.png
>
> Also the density is quite close to Aspartate, so PO4 may not be right. Can it 
> be dihydrogen phosphate as two positively charged residues (Specially the 
> lysine) are also nearby to neutralize positive charge? Other ions in the 
> crystallization condition are Cl-, K+ and Na+. These are not put as both 
> aspartate and lysine are at comparable distances from the density. The pH is 
> 6.2 in which dihydrogen phosphate is reported to interact with aspartate 
> (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5855859/).
>
> Waiting eagerly for your reply.
> --
>
> Thanks and Merry Christmas in advance.
> Best Regards,
> Arpita
>
> ---
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[ccp4bb] BCA Biological Structures Group Winter (BSG) Meeting, Mon 11th Dec 2023

[Jon Cooper]

We are fast approaching the BSG Winter Meeting, which will be held within the 
Dorothy Crowfoot Hodgkin Building at the University of Oxford, on Monday 11th 
December 2023.

Speakers include:

- Dr Jo Parker (University of Oxford) - Drug recognition and transport via 
Solute Carriers.
- Prof. Xiaodong Zhang (Imperial College London) - Molecular machines that open 
up double-stranded DNA for gene transcription.
- Dr Andrew Carter (MRC LMB) - Cargo transport by dynein/dynactin
- Dr Giulia Zanetti (UCL Birkbeck) - Membrane trafficking mechanisms in the 
early secretory pathway.
- Prof. Elton Zeqiraj (University of Leeds) - Discovery of molecular glues that 
regulate activity and conformation of dynamic protein complexes.

For registration and to view the preliminary programme, please 
click[here](https://registrations.hg3conferences.co.uk/hg3/frontend/reg/thome.csp?pageID=107555&eventID=275).

- - - - - - - - - - - - - - - - - - - - - - - - - -

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

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Re: [ccp4bb] Quaternary Structure concept

[Jon Cooper]

Hello, it sounds like a monomeric protein which has been cleaved in 4 places so 
that would not give it 'quaternary' structure. If the nicked monomers assembled 
into dimers or timer, etc, then it becomes quaternary.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 22 Nov 2023, 20:58, BRUNO DI GERONIMO QUINTERO wrote:

> Dear CCP4BB comunnity;
>
> I am not a structural biologist thus far.
>
> I would like to inquire about the concept of quaternary structure and its 
> applicability to the system I am currently investigating. The protein under 
> study is a human lysosomal protein (Gene MAN2B1) that initially presents as a 
> single chain. Upon entry into the lysosome (facilitated by the signal 
> peptide), it undergoes cleavage four times in four external loops, resulting 
> in the formation of five different "chains." The tertiary structure remains 
> unchanged, and only after denaturation and purification, it becomes possible 
> to observe the five distinct peptides. If the protein remains in the 
> endoplasmic reticulum (ER), it exists as a single chain, as there is no 
> cleavage due to the higher pH in the ER.
>
> My question is as follows: can we consider the protein inside the lysosome as 
> having a quaternary structure? It originates from a monomer, and the subunits 
> exhibit different sequences while interacting with each other. But indeed, 
> there are 5 different peptides.
>
> I would appreciate your expertise and consideration of this perhaps 
> unconventional question, which is causing me significant concern.
>
> Best regards, Bruno Di Geronimo.
>
> ---
>
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Re: [ccp4bb] low resolution data refinement

[Jon Cooper]

Not sure if it's been mentioned that NCS can help a lot at that resolution. We 
did some mutants derived from a 2 Angstrom native structure at about that 
resolution with 4-fold NCS and the maps were quite convincing, well, I thought 
anyway. That was in the days of RESTRAIN which, I think, had an implementation 
of NCS refinement that was a bit different from current progs. Ian will know ;-0

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

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 Original Message 
On 21 Nov 2023, 20:27, Albert Castellvi Toledo wrote:

> Also forget to observe side chains at 4A! At this resolution is crucial to 
> critically assess the position of each amino acid in your model, taking into 
> account factors such as hinges in your structure, hydrophobic and hydrophilic 
> regions, and the types of contacts between secondary structure elements. 
> Paying attention to these details can enhance the accuracy and reliability of 
> your model.
>
> Good luck!
>
> Albert Castellví
>
> On 11/21/23 20:57, Albert Castellvi Toledo wrote:
>
>> Hello,
>>
>> At low resolutions, model bias becomes a significant issue, capable of 
>> yielding inaccurate MR solutions even with favorable figures of merit. In my 
>> experience, it is always necessary to validate MR solutions at low 
>> resolution. One effective approach involves systematically omitting small 
>> fragments from the model and see if the resulting maps suggest you the 
>> placement of the omitted fragment or not. This method enables the 
>> identification of whether the solution is genuinely robust or if it is 
>> highly influenced by model bias.
>>
>> Salut,
>>
>> Albert Castellví
>>
>> On 11/21/23 13:02, Yahui Liu wrote:
>>
>>> Dear all,
>>> I got a protein crystal dataset of 4.3 A and would like to some the 
>>> structure with MR.
>>> Now I am suffering with the refinement. I used both Refmac and Phenix.
>>>
>>> Someone could give me a hand or any suggestions?
>>>
>>> All the best
>>>
>>> ---
>>>
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Re: [ccp4bb] Problem with ligand identification

[Jon Cooper]

How does it look with gl gl... glycerol fitted ;-?

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 Original Message 
On 15 Nov 2023, 14:00, Rafal Dolot wrote:

> Hello everyone,
>
> I need help identifying the ligand I found on the electron density maps. I 
> have soaked ribonuclease A crystals with the phosphorothioate dinucleotide. 
> The diffraction experiment was performed on a home source (Cu). When I 
> analysed the data, I found both the dinucleotide and this strange object near 
> two histidines. Since I did not find anything similar on the list of possibly 
> used compounds, it could be a contamination but still unknown to me. I tried 
> modelling glycolic acid (GOA) here, but it looks like the electron density 
> around the hydroxyl group is greater. Maybe a sulphur containing compound - 
> MCR? Do you have any other idea?
>
> RegardsRafal
> --
>
> --
> Rafal Dolot, Ph.D.
> Polish Academy of Sciences
> Centre of Molecular and Macromolecular Studies
> Division of Bioorganic Chemistry
> Macromolecular Crystallography Laboratory
> Sienkiewicza 112
> 90-363 Lodz, Poland
> Phone: +48(42)6803325
> Cell: +48 502897781
> --
>
> -
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[ccp4bb] Video link for RSC meeting on "British X-ray Crystallographers."

[Jon Cooper]

Message from the conference organiser:

Dear all,

I am very glad to be able to tell you that all the talks given on 18th October 
have been put up on the RSC Historical Group YouTube playlist:

[https://www.youtube.com/playlist?list=PLLnAFJxOjzZu7N0f5-nVtHcLNxU2tKmpC](https://outlook.office.com/owa/redir.aspx?REF=KhF6iKBxs0JkDI3WrY44a3dAn3iCufRejcJaQY1nDL7uQ25cduHbCAFodHRwczovL3d3dy55b3V0dWJlLmNvbS9wbGF5bGlzdD9saXN0PVBMTG5BRkp4T2p6WnU3TjBmNS1uVnRIY0xOeFUydEttcEM.)

My thanks for Professor Stephen Neidle for recording his talk without an 
audience in the following week and toKathryn Espino of RSC Networks for 
uploading them to YouTube.

Best wishes,

Peter Morris

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

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Re: [ccp4bb] 3D viewing on PC

[Jon Cooper]

Hello Oliviero

If you look in the ccp4bb archive (my apologies if you already have) there are 
quite a few posts about this at the end of July - early Aug 2020 i.e. >3 years 
ago. A quick look shows that the options then were mainly based on 2nd hand 
bits and bobs, though.

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 Original Message 
On 12 Oct 2023, 07:34, Oliviero Carugo wrote:

> I am looking for information on methods of stereoscopic (3D) viewing of 
> macromolecular structures on the PC monitor (manufacturers, vendors, prices 
> etc.). Thank you, Oliviero 
>  To 
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Re: [ccp4bb] Intractable outliers in wwPDB validation report

[Jon Cooper]

Hello, unless it's changed over the last couple of years, the pdb rightly used 
to let you deposit a structure with outliers, hopefully not too many, though ;-0

I take it the stalling you reported probably comes from whoever is looking over 
your shoulder.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

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 Original Message 
On 23 Sept 2023, 02:29, Nitin Kulhar wrote:

> Dear all
>
> We have refined (Refmac5) a crystallographic structure with Rw/Rf values 
> 0.19/0.22 (Resln 2.67). However, the deposition has stalled on account of the 
> wwPDB's preliminary validation report, which indicates map/model and geometry 
> issues, with each criterion containing a few instances. We tried to correct 
> these by varying overall geometry restraint weights, e.g. decreasing overall 
> weights from default value of 1.0, incementally decreasing sigmas 
> corresponding to the planarity restraint term. This did not resolve the 
> issues.
>
> In another approach, real space refinement by hand (against 2fo-fc) in coot 
> brought the geometry parameters within acceptable limits in addition to 
> improved apparent agreement with electron density (2fo-fc, sigma=1), but 
> uploading the resultant coordinates seems to undo the changes made in coot, 
> as indicated by reappearance of same outliers in the subsequent validation 
> report.
>
> I request your kind suggestions in this regard. Please also revert for any 
> further information.
>
> Thanks
> Nitin Kulhar
> PhD student
> c/o Dr Rajakumara Eerappa
> Macromolecular Structural Biology Group
> Department of Biotechnology
> Indian Institute of Technology Hyderabad
> Kandi, Sangareddy
> Telangana, India 502284
>
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Re: [ccp4bb] Forthcoming RSC meeting

[Jon Cooper]

Dear all

There are 20 more places available for the in-person RSC meeting on British 
X-ray Crystallographers in London on 18th October. There is also the option to 
attend remotely and those wishing to do so should contact the organiser (Peter 
Morris) whose e-mail address is on the meeting web page:

https://www.rsc.org/events/detail/76719/british-x-ray-crystallographers

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

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--- Original Message ---
On Wednesday, September 20th, 2023 at 22:23, Jon Cooper 
 wrote:

> A reminder that the registration deadline for the free one-day RSC meeting on 
> British X-ray Crystallographers is fast approaching. More details can be 
> found here:
>
> https://www.rsc.org/events/detail/76719/british-x-ray-crystallographers
>
> Best wishes, Jon Cooper.
> jon.b.coo...@protonmail.com
>
> Sent with [Proton Mail](https://proton.me/) secure email.



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Re: [ccp4bb] Forthcoming RSC meeting

[Jon Cooper]

I am also asking about remote access and recording as I not up to date on that 
either. There will be a fairly detailed report in Crystallography News and 
volunteers for writing it are most welcome ;-0

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 21 Sept 2023, 15:13, Jon Cooper wrote:

> Folk are reporting that registration is full, sorry. I will contact the 
> organiser and ask if there might be an overflow option.
>
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>
> Sent from Proton Mail mobile
>
>  Original Message 
> On 20 Sept 2023, 22:23, Jon Cooper wrote:
>
>> A reminder that the registration deadline for the free one-day RSC meeting 
>> on British X-ray Crystallographers is fast approaching. More details can be 
>> found here:
>>
>> https://www.rsc.org/events/detail/76719/british-x-ray-crystallographers
>>
>> Best wishes, Jon Cooper.
>> jon.b.coo...@protonmail.com
>>
>> Sent with [Proton Mail](https://proton.me/) secure email.
>>
>> ---
>>
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>>
>> ---
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Re: [ccp4bb] Forthcoming RSC meeting

[Jon Cooper]

Folk are reporting that registration is full, sorry. I will contact the 
organiser and ask if there might be an overflow option.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 20 Sept 2023, 22:23, Jon Cooper wrote:

> A reminder that the registration deadline for the free one-day RSC meeting on 
> British X-ray Crystallographers is fast approaching. More details can be 
> found here:
>
> https://www.rsc.org/events/detail/76719/british-x-ray-crystallographers
>
> Best wishes, Jon Cooper.
> jon.b.coo...@protonmail.com
>
> Sent with [Proton Mail](https://proton.me/) secure email.
>
> ---
>
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[ccp4bb] Forthcoming RSC meeting

[Jon Cooper]

A reminder that the registration deadline for the free one-day RSC meeting on 
British X-ray Crystallographers is fast approaching. More details can be found 
here:

https://www.rsc.org/events/detail/76719/british-x-ray-crystallographers

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent with [Proton Mail](https://proton.me/) secure email.



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Re: [ccp4bb] High Temperature Factors with TLS

[Jon Cooper]

Hello, is it definitely due to the TLS refinement? I guess you have tried 
without TLS and don't see the same effect i.e. the B-factors are more 
consistent. It would be good to know.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

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 Original Message 
On 2 Aug 2023, 15:42, Thomas, Leonard M. wrote:

> Hello All,
>
> A general questions though phenix.refine is being used for refinement. A 
> student I am working with has a structure that was solved and initially 
> refined using TLS and NCS parameters. They were given the structure to gain 
> some experience in refinement and they have been asking me some questions, I 
> was not involved in the initial work. While everything seems to be happy and 
> the model is correct with good refinement statistics for the most part one 
> thing that I am unsure of is some of the heavier atoms (Phosphate and Sulfer) 
> have very high temperature factors when looking at individual residues or 
> ligands. The temperature factors are at least twice as high as the lighter 
> atoms they are associated with.
>
> I am at a loss to explain what is going on, I really have not used TLS 
> refinement a lot so there is that. Resolution is about 2.5 angstroms with 
> good completeness.
>
> Thoughts?
>
> Thank You in advance
> Len Thomas
>
> Leonard Thomas, Ph.D.
> Biomolecular Structure Core, Director
>
> Oklahoma COBRE in Structural Biology
> Price Family Foundation Institute of Structural Biology
> University of Oklahoma
> Department of Chemistry and Biochemistry
> 101 Stephenson Parkway
> Norman, OK 73019-5251
> Office: (405)325-1126
> lmtho...@ou.edu
> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl
>
> ---
>
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Re: [ccp4bb] anomalous map in Coot - Linux vs. Win difference?

[Jon Cooper]

It looks like it is not applying the 90 degree phase shift for anomalous data.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 2 Aug 2023, 14:32, Andrea Smith wrote:

> Dear Eleanor,
>
> yes, I made the printscreen with the setting that shows both maps contoured 
> at 0.08 = 3 rmsd.
>
> I also attach a printscreen from a site where I believe a Zn ion is bound 
> (from my condition). Can see that Wincoot is drawing the map wrong...
> Andrea
>
> On Wednesday, August 02, 2023 15:28 CEST, Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hmmm -are the two ano maps contoured at the same level?
>> You can check this by setting the SCROLL option to the ano map.
>>
>> The 2mFo-DFc maps look pretty identical..which suggests the two input mtz 
>> files are similar.
>> You can get more information by viewing the inputs to make sure the values 
>> are the same..
>> Eleanor
>>
>> On Wed, 2 Aug 2023 at 13:53, Andrea Smith  wrote:
>>
>>> Dear all,
>>>
>>> I used refmac in CCP4Cloud and then I opened the generated .pdb and .mtz 
>>> from the CCP4Cloud job both in Linux Coot 0.9.6. and WinCoot 0.9.6. I can 
>>> see different anomalous maps in Coot and Wincoot - see attached printscreen 
>>> where on the left there is a green electron density between the aspartates 
>>> while on the right there is none. I tried to search if this is a bug but 
>>> couldn't find info about this.
>>>
>>> Am I doing something wrong? Do I have a local software issue?
>>>
>>> Any advice would be appreciated, best,
>>> Andrea
>>>
>>> ---
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>> ---
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> ---
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Re: [ccp4bb] Dry shipper in limbo

[Jon Cooper]

Hello, I don't do anything MAC but maybe shipping dewars would be a good 
situation for an Apple Airtag, which I read about recently, or equivalent, if 
there are any?

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 28 Jul 2023, 08:56, Savvas Savvides wrote:

> Dear Kevin,
>
> A similar incident from just two weeks ago, in Europe in our case, was 
> resolved by travelling to the regional FedEx package collection/distribution 
> center to recover the dry-shipper in person. This involved gaining access to 
> the FedEx center and talking to the right people.
>
> I would absolutely not wait this out because your shipment is probably 
> somewhere in the corner of a distribution center used as a seat by employees 
> taking a break. I can attest to the fact that they do have such corners where 
> “problematic" shipments are piled up!
>
> Despite what you were told on the phone or could deduce from any online 
> tracking systems (in our case the dry-shipper was not even trackable), there 
> is still a (very good) chance that your shipment might still be at a regional 
> collection/distribution center.
>
> The key is to get to any information about where this place might be, talk to 
> the local people, and find out what the actual route of the shipment might 
> have been after getting picked up from your lab. The routes often involve 
> intermediate collection/distribution sites.
>
> To their credit, and in contrast to the general FedEx customer service, the 
> people at the regional FedEx distribution center (including the shift 
> manager) were very empathic and helpful, and used means that go above and 
> beyond SOPs to help. This included sharing photos of the shipment via 
> WhatsApp with drivers/employees of the three previous shifts etc… Despite the 
> volumes of work they handle, drivers and other courier employees actually do 
> remember unusually looking shipments, such as a shipping-case containing a 
> dry-shipper!
>
> Best of luck and wishes,
> Savvas
>
>> On 28 Jul 2023, at 08:15, Savvas Savvides  wrote:
>>
>> Best wishes,
>> Savvas
>>
>> Begin forwarded message:
>>
>>> From:"Dr. Kevin M Jude" 
>>> Date:28 July 2023 at 05:16:39 CEST
>>> To:CCP4BB@jiscmail.ac.uk
>>> Subject:[ccp4bb] Dry shipper in limbo
>>> Reply-To:"Dr. Kevin M Jude" 
>>
>>> 
>>> My first adventure in international crystallography is off to an 
>>> inauspicious start. On Monday, I sent a dry shipper “overnight” from 
>>> California to Saskatchewan, but it has been stuck in the Memphis FedEx 
>>> facility for a few days. I’ve gotten several conflicting explanations of 
>>> the status from FedEx on the phone, but the most likely seems that it has 
>>> “pre-cleared” customs and yet has not yet made it to Calgary. It’s not 
>>> clear whether anyone actually knows where the shipping case is, since I was 
>>> asked to give a physical description of it. Is there anything else I can do 
>>> from a few thousand miles away, or do I just have to wait this out?
>>>
>>> --
>>>
>>> Kevin Jude, PhD
>>>
>>> Structural Biology Research Specialist, Garcia Lab
>>>
>>> Howard Hughes Medical Institute
>>>
>>> Stanford University School of Medicine
>>>
>>> Beckman B177, 279 Campus Drive, Stanford CA 94305
>>>
>>> Phone:[(650) 723-6431](tel:%28650%29%20723-6431)
>>>
>>> ---
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> ---
>
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Re: [ccp4bb] How to deal with tNCS?

[Jon Cooper]

Hello again, the R- and R-free are pretty high so there might be a problem with 
the space group or you may not have found all the molecules in the asymmetric 
unit. Are there big gaps in the packing with electron density to suggest 
additional molecules? Have you tried the option to input the current solution 
as a starting structure to see if the MR finds any more subunits. Is there any 
flexibility within your structure which could lead to domains having different 
orientations or visibility in your map? Can the model be split further into 
domains? The diffraction pattern does show a fair amount of splitting. MOSFLM 
might even be able to get additional lattices for you. I haven't done this 
stuff for a bit so others will know more about DIALS, etc ;-0 It would be good 
to see the results of twinning tests, if you have any. The one from CTRUNCATE, 
if you have it, is quite good.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 21 Jul 2023, 04:10, Lande wrote:

> Dear Eleanor and Jon,
>
> Thank you for your replies. My good datasets are in P212121 space group and 
> unit cell 56.67 60.53 67.51 90.00 90.00 90.00 ,2 copies in ASU. The tNCS one 
> is in C2221 space group and unit cell 122.32 134.88 55.45 90.00 90.00 90.00. 
> Matthews suggests 4 copies and I tried 4-6 copies to search in phaser (only 4 
> copies in solutions). For fractional coordinate, it is 1/2 and the 
> Rfree/Rwork is 0.4877/0.4466. This is another topic I can hardly found in 
> modern crystallography textbooks..
>
> Here I also attached the self rotaion fuction. I guess there might be 8 peaks 
> but honestly I have no idea how to read those graphs. There is another 
> screenshot of "more tNCS" image.
>
> Many thanks to your help.
>
> regards,
> Lande Fu
>
> ---
>
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Re: [ccp4bb] How to deal with tNCS?

[Jon Cooper]

Hello Lande, the map which you have fitted looks quite good, as does the 
diffraction pattern. At that resolution it will benefit from anisotropic 
refinement, I think. What sort of R-and R-free do you have? You mentioned they 
are high with some of your solutions. What does the solvent content suggest for 
the number of molecules per asymmetric unit and have you found them all? With 
MR, there is usually a bewildering array of peaks with the same height, due to 
the high symmetry of the translation function. The programs will sort that out 
for you, usually. Is that what you mean with 48 solutions? Are you sure of the 
space group? The main MR progs can try all possibilities, I think, so I assume 
you have done this. Also, my first and most memorable encounter with tNCS was 
with a crystal which had an NCS 2-fold parallel with a crystallographic 2(1) 
screw-axis. To my mind tNCS is just rotational NCS with a screw translation? 
Others will probably disagree ;-0

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 18 Jul 2023, 10:06, Lande wrote:

> How to deal with tNCS? Dear all, I have read topics talking about tNCS 
> problem a few years ago and have faced many tNCS data during my work. 
> Generally, I just turned that tNCS button on in phaser during MR, and ignored 
> high R/R-free if the MR solutions were correct. However, I always thought 
> about what made tNCS to occur and what I can do further on tNCS data. 
> Recently, I got sub 1.5A diffraction data of a simple protein (~100 amino 
> acid) soaking with a large ligand and it seems it suffers severe tNCS. It is 
> very clear that two of its unit cell axis are doubled and there is many ghost 
> density around the model. The other 10 datasets with different soaking time 
> and concentration do not have tNCS, No ligand in there after modeling. So all 
> my hope lays on that tNCS one. Here are my questions: 1. I know some proteins 
> tend to form tNCS crystal but what causes tNCS in this crystal only? 2. In MR 
> 48 solution were found and currently I have 4 copies in ASU. There seems to 
> be more to fit the empty density. The map is messy and I cannot determinate 
> the ligand status. What can I do now? Here I linked some screenshots. Any 
> suggestions or articles to read will be helpful. Regards, Lande Fu
>
> ---
>
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Re: [ccp4bb] British X-ray Crystallographers

[Jon Cooper]

The organiser has confirmed it is free.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

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 Original Message 
On 26 May 2023, 22:30, Jon Cooper wrote:

> I've just registered as a non-member and there's no fee, right?
>
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>
> Sent from Proton Mail mobile
>
>  Original Message 
> On 24 May 2023, 09:26, Harry Powell wrote:
>
>> Hi Jon “Preaching to the choir”! Harry > On 23 May 2023, at 23:16, Jon 
>> Cooper wrote: > > I am biased, but this looks like an interesting meeting: > 
>> > https://www.rsc.org/events/detail/76719/british-x-ray-crystallographers > 
>> > Best wishes, Jon Cooper. > jon.b.coo...@protonmail.com > > Sent with 
>> Proton Mail secure email. > > To unsubscribe from the CCP4BB list, click the 
>> following link: > 
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Re: [ccp4bb] Issue with CSO in Coot & Refmac

[Jon Cooper]

Hello, is the CSO going into the PDB file as ATOM'S or HETATM's?

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

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 Original Message 
On 27 May 2023, 00:43, Nicholas Clark wrote:

> I have a cysteine residue that is oxidized and needs to be modeled as CSO. In 
> the past, when "replace residue" was used to substitute for CSO, the CSO 
> would "behave" during real-space refinement and essentially take the place of 
> the Cys. However, when Cys is replaced by CSO now the CSO is behaving as an 
> "external ligand" and does not maintain covalent bonds to the residue before 
> or after (repulsion between CSO & preceding and subsequent residue). The only 
> way I can get it to maintain covalent bonds in Coot is to add CSO as a 
> monomer and place it before merging into the chain and renumbering the 
> residue (afterwards, real space refinement behaves the same as direct 
> replacement of CYS->CSO). Similarly, during refinement with Refmac, only one 
> of the CSO conformations will maintain its position, the alternate 
> conformation breaks the linkage to the preceding residue.
>
> TLDR: CSO replacement of CYS not working in Coot or Refmac, acting as 
> external ligand.
>
> I've tried adding a "Link" definition to the header for both conformations 
> but this does not fix it. Any suggestions on how to resolve this issue?
>
> Best regards,
>
> Nick Clark
>
> --
>
> Nicholas D. Clark (He/Him)
> PhD Candidate
> Malkowski Lab
> University at Buffalo
> Department of Structural Biology
> Jacob's School of Medicine & Biomedical Sciences
> 955 Main Street, RM 5130
> Buffalo, NY 14203
>
> ---
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Re: [ccp4bb] British X-ray Crystallographers

[Jon Cooper]

I've just registered as a non-member and there's no fee, right?

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

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 Original Message 
On 24 May 2023, 09:26, Harry Powell wrote:

> Hi Jon “Preaching to the choir”! Harry > On 23 May 2023, at 23:16, Jon Cooper 
> wrote: > > I am biased, but this looks like an interesting meeting: > > 
> https://www.rsc.org/events/detail/76719/british-x-ray-crystallographers > > 
> Best wishes, Jon Cooper. > jon.b.coo...@protonmail.com > > Sent with Proton 
> Mail secure email. > > To unsubscribe from the CCP4BB list, click the 
> following link: > 
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>  To 
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[ccp4bb] British X-ray Crystallographers

[Jon Cooper]

I am biased, but this looks like an interesting meeting:

https://www.rsc.org/events/detail/76719/british-x-ray-crystallographers

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

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Re: [ccp4bb] isopeptide bond and shelx topology file

[Jon Cooper]

Hello Amit, without PRODRG I don't know of another way to make the SHELX 
dictionary restraints but it can be done by hand with a small-molecule 
structure to measure the bond lengths and 1-3 atom distances from. You can also 
use general values for the ideal bond lengths and angles and the cosine rule 
will give you the 1-3 distances, if things get really desperate. It would be 
worth looking at pdb2ins. I remember Ian Tickle wrote a program to make 
distance restraints for Restrain from a ligand pub file and I have a copy 
somewhere. The restrain dictionary was similar to the shelx one.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

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 Original Message 
On 28 Apr 2023, 08:41, StrBio wrote:

> Hello,
>
> Can you suggest how to make isopeptide bond in coot and generate .cif file to 
> refine the structure in phenix?
>
> Also need suggestions to create shelxl topology file for non standard amino 
> acids.
> I used PRODGR before but seems like the sever is down last couple of months. 
> Any alternatives?
>
> Thank you
> Amit
>
> ---
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Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

[Jon Cooper]

Hello, can you give us a screenshot of a diffraction image, with the caveat 
that they never look all that good with fine-slicing, still it might help ;-0 
Also, an idea of the R-merge, R-meas, CC-half in some of those space groups.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

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 Original Message 
On 21 Mar 2023, 16:43, Gianluca Cioci wrote:

> Dear All,
>
> I have collected a dataset from a small protein diffracting at 2.7A 
> resolution, here is the space-group determination from XDS:
>
> * 44 aP 0.0 66.3 66.3 83.9 90.2 90.1 98.7
> * 31 aP 1.2 66.3 66.3 83.9 89.8 90.1 81.3
> * 14 mC 1.3 86.4 100.6 83.9 90.0 90.2 90.0
> * 34 mP 2.9 66.3 83.9 66.3 90.2 98.7 90.1
> * 13 oC 3.7 86.4 100.6 83.9 90.0 90.2 90.0
> * 10 mC 4.9 100.6 86.4 83.9 89.8 90.0 90.0
>
> Clearly, something weird is going on...
>
> The structure can be solved in C2/P21/C2221 with different number of 
> molecules in the AU, with Phaser complaining about strong tNCS modulation.
>
> However the maps look bad and the structure is impossible to refine (Rfact > 
> 0.5) in all the space-groups that I have tried so far...
>
> Thanks in advance for any advice on how to rescue these data !
>
> Cheers,
>
> GIA
>
> [Click to zoom the image]
>
> --
> Dr. Gianluca CIOCI
> Toulouse Biotechnology Institute (TBI)
> http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
> PICT - Plateforme Intégrée de Criblage de Toulouse
> http://www.pict.ipbs.fr/
> Tel: +33 (0)5 61 55 97 68
> E-mail:
> ci...@insa-toulouse.fr
> TBI - INSA Toulouse
> 135 avenue de Rangueil
> 31077 Toulouse CEDEX 04
> http://www.toulouse-biotechnology-institute.fr
>
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Re: [ccp4bb] anomalous data usage

[Jon Cooper]

Hello Ian,

if I understand you and Eleanor correctly, this is the philosophy of the 
mini-MTZ, i.e. if you are doing anything independent of i2, you have to dig 
around a bit to find which output file contains the columns you need.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

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 Original Message 
On 13 Mar 2023, 23:27, Ian Tickle wrote:

> Eleanor, which program is doing that and more to the point, why?
>
> -- Ian
>
> On Mon, 13 Mar 2023 at 20:17, Eleanor Dodson  
> wrote:
>
>> fIf you are using ccp4I2 for some forgotten reason the final output has one 
>> reflection with I+ and I-, another with Imean, another with Fmean - aagghh
>>
>> On Mon, 13 Mar 2023 at 19:40, Ian Tickle  wrote:
>>
>>> Hi Gottfried
>>>
>>> AIMLESS definitely outputs IMEAN (and SIGIMEAN) by default.
>>>
>>> Cheers
>>>
>>> -- Ian
>>>
>>> On Mon, 13 Mar 2023 at 18:53, Palm, Gottfried  
>>> wrote:
>>>
>>>> Dear all,
>>>>
>>>> I have a few questions handling (non) anomalous data:
>>>> By default aimless seems to produce Iplus and Iminus columns. Can I force 
>>>> it to (also) create an Imean column?
>>>> What does refmac do, when it gets Iplus and Iminus (and their sigmas) as 
>>>> input. Does it take only one of them or does it calculate and use Imean?
>>>> Greetings
>>>>
>>>> Gottfried
>>>>
>>>> ---
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Re: [ccp4bb] Mini map aide updates

[Jon Cooper]

I am cautiously optimistic that there have been some improvements to my Mini 
Map Aide (a basic map viewer mainly for mobile devices): http://minimapai.de

- The browser does not accidentally 'go back' on scrolling upwards in the 
graphics window.
- Atom selection is now more accurate i.e. it almost works reliably, unlike 
before.
-

Better memory management - it can go through several hundred residues without 
crashing!

-

New virtual server!

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

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--- Original Message ---
On Wednesday, November 9th, 2022 at 00:30, Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> For info, or more likely amusement, the Mini Map Aide website which I put 
> together a few months ago for looking at electron density maps, primarily on 
> mobile devices:
>
> http://minimapai.de
>
> now allows tweaks to be made to individual amino acids and basic 
> regularisation to be done, so there definitely is no excuse to shrink from 
> building, or at least tweaking, models. It is still a bit harebrained and I'm 
> not sure how the results of my geometry minimiser would stand up in any 
> validation tests but, used cautiously, it seems to give better rmsd's than 
> the 1974 lysozyme models ;-0
>
> Best wishes, Jon Cooper.
> jon.b.coo...@protonmail.com
>
> Sent with [Proton Mail](https://proton.me/) secure email.
>
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Re: [ccp4bb] To Trim or Not to To Trim

[Jon Cooper]

Hello, yes, the trimming and occupancy tricks can be confusing and they can be 
a bit of a cheeky way to improve the model statistics. I prefer to build the 
whole side chain and if you can't see all or part of it, then that's just too 
bad, but I have erred.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

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 Original Message 
On 10 Mar 2023, 01:25, Rhys Grinter wrote:

> Hi All,
>
> I'm trying to crowdsource an opinion on how people deal with modelling side 
> chains with poorly resolved electron or cryoEM density.
>
> My preference is to model the sidechain and allow the B-factors to go high in 
> refinement to represent that the side chain is flexible. However, I'm aware 
> that some people truncate sidechains if density is not present to justify 
> modelling. I've also seen models where the sidechain is modelled but with 
> zero occupancy if density isn't present.
>
> Is there a consensus and justifying arguments for why one approach is better?
>
> Cheers,
>
> Rhys
>
> ---
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Re: [ccp4bb] Structural alignment and classification

[Jon Cooper]

Coot's ssm superposition does give the C-alpha rmsd, though, most easily seen 
if you run it from a terminal window? I guess it can't be miles different from 
a least-squares fit ;-?

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

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 Original Message 
On 9 Mar 2023, 13:55, Paul Emsley wrote:

> On 06/03/2023 07:35, Armando Albert wrote: > I want to align several 
> structures we obtained from a fragment screening campaign and cluster them 
> according to RMSD. > To what end, may I ask? I would use LSQKAB, parse the 
> log files for the RMSD and create an input file for R. (One cannot just do 
> this in Coot, because, for LSQ fitting, Coot only returns the transformation 
> matrix, not any fitting statistics - in retrospect this is obviously an 
> oversight.) Paul. 
>  To 
> unsubscribe from the CCP4BB list, click the following link: 
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Re: [ccp4bb] C6 Webtool

[Jon Cooper]

Cheeky question: if its 'just' an asp script, a virtual private server is about 
£10 per year. Does it need a huge database or something?

Cheers all, Jon Cooper

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 Original Message 
On 17 Jan 2023, 20:34, Janet Newman wrote:

> CSIRO has taken this resource offline. Hopefully it will return, but hopes 
> are often dashed.
>
> janet
>
> ---
>
> From: CCP4 bulletin board  on behalf of Leonhard Kick 
> 
> Sent: Thursday, January 12, 2023 7:56 PM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: [ccp4bb] C6 Webtool
>
> You don't often get email from leonhard.k...@wuxiapptec.com. [Learn why this 
> is important](https://aka.ms/LearnAboutSenderIdentification)
>
> Hi all and a belated Happy New Year,
>
> I was wondering if any of you noticed that the C6 Webtool from Janet Newman 
> (https://c6.csiro.au/C6.asp) is discontinued and offline.
>
> We used it quite extensively to get a short and meaningful comparison of 
> commercial screens (differences and similarities, mostly).
>
> Do you know if the service was conserved somewhere? Or do you have 
> alternatives that you preferred anyway? Would be great if you could share 
> your experiences.
>
> Thank you all
>
> Cheers
>
> Leo
>
> 
>
> Leonhard Kick
>
> Deputy Head Crystallography
>
> Crelux GmbH – A WuXi AppTec Company
>
> Am Klopferspitz 19a
>
> 82152 Martinsried
>
> Germany
>
> ---
>
> Save paper. Protect the environment. Print only when necessary.
>
> This email message is intended only for use by the intended recipient and may 
> contain confidential and privileged information. Any unauthorized review, 
> use, disclosure or distribution is prohibited. If you are not the intended 
> recipient, then please contact the sender by reply email and destroy all 
> copies of the original message.
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Re: [ccp4bb] Careless and negative Wilson B-factor

[Jon Cooper]

Hello, are the data from serial crystallography? The redundancy and the CC's 
are very good but the R-merge (an unpopular metric these days) is quite high?

Cheers, Jon Cooper2

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 Original Message 
On 6 Jan 2023, 08:17, 조규혁 wrote:

> Dear all,
>
> I recently tested a novel merging tool for crystallography data called 
> Careless (https://github.com/rs-station/careless).
>
> When I used it on our 2.6 A-resolution structure in the I23 space group with 
> a lipid bound structure, I noticed that the electron density surrounding the 
> acyl chain was significantly improved.
>
> However, I am concerned about the Wilson B-factor. The Phenix.table_one tool 
> reports that the Wilson B-factor of the merged mtz file is -0.91. 
> Phenix.Xtriage warns that a negative Wilson B-factor can be an indication of 
> unusual pathology or artificial manipulation.
>
> Has anyone else encountered similar conditions? Are there any circumstances 
> in which a negative Wilson B-factor can be rationalized?
>
> Thank you,
> Gyuhyeok
>
> P.S. Here is the part of the output of Phenix.table_one.
>
> Wavelength1.
> Resolution range  37.98 - 2.60
> (2.69 - 2.60)
> Space group   I 2 3
> Unit cell 161.128 161.128 161.128
> 90 90 90
> Total reflections 886846 (79364)
> Unique reflections21520 (2135)
> Multiplicity  41.2 (37.2)
> Completeness (%)  99.95 (100.00)
> Mean I/sigma(I)
>
> 14.2 (0.8)
>
> Wilson B-factor   -0.91
> R-merge   0.240 (4.566)
> R-meas0.243 (4.629)
> R-pim 0.038 (0.757)
> CC1/2 0.998 (0.362)
> CC*   0.999 (0.729)
>
>>> PhD student
>>>
>>> Department of Chemistry
>>>
>>> Gwangju Institute of Science and Technology (GIST)
>>>
>>> 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005
>>>
>>> Republic of Korea
>>>
>>> Tel. +82 62-715-4633
>>>
>>> e-mail: gyuhyeok...@gist.ac.kr
>
> ---
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Re: [ccp4bb] Fwd: Re: [ccp4bb] Calculate charge on protein surface

[Jon Cooper]

Dear Boaz

I think your original answer must have been steganographic ;-0 Maybe white text 
on a white background ;-? Anyway, I can see it below now that I have started 
typing this reply, and advice is excellent.

My answer to Rafael's question would be to look at apbs:

https://www.poissonboltzmann.org/

This gives you a map of the potential. It's a while since I dabbled with it, 
but I remember using it and it was all pretty workable as a standalone program, 
even for an electrostatics non-specialist. You might need to do some scripting 
to sum up charges, etc, though.

Good luck. Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 28 Dec 2022, 15:57, Boaz Shaanan wrote:

> Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben Gurion University
> Beer Sheva, Israel
> -- Forwarded message --
> From: בעז שאנן 
> Date: Dec 28, 2022 17:13
> Subject: Re: [ccp4bb] Calculate charge on protein surface
> To: Rafael Marques 
> Cc:
>
>> Hi
>> In ucsf-chimera you can "walk" with the cursor on the surface and it'll show 
>> the actual porential value at each point in the command line. You have to 
>> enable this option in the surface drawing panel. I've used this option quite 
>> often. There may be a similar option in chimerax by now.
>> My 2p.
>> Cheers,
>> Boaz
>>
>> Boaz Shaanan, Ph.D.
>> Dept. of Life Sciences
>> Ben Gurion University
>> Beer Sheva, Israel
>>
>> On Dec 28, 2022 17:03, Rafael Marques  wrote:
>>
>> Hello guys. I hope you are having a great break and still eating the 
>> leftovers of your Xmas turkey.
>>
>> I wonder if there is any software that could provide me numbers regarding 
>> the formal charge of different sides of my structure. Although I can clearly 
>> see that one face of it is pretty red, I would like to know “how much” red 
>> it is.
>>
>> Best wishes
>>
>> Rafael Marques da Silva
>>
>> PhD Student – Structural Biology
>>
>> University of Leicester
>>
>> Mestre em Física Biomolecular
>>
>> Universidade de São Paulo
>>
>> Bacharel em Ciências Biológicas
>>
>> Universidade Federal de São Carlos
>>
>> phone: +55 16 99766-0021
>>
>> "A sorte acompanha uma mente bem treinada"
>>
>> 
>>
>> ---
>>
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Re: [ccp4bb] Copying NCS chain to heteroligomer

[Jon Cooper]

Hello, this sounds like a good case for electron density averaging which would 
allow you to build one chain into the averaged density and then generate the 
full set of 12 by NCS for refinement. Even better would be using the NCS in 
refinement of the one chain you have built. Anyway, I would have to look at the 
GUIs to see how practical this is nowadays, sorry. Cheers, Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 17 Nov 2022, 19:03, Alessandro S. Nascimento wrote:

> Dear all,
>
> We are refining a 24-mer complex composed of 12 copies of protein A and 12 
> copies of protein B. Since the resolution is not very high (~3.0 Ang), we 
> will probably want to copy the modifications made in Coot for one chain to 
> the other chains of the same protein (but not for the other protein).
>
> Unfortunately, we did not find a way to do that in Coot. Is there any option 
> for this?
>
> Thanks a lot in advance,
>
> Alessandro
>
> --
>
> *
> * Alessandro S. Nascimento *
>
> * Associate Professor - Sao Carlos Institute of Physics *
> * University of São Paulo (IFSC/USP) *
> * E-mail: asnascime...@ifsc.usp.br *
> *
>
> ---
>
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Re: [ccp4bb] hydrogens?

[Jon Cooper]

I used to use the riding hydrogens from shelx when I was doing a neutron 
refinement a few years ago, now. It might be worth looking at some recent 
neutron papers to see how the H/D atoms are handled. I think it is mainly done 
with phenix these days ;-0

If you have electrostatic calculations or other arguments re placing the 
exchangeable hydrogens, I would just exercise your best judgement. Ultimately 
your model would have to be acceptable to referees. I am not aware of a server 
which places hydrogens based on electrostatics, but probably there is?

Good luck with it. Jon.C.

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 Original Message 
On 11 Nov 2022, 19:46, Murpholino Peligro wrote:

> Hi
>
> What is the best way to add hydrogens to a pdb file for a, probably, last 
> round of refinement?
>
> Can hydrogens be added in a pH/pka-dependent manner? Something like this 
> (https://server.poissonboltzmann.org/) but get a pdb file ready for 
> phenix.refine/buster/refmac?
>
> Thanks
>
> ---
>
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[ccp4bb] Mini map aide updates

[Jon Cooper]

For info, or more likely amusement, the Mini Map Aide website which I put 
together a few months ago for looking at electron density maps, primarily on 
mobile devices:

http://minimapai.de

now allows tweaks to be made to individual amino acids and basic regularisation 
to be done, so there definitely is no excuse to shrink from building, or at 
least tweaking, models. It is still a bit harebrained and I'm not sure how the 
results of my geometry minimiser would stand up in any validation tests but, 
used cautiously, it seems to give better rmsd's than the 1974 lysozyme models 
;-0

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

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Re: [ccp4bb] Jenkins?

[Jon Cooper]

It'll just be Hugh hacking your system again ;-0

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 Original Message 
On 25 Sep 2022, 15:37, David J. Schuller wrote:

> CCP4 8.0.004
> Scientific Linux 7, kernel 3.10.0-1160.76.1.el7.x86_64
> mate-desktop-1.16.2-1.el7.x86_64
>
> This morning I updated my Nvidia graphics driver, then rebooted. When I 
> logged in again, my desktop (Mate) was all messed up, no applications menus, 
> etc. I perused the log files and found many lines similar to these in 
> /var/log/messages:
>
> Sep 25 09:45:32 titan mate-session[1718]: WARNING: Could not connect to 
> Systemd: Failed to connect to socket 
> /home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket:
>  No such file or directorySep 25 09:45:34 titan journal: Error connecting to 
> system bus: Failed to connect to socket 
> /home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket:
>  No such file or directory
> Sep 25 10:12:35 titan pulseaudio[22894]: [alsa-sink-ALC887-VD Analog] 
> core-util.c: Failed to connect to system bus: Failed to connect to socket 
> /home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket:
>  No such file or directory
> Sep 25 10:12:40 titan pulseaudio[23162]: [pulseaudio] core-util.c: Failed to 
> connect to system bus: Failed to connect to socket 
> /home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket:
>  No such file or directory
> Sep 25 10:12:40 titan pulseaudio[23162]: [pulseaudio] core-util.c: Failed to 
> connect to system bus: Failed to connect to socket 
> /home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket:
>  No such file or directory
>
> I do not have, and have never had, a user "jenkins" on my system. Note that 
> the CCP4 workspace is implicated.
>
> I took the CCP4 startup stuff out of my .cshrc login script and restarted, 
> and everything appeared to be normal.
> # source /usr/local/xtal/ccp4/bin/ccp4.setup-csh >& /dev/null
>
> Why is jenkins mucking about with my desktop settings, and how do I keep him 
> from doing so?
>
> ===
> All Things Serve the Beam
> ===
> David J. Schuller
> modern man in a post-modern world
> MacCHESS, Cornell University
> schul...@cornell.edu
>
> ---
>
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Re: [ccp4bb] Lower b-factors with increasing T

[Jon Cooper]

Cool, typed a long reply but only about 1/3 of it is still relevant and is 
given below.

The crystal would have to be capillary mounted for these data collections or 
the humidity controlled somehow. Only 253 K would be a good one to use. 
Pre-cryo, this used to give good data at SRS! Interested in the oil method you 
mentioned. Anyway, for capillary work:

253 K = -20 C = good temp to use
273 K = 0 C = maybe OK
293 K = 20 C = OK
313 K = 30 C = maybe OK

> Re: In addition, I computed the wilson B.s
253 - 41
273 - 35.4
293 - 36.5
313 - 0.19

Assuming the last one is a typo, unless it's a neutron dataset - no B-factor ;-)

Cheers, Jon.C.

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 Original Message 
On 8 Sep 2022, 14:39, Matt McLeod wrote:

> Hi all, This is my first JISC post so I am still working on how to navigate 
> this. I have to say I feel like there is a much better way to have a forum on 
> structural biology... I could imagine a discord server where we can post 
> individual questions, have live chats, etc. I'd be happy to set this up if 
> people are interested. The data collection was done on a single crystal, 
> using vector scanning to minimize radiation damage, and using oil to prevent 
> dehydration. I have since gone back and re-processed the 313K dataset with an 
> updated DIALS and the problem seems to have gone away (and gave me better 
> scaling statistics)...my guess is that the scaling program is just improving 
> some of these "bugs". This high temp dataset now has the highest average 
> B-factor. Regardless, there does seem to be not much variation with the 
> temperature at the modest temperatures which may be in line with the 
> biological story but these values make much more sense now. Thanks everyone 
> for all the suggestions with regards to scaling the data together, SCALEIT, 
> etc. I have a few different options to interpret the data now. Matt 
>  To 
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[ccp4bb]

[Jon Cooper]

Hello, K will always have a higher B-factor for a given piece of density due to 
it having a larger atomic number. Is the K B-factor much higher than those of 
neighbouring atoms and, if not, it's probably the best interpretation? Cheers, 
Jon.C.

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 Original Message 
On 8 Sep 2022, 14:07, smita yadav wrote:

> Dear Community,
> Can you tell me. if we fit some metal in X-ray structure and its geometry and 
> other properties are satisfied but showing some higher B-factor. does it 
> validate to put that metal-ligand.ligand. At one site 2 metals such as K and 
> NA fit, but K shows a higher B-factor, but other parameters such as geometry 
> and other fit better for K instead of NA. So, out of the two ligands at the 
> same site which one would be more favorable to be fit. --
>
> On Thu, Sep 8, 2022 at 6:35 PM smita yadav  wrote:
>
>> Dear Community,
>> Can you tell me. if we fit some metal in X-ray structure and its geometry 
>> and other properties are satisfied but showing some higher B-factor. does it 
>> validate to put that metal-ligand.ligand. At one site 2 metal such as K and 
>> NA fits, but K shows higher
>> --
>>
>> Regards,
>> Smita Yadav
>> Ph.D SRF
>> Regional Centre for biotechnology,
>> Haryana-121001.
>
> --
>
> Regards,
> Smita Yadav
> Ph.D SRF
> Regional Centre for biotechnology,
> Haryana-121001.
>
> ---
>
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Re: [ccp4bb] Polymer ligand (Jefffamin) modeling in low resolution maps

[Jon Cooper]

Hello Jan

Not a very helpful suggestion, but using rcsb's ligand-expo site I did find 
some structures of similar resolution in the PDB with jeffamine present. I 
don't know if looking at them would be helpful and you have probably done that 
already.

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 Original Message 
On 18 Aug 2022, 10:37, Jan Stransky wrote:

> Dear all, we have a structure at not the greatest resolution (~2.6A) of which 
> crystal was grown in crystallization condition with Jeffamin. In the maps, we 
> see typical PEG-like sausages. Jeffamin is basically a PEG decorated with 
> some methyl groups and it is terminated with amine groups. Now, the question 
> is how to interpret such blobs? To my understanding the methyl decoration is 
> not regular, and it is not obviously visible in the maps. Nor is clear, if 
> there is a contact to the amine group. When we tried to put in PEG models as 
> placeholders, it explains the density fine, but the contacts are nothing 
> great, e.g. position of the oxygens in the polymer is not clear. Calculating 
> Polder maps does not clear things up. How would you deal with interpretation 
> such maps? Thank you for your ideas :-) Jan 
>  To 
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Re: [ccp4bb] Checking X-ray sequence (no more protein).

[Jon Cooper]

Thank you very much for all the helpful replies. I have summarised the 
discussion here:

https://justpaste.it/9cfl9

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent with [Proton Mail](https://proton.me/) secure email.



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Re: [ccp4bb] Checking X-ray sequence (no more protein).

[Jon Cooper]

Thank you, yes, threading style tools to assess the likelihood of having a 
given amino acid in a certain position in the fold would be a good approach. I 
have tried one but wasn't hugely informative, in my hands anyway. All 
suggestions very welcome but big database science is a bit outside my skill 
set. Of course, sequence conservation in the family helps a lot with the 
assignment but there are bigger ambiguities in less conserved surface regions 
e.g. a disordered Lys can refine well as a Ser, Ala or Gly even, but e.g. 
nearby conserved acidic groups might suggest the presence of the basic amino 
acid which could salt-bridge with them, but why then would it be so disordered? 
Tangles we weave...

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 Original Message 
On 29 Jul 2022, 14:17, Clemens Vonrhein wrote:

> Maybe a crazy idea, but couldn't one use various model/geometry validation 
> tools to figure out some of those ambiguities? As a test one could take a 
> very good 1.7A structure and do some random ASN->ASP, THR->VAL etc mutations 
> followed by refinement (including hydrogens). Wouldn't some validation tool 
> pick up unfavourable conformations, poor rotamers and/or hydrogen clashes and 
> poor H-networks (compared to the initial, correct sequence)? Maybe there is 
> some kind of "fingerprint" in validation results for such incorrect residue 
> assignments that can distinguish correct from incorrect sequences ... Or put 
> another way, if model validation can not pick up such sequence errors: should 
> we be worried about the reliability of our validation criteria? A large scale 
> re-refinement of deposited structures with (1) the current/correct sequence 
> and (2) those ASN/ASP, THR/VAL etc ambiguities artificially introduced, could 
> provide a clever algorithm (AI?) with the data basis to figure out those 
> "fingerprints". Maybe even for the ASN/GLN/HIS side-chain orientations when 
> the sequence is actually correct. Cheers Clemens On Fri, Jul 29, 2022 at 
> 12:08:58PM +, Jon Cooper wrote: > Thank you so much for your replies. I 
> apologise for being unclear. The protein is purified from a plant that hasn't 
> had its genome sequence determined. We know the enzyme family of the protein 
> and therefore the structure was originally solved by MR. The 'X-ray sequence' 
> we have is just determined from looking at the 1.7 Angstrom density, which is 
> good, over several refinement and rebuilding rounds. The resulting sequence 
> has been run through blast and it is up to 58% identical with other family 
> members. To me this seemed low but that degree of identity is typical of 
> other family members. The postgrad who did the work did obtain some peptide 
> sequences and prior to that about 20% of the sequence was determined by the 
> Edman method with the usual Asp/Asn and Glu/Gln ambiguity. However, there 
> isn't any prospect of us doing further experimental work, sorry, but that's 
> the way it is!! > > Best wishes, Jon.C. > > Sent from ProtonMail mobile > > 
>  Original Message  > On 29 Jul 2022, 12:23, Jan Dohnalek 
> wrote: > > > If you know at least something about your protein, organism, 
> type of molecule, ..., you could try mass spectrometry peptide mapping to 
> known sequences, this may give you some answers for the ambiguities you might 
> be seeing, if nothing else .. > > > > Jan > > > > On Fri, Jul 29, 2022 at 
> 12:15 PM Jon Cooper wrote: > > > >> Hello, I am looking for suggestions of 
> ways to check a 1.7 Angstrom X-ray sequence for a protein where it is 
> impractical to do experimental sequencing, protein or DNA. The structure 
> refines to publishable R/R-free and the main ambiguities seem to be Thr/Val, 
> Asp/Asn and Glu/Gln where alternative H-bonding networks are possible. 
> Running alpha-fold seems an interesting option? Any suggestions much 
> appreciated. > >> > >> Cheers, Jon.C. > >> > >> Sent from ProtonMail mobile > 
> >> > >> --- > >> 
> > >> To unsubscribe from the CCP4BB list, click the following link: > >> 
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > -- > 
> > > > Jan Dohnalek, Ph.D > > Institute of Biotechnology > > > > Academy of 
> Sciences of the Czech Republic > > Biocev > > Prumyslova 595 > > 252 50 
> Vestec near Prague > > Czech Republic > > Tel. +420 325 873 758 > > 
>  > > 
> To unsubscribe from the CCP4BB list, cli

Re: [ccp4bb] Checking X-ray sequence (no more protein).

[Jon Cooper]

Thank you so much for your replies. I apologise for being unclear. The protein 
is purified from a plant that hasn't had its genome sequence determined. We 
know the enzyme family of the protein and therefore the structure was 
originally solved by MR. The 'X-ray sequence' we have is just determined from 
looking at the 1.7 Angstrom density, which is good, over several refinement and 
rebuilding rounds. The resulting sequence has been run through blast and it is 
up to 58% identical with other family members. To me this seemed low but that 
degree of identity is typical of other family members. The postgrad who did the 
work did obtain some peptide sequences and prior to that about 20% of the 
sequence was determined by the Edman method with the usual Asp/Asn and Glu/Gln 
ambiguity. However, there isn't any prospect of us doing further experimental 
work, sorry, but that's the way it is!!

Best wishes, Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 29 Jul 2022, 12:23, Jan Dohnalek wrote:

> If you know at least something about your protein, organism, type of 
> molecule, ..., you could try mass spectrometry peptide mapping to known 
> sequences, this may give you some answers for the ambiguities you might be 
> seeing, if nothing else ..
>
> Jan
>
> On Fri, Jul 29, 2022 at 12:15 PM Jon Cooper 
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hello, I am looking for suggestions of ways to check a 1.7 Angstrom X-ray 
>> sequence for a protein where it is impractical to do experimental 
>> sequencing, protein or DNA. The structure refines to publishable R/R-free 
>> and the main ambiguities seem to be Thr/Val, Asp/Asn and Glu/Gln where 
>> alternative H-bonding networks are possible. Running alpha-fold seems an 
>> interesting option? Any suggestions much appreciated.
>>
>> Cheers, Jon.C.
>>
>> Sent from ProtonMail mobile
>>
>> ---
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> --
>
> Jan Dohnalek, Ph.D
> Institute of Biotechnology
>
> Academy of Sciences of the Czech Republic
> Biocev
> Prumyslova 595
> 252 50 Vestec near Prague
> Czech Republic
> Tel. +420 325 873 758



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[ccp4bb] Checking X-ray sequence (no more protein).

[Jon Cooper]

Hello, I am looking for suggestions of ways to check a 1.7 Angstrom X-ray 
sequence for a protein where it is impractical to do experimental sequencing, 
protein or DNA. The structure refines to publishable R/R-free and the main 
ambiguities seem to be Thr/Val, Asp/Asn and Glu/Gln where alternative H-bonding 
networks are possible. Running alpha-fold seems an interesting option? Any 
suggestions much appreciated.

Cheers, Jon.C.

Sent from ProtonMail mobile



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Re: [ccp4bb] Comparing two datasets

[Jon Cooper]

Hello again, as far as I can tell, the question is about two already 
merged/unique datasets which Mirek wishes to merge into one. As far as I can 
tell/remember, Scaleit is for scaling datasets side-by-side to get isomorphous 
differences, etc, and I don't know of a way that you could get it to merge 2 
datasets as Mirek requested. Probably I am wrong but Scaleit R-factors are 
different from R-merge, although the latter might be a bit dubious in the 
circumstances. Anyway, I think the Combat route is a viable way of achieving 
what the questioner wants to achieve ;-0

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 Original Message 
On 26 Jul 2022, 12:25, John R Helliwell wrote:

> Dear Colleagues,
> Scaleit is a terrific program.
> Amongst its strengths already listed I would also mention its breakdown table 
> with F so that in the strongest F reflections bin any systematic errors 
> between the two data sets can show up if the Rfactor is greater than about 1%.
> Greetings,
> John
>
> Emeritus Professor John R Helliwell DSc
>
>> On 26 Jul 2022, at 11:40, Eleanor Dodson 
>> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> 
>> Not only does SCALEIT do the job - it presented useful plots and an 
>> informative log file..
>> Eleanor
>> (You need to run CAD hklin1 Xtal1.mtz hklin2 Xtal2.mtz ...and obviously the 
>> columns from each Xtal will need different labels..)
>>
>> On Tue, 26 Jul 2022 at 09:45, Phil Evans  wrote:
>>
>>> If you give Pointless Fs, it squares them to Is (not correct if the Fs have 
>>> been derived from the truncate procedure, but not too bad). It will then 
>>> give you a comparison. If you give the two datasets to Pointless, labelling 
>>> them as different datasets, you can use Aimless to compare them
>>>
>>> But as Andrew said, the appropriate CCP4 program is Scaleit: it’s old but 
>>> still works and gives lots of statistics
>>>
>>> Phil
>>>
>>> Sent from my iPhone
>>>
 On 26 Jul 2022, at 09:37, Andrew Leslie - MRC LMB 
  wrote:
>>>
 I think that POINTLESS works with intensities rather than structure 
 factors (I’m not sure if this can be changed). Also, SCALEIT gives a much 
 more detailed breakdown (R factors as a function of resolution and 
 differences in terms of sigmas etc) than POINTLESS WILL.

 Cheers,

 Andrew

> On 26 Jul 2022, at 09:24, LEGRAND Pierre 
>  wrote:
>
> Hello Mirek,
>
> A very quick approach for that is offered by pointless:
>
> pointless HKLREF 1_1_aimless.mtz HKLIN 2_1_aimless.mtz
> or
> pointless HKLREF 1_1_aimless.mtz XDSIN XDS_ASCII.HK
>
> You will obtain a table looking like that, taking into account to 
> possible reindexing:
>
> Alternative indexing scores relative to reference
> Alternative reindexing Lklhd CC R(E^2) Number Cell_deviation
> 1 [h,k,l] 0.993 0.962 0.118 19150 0.08
> 2 [-k,h,l] 0.007 0.078 0.512 19150 0.87
>
> Best wishes,
>
> Pierre Legrand
> PROXIMA-1 Beamline
> Synchrotron SOLEIL
>
> ---
>
> De: "Nicolas Foos" 
> À: CCP4BB@JISCMAIL.AC.UK
> Envoyé: Mardi 26 Juillet 2022 08:36:35
> Objet: Re: [ccp4bb] Comparing two datasets
>
> Hi Mirek,
>
> I am pretty sure XSCALE will do that for you : 
> https://xds.mr.mpg.de/html_doc/xscale_program.html
>
> If not, maybe have a look on SHELXC in SIR mode.
>
> Hope this help.
>
> Nicolas
>
> On 25/07/2022 21:52, Cygler, Miroslaw wrote:
>
>> Hi,
>> I would like to calculate the R-merge for Fs from two datasets processed 
>> from two different crystals. Tried to use Blend but got the message that 
>> Blend requires R. Downloaded R but do not know how to tell CCP4 where it 
>> is located on my Mac. Is there another program that would take two mtg 
>> files and merge the Fs?
>> Any help would be greatly appreciated.
>>
>> Mirek
>>
>> ---
>>
>> To unsubscribe from the CCP4BB list, click the following link:
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>
> --
> Nicolas Foos PhD - ARISE fellow
> https://orcid.org/-0003-2331-8399
> EMBL Grenoble, McCarthy Team
> 71 av. des Martyrs,
> 38000 Grenoble FRANCE
>
> +33 4 57 42 84 67
>
> ---
>
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 ---

>

Re: [ccp4bb] Comparing two datasets

[Jon Cooper]

Hello, I looked thru the program list in ccp4i and Combat caught my eye. Seems 
you can input an MTZ file of amplitudes and output a multirecord MTZ, and you 
can specify a batch number. If you did the same for your second dataset with a 
different batch number you could then append them with Sortmtz and run Scala, 
Pointless, Aimless, etc, to get the usual stats.

If you scaled the F and sigF columns as Andrew suggested, Sftools has a MERGE 
or MERGE AVERAGE option which *might* work!!

Cheers, Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 25 Jul 2022, 20:52, Cygler, Miroslaw wrote:

> Hi,
> I would like to calculate the R-merge for Fs from two datasets processed from 
> two different crystals. Tried to use Blend but got the message that Blend 
> requires R. Downloaded R but do not know how to tell CCP4 where it is located 
> on my Mac. Is there another program that would take two mtg files and merge 
> the Fs?
> Any help would be greatly appreciated.
>
> Mirek
>
> ---
>
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Re: [ccp4bb] Unidentified electron density

[Jon Cooper]

Agreed, it doesn't look like a zinc site, or indeed any metal site, with all 
those basic residues around it, but just being a bad loser ;-0 Cheers, Jon.C.

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 Original Message 
On 2 Jul 2022, 08:14, Eleanor Dodson wrote:

> Did you check anomalous difference peaks? They would show zn very clearly.
>
> On Sat, 2 Jul 2022 at 08:08, Sayan Saha  wrote:
>
>> Dear all,
>> As suggested by most people, we modeled Zn2+ ions coordinated with three 
>> water molecules.
>> Thanks for everyone’s response.
>>
>> With best regards,
>> Sayan Saha
>>
>> On Fri, Jul 1, 2022 at 8:04 PM Jon Cooper  
>> wrote:
>>
>>> Hello, I wonder if it is disorder i.e. alternative conformations of the Asp 
>>> and flexible Lys.
>>>
>>> Do let us know your final interpretation as we don't often, or indeed ever, 
>>> hear the final outcome of these mystery density competitions and I would 
>>> love to learn more from them.
>>>
>>> Cheers, Jon.C.
>>>
>>> Sent from ProtonMail mobile
>>>
>>>  Original Message 
>>> On 30 Jun 2022, 08:03, Sayan Saha < ssaha43...@gmail.com> wrote:
>>>
>>>> Dear All,
>>>>
>>>> I am trying to refine a protein structure. I observed an additional 
>>>> electron density (Figures attached) connected to the aspartate residue.
>>>>
>>>> Any suggestion in this regard would be appreciated.
>>>>
>>>> With best regards,
>>>> Sayan Saha.
>>>>
>>>> ---
>>>>
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Re: [ccp4bb] Unidentified electron density

[Jon Cooper]

Hello, I wonder if it is disorder i.e. alternative conformations of the Asp and 
flexible Lys.

Do let us know your final interpretation as we don't often, or indeed ever, 
hear the final outcome of these mystery density competitions and I would love 
to learn more from them.

Cheers, Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 30 Jun 2022, 08:03, Sayan Saha wrote:

> Dear All,
>
> I am trying to refine a protein structure. I observed an additional electron 
> density (Figures attached) connected to the aspartate residue.
>
> Any suggestion in this regard would be appreciated.
>
> With best regards,
> Sayan Saha.
>
> ---
>
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Re: [ccp4bb] Patterson map

[Jon Cooper]

Hello, in P21, FFT swaps the axes around so Y will be the slowest changing axis 
i.e. along W in the Patterson, I think.

How many atoms are in your model? Very hard to be sure it's not working as the 
Patterson is so very convoluted with a large model.

Cheers, Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 21 Jun 2022, 14:11, fuxingke wrote:

> In ccp4, I can use "Generate Patterson Map" to generate Patterson map in "Map 
> & Mask Utilities". But, I found a serious problem. When I use a set of data 
> with spacegroup P21 and the position of atom is kown, the length of w-axis in 
> the Patterson map is not equal to cell parameters c. What's more, the 
> position of Patterson peaks are also different from the interatomic vectors. 
> The parameter is as below.
> Why the Patterson map is different? How can I avoid this problem？Is there any 
> other better method to calculate the Patterson map?
>
> I'm looking forward to your reply.
>
> Regards
>
> Best wishes,
>
> Fu Xingke
>
> Institute of Physics CAS
>
> ---
>
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Re: [ccp4bb] Maps on mobile phones.

[Jon Cooper]

For info, this website of mine ('mini map aide'):

[minimapai.de](http://minimapai.de/)

should now work with MTZ files.

Thank you to Marcin Wojdyr (CCP4/Global Phasing) for letting me use gemmi 
sf2map on the server to do the conversion from MTZ to CCP4 map format. I gather 
it uses pocket FFT!

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent with [ProtonMail](https://protonmail.com/) secure email.

--- Original Message ---
On Saturday, May 21st, 2022 at 00:20, Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> For info, barring disasters, the mini map viewer I put together 
> (minimapai.de) should now work with maps produced by Gemmi sf2map.
>
> I did not realise the default axis order (i.e. fast, medium, slow) had 
> changed. Anyway, I think it now works with both the new- and old-style maps.
>
> Cheers, Jon.C.
>
> Sent from ProtonMail mobile
>
>  Original Message 
> On 7 Apr 2022, 01:03, Jon Cooper < 
> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Thank you to those who replied a week or two ago about this. In the end, I 
>> put a revised version here:
>>
>> http://minimapai.de/
>>
>> I'm not sure if that (econo) domain name is a play on words or an aide 
>> memoire ;-?
>>
>> Anyway, with practice, it seems to keep working for ~100 or more residues,at 
>> a time, which might even be useful to somebody ;-?
>>
>> Best wishes, Jon Cooper.
>> jon.b.coo...@protonmail.com
>>
>> Sent with [ProtonMail](https://protonmail.com/) secure email.
>>
>> --- Original Message ---
>> On Monday, March 28th, 2022 at 16:33, Jared Sampson 
>>  wrote:
>>
>>> Hi Phoebe -
>>>
>>> Your email got me wondering about this as well, so over the weekend I 
>>> downloaded BioViewer (simple and relatively intuitive, few customizable 
>>> options), and iMolview (more complex user interface, with more 
>>> information—e.g. sequence, chain IDs—and more granular control of 
>>> representation) on iOS. Not sure if there is an Android version for either 
>>> of those but if you're working with iPads, they might be worth a closer 
>>> look.
>>>
>>> Cheers,
>>> Jared
>>>
>>> On Sun, Mar 27, 2022 at 4:00 PM Phoebe A. Rice  wrote:
>>>
>>>> Oo that looks handy!
>>>>
>>>> And it reminds me to ask the community: if you wanted to do outreach to 
>>>> high schoolers and get them to, say, look at a DNA structure, is there a 
>>>> PyMol-like program that works on tablets? I see PyMol for ipad has been 
>>>> discontinued.
>>>>
>>>> Thanks,
>>>>
>>>> Phoebe
>>>>
>>>> From: CCP4 bulletin board  on behalf of Paul Emsley 
>>>> 
>>>> Reply-To: Paul Emsley 
>>>> Date: Sunday, March 27, 2022 at 11:11 AM
>>>> To: "CCP4BB@JISCMAIL.AC.UK" 
>>>> Subject: Re: [ccp4bb] Maps on mobile phones.
>>>>
>>>> On 27/03/2022 00:17, Jon Cooper wrote:
>>>>
>>>>> Hello, I have been trying to put together a thing for viewing small 
>>>>> blocks of CCP4 electron density maps with a mobile web browser. If anyone 
>>>>> is interested, the current state of it is here:
>>>>>
>>>>> http://ic50.org/jbctest14.html
>>>>
>>>> Have you seen/heard about uglymol? The name is an insult but the project 
>>>> is interesting.
>>>>
>>>> https://github.com/uglymol/uglymol
>>>>
>>>>> Sorry, the link is not https yet, but nothing gets uploaded to the 
>>>>> server! It seems to work OK on Android and iPhone and the maps (note: 
>>>>> only maps; it doesn't do MTZ's, sorry) look similar when viewed in Coot 
>>>>> (taken as the gold standard ;-),
>>>>
>>>> For the record, I've never much liked the contouring of Coot - too many 
>>>> close lines and tiny triangles. I've wanted to change it for a long time, 
>>>> but it's never been the most important thing to fix.
>>>>
>>>>> but I have a few questions about the contouring algorithm that I have 
>>>>> used. It is "surfacenets.js" from here:
>>>>>
>>>>> https://github.com/mikolalysenko/isosurface
>>>>>
>>>>> and a paper describing it is here:
>>>>>
>>>>> https://www.merl.com/publications/docs/TR

Re: [ccp4bb] Maps on mobile phones.

[Jon Cooper]

For info, barring disasters, the mini map viewer I put together (minimapai.de) 
should now work with maps produced by Gemmi sf2map.

I did not realise the default axis order (i.e. fast, medium, slow) had changed. 
Anyway, I think it now works with both the new- and old-style maps.

Cheers, Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 7 Apr 2022, 01:03, Jon Cooper wrote:

> Thank you to those who replied a week or two ago about this. In the end, I 
> put a revised version here:
>
> http://minimapai.de/
>
> I'm not sure if that (econo) domain name is a play on words or an aide 
> memoire ;-?
>
> Anyway, with practice, it seems to keep working for ~100 or more residues,at 
> a time, which might even be useful to somebody ;-?
>
> Best wishes, Jon Cooper.
> jon.b.coo...@protonmail.com
>
> Sent with [ProtonMail](https://protonmail.com/) secure email.
>
> --- Original Message ---
> On Monday, March 28th, 2022 at 16:33, Jared Sampson 
>  wrote:
>
>> Hi Phoebe -
>>
>> Your email got me wondering about this as well, so over the weekend I 
>> downloaded BioViewer (simple and relatively intuitive, few customizable 
>> options), and iMolview (more complex user interface, with more 
>> information—e.g. sequence, chain IDs—and more granular control of 
>> representation) on iOS. Not sure if there is an Android version for either 
>> of those but if you're working with iPads, they might be worth a closer look.
>>
>> Cheers,
>> Jared
>>
>> On Sun, Mar 27, 2022 at 4:00 PM Phoebe A. Rice  wrote:
>>
>>> Oo that looks handy!
>>>
>>> And it reminds me to ask the community: if you wanted to do outreach to 
>>> high schoolers and get them to, say, look at a DNA structure, is there a 
>>> PyMol-like program that works on tablets? I see PyMol for ipad has been 
>>> discontinued.
>>>
>>> Thanks,
>>>
>>> Phoebe
>>>
>>> From: CCP4 bulletin board  on behalf of Paul Emsley 
>>> 
>>> Reply-To: Paul Emsley 
>>> Date: Sunday, March 27, 2022 at 11:11 AM
>>> To: "CCP4BB@JISCMAIL.AC.UK" 
>>> Subject: Re: [ccp4bb] Maps on mobile phones.
>>>
>>> On 27/03/2022 00:17, Jon Cooper wrote:
>>>
>>>> Hello, I have been trying to put together a thing for viewing small blocks 
>>>> of CCP4 electron density maps with a mobile web browser. If anyone is 
>>>> interested, the current state of it is here:
>>>>
>>>> http://ic50.org/jbctest14.html
>>>
>>> Have you seen/heard about uglymol? The name is an insult but the project is 
>>> interesting.
>>>
>>> https://github.com/uglymol/uglymol
>>>
>>>> Sorry, the link is not https yet, but nothing gets uploaded to the server! 
>>>> It seems to work OK on Android and iPhone and the maps (note: only maps; 
>>>> it doesn't do MTZ's, sorry) look similar when viewed in Coot (taken as the 
>>>> gold standard ;-),
>>>
>>> For the record, I've never much liked the contouring of Coot - too many 
>>> close lines and tiny triangles. I've wanted to change it for a long time, 
>>> but it's never been the most important thing to fix.
>>>
>>>> but I have a few questions about the contouring algorithm that I have 
>>>> used. It is "surfacenets.js" from here:
>>>>
>>>> https://github.com/mikolalysenko/isosurface
>>>>
>>>> and a paper describing it is here:
>>>>
>>>> https://www.merl.com/publications/docs/TR99-24.pdf
>>>>
>>>> Unfortunately, my maths is not good enough to tell if it matters if you 
>>>> give it fractional coordinates, rather than orthogonal. I simply give it 
>>>> the electron density values on the CCP4 map grid coordinates, which will 
>>>> be on non-orthogonal axes for unit cells with non-90 degree angles. It 
>>>> seems to give qualitatively similar results to Coot in these cases, so I 
>>>> am cautiously optimistic, but not sure.
>>>
>>> uglymol makes the transformation that you need - so does CootVR for that 
>>> matter
>>>
>>> https://github.com/hamishtodd1/hamishtodd1.github.io/tree/master/cvr
>>>
>>> Here's Chris Hassall playing with it:
>>>
>>> https://www.youtube.com/watch?v=-wfopgdN8o4
>>>
>>> Just to be clear, this is running inside Firefox.
>>>
>>> (It looks like he discovered a contouring b

Re: [ccp4bb] Specifics of different SCALEIT refinements

[Jon Cooper]

Hello, scaleit is for derivative-to-native scaling whereas the Fox and Holmes 
method is generally for batch scaling and merging, as done, for example, by 
scala and its successors, but it is all non-linear least squares, so the 
methods will be fundamentally the same. Hope this helps a bit, Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 12 May 2022, 22:43, Fadini, Alisia wrote:

> Dear all,
>
> I am having trouble following from the documentation what specific functions 
> are minimized in SCALEIT for the different REFINE options and how the 
> Fox&Holmes method is applied. Any insight would be very helpful!
>
> All the best,
> Alisia
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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Re: [ccp4bb] To print the results of CCP4 CONTACT

[Jon Cooper]

Hello, something like:

ccp4prog xyzin input.pdb > output.log

Or:

ccp4prog xyzin input.pdb > & output.log

if output.log already exists.

HTH, Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 11 May 2022, 15:48, Rafiga Masmaliyeva wrote:

> Hi.
>
> I run CCP4 CONTACT with command line.
> Which command do I need to add to be able to print the results to a text file 
> if it is possible?
>
> Thank you in advance.
>
> Best regards
> Rafiga
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
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Re: [ccp4bb] Regrading Naccess

[Jon Cooper]

Hello, I would try deleting the header records i.e. REMARKs, etc, leaving only 
ATOMS and possibly HETATMs. Also, your filename (_2H ?) suggests the PDB file 
has riding hydrogen atoms in it which might throw naccess off course. Best 
wishes, Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 2 May 2022, 12:45, Abhilasha Thakur wrote:

> Hello !!
> Greeting of the day
>
> I have successfully downloaded the naccess but cant be able to use it while 
> executing the command in the terminal $ naccess file.pdb it showed an error 
> that usage: you must supply a pdb format file I have attached an image of 
> error please help me to solve this problem.
>
> Thankyou
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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Re: [ccp4bb] Regarding NACCESS Server for Protein solvent accessible surface

[Jon Cooper]

Hello, naccess and psa are golden oldies but there is areaimol in ccp4 which 
might also help. For naccess, the best contact would be the author (Simon 
Hubbard, Manchester). You could even say you were sent by his examiner ;-0

Good luck with it. Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 22 Apr 2022, 12:14, Abhilasha Thakur wrote:

> Hello Everyone!!
> Greeting of the day
>
> I want to use the NACCESS Server for the calculation of solvent accessible 
> surfaces but I cant be able to install it after downloading it. I have tried 
> linux based but cant be able to install it. PLease guide me how to install it 
> and If there are other Server which can be used for solvent accessible 
> surface calculation please suggest to me but it can be handled or operable by 
> the Shell script in linux system.
>
> Thankyou
>
> ---
>
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Re: [ccp4bb] How to prevent acetate ion clash into ZN in refmac5 and COOT?

[Jon Cooper]

Hello, could this be a case of the ZN not being shifted one place to the left 
in the PDB file to give it the right scattering factor ? ? The progs are 
pushing neighbouring atoms into the Zn density to account for its scattering 
power ? ? Maybe these problems don't happen any more.

Sent from ProtonMail mobile

 Original Message 
On 11 Apr 2022, 15:55, Martin Moche wrote:

> Dear colleagues,
>
> We are refining a structure where an acetate ion (ACT) binds a zinc ion, Zn+2 
> (ZN), using an excellent quality 1.38Å dataset, however the acetate oxygen 
> ends up too close (1.2Å) to the ZN during restrained refinement in refmac5? 
> Moreover, the ACT ion gets “deformed” so that the acetate oxygen-carbon bond 
> gets extended into 1.4Å?
>
> When doing COOT sphere refinement, the acetate ion moves on top of the ZN? 
> like the ZN was not there? And we think this would happen also in refmac5, if 
> the electron density were not holding acetate ion back from entering the zinc 
> site. We guess on a “tug of war” between ZN site attraction for acetate 
> oxygen, and electron density for other three acetate atoms, is deforming the 
> acetate ion. Why is the acetate ion not aware of the ZN in COOT? and refmac5…
>
> In the attached image, we removed the deformed acetate ion from refinement 
> resulting in the green difference density contoured at 5σ. The deformed 
> acetate from previous refinements (gold color carbons) has a carbon-oxygen 
> bond of 1.4Å and an oxygen-zinc distance of 1.2Å. The oxygen-zinc distance is 
> typically around 1.8Å for previous acetate ions (magenta carbons) modeled in 
> other PDB entries of the same enzyme.
>
> To get more reasonable refinement we manually attempted to add LINK (and 
> LINKR) restraints in the PDB file for the oxygen-zinc bond but that had no 
> impact on refmac5 and COOT refinement? although notified in the refmac5 
> logfiles (attached).
>
> COOT is intended to parse LINK records and are not using nonbonded restraints 
> (1). We share our LINK records here for review.
>
> LINK ZN ZN A 625 OE1 GLU A 318 1555 1555 2.060
>
> LINK ZN ZN A 625 OE2 GLU A 318 1555 1555 2.060
>
> LINK O ACT A 623 ZN ZN A 625 1555 1555 2.060
>
> LINKR O ACT A 623 ZN ZN A 625 1555 1555ACT-ZN
>
> LINKR ZN ZN A 625 NE2 HIS A 299 ZN-HISNE
>
> LINKR ZN ZN A 625 NE2 HIS A 295 ZN-HISNE
>
> We tried with one LINK or LINKR row or with both present in PDB (as above) 
> and used various checkboxes under “Advanced options” (pictured) under 
> Refinement-Refmac5 > Inputs > Restraints
>
> Metal coordination vary with oxidation state and despite AceDRG (2) and 
> recent CCP4 developments (3) we are now struggling with Zinc and acetate ion 
> in our refinement.
>
> Maybe we have run into a BUG? or how should we proceed?
>
> Best regards,
>
> Martin
>
> P.S.
>
> Also, in phenix.refine the acetate ion moves too close to the ZN? And one if 
> the zinc coordinated water molecules left its electron density and moved 
> towards the ZN..?
>
> D.S.
>
> 1. Casanal A, Lohkamp B, Emsley P. Current developments in Coot for 
> macromolecular model building of Electron Cryo-microscopy and 
> Crystallographic Data. Protein Sci. 2020;29(4):1069-78.doi:10.1002/pro.3791.
>
> 2. Nicholls RA, Joosten RP, Long F, Wojdyr M, Lebedev A, Krissinel E, 
> Catapano L, Fischer M, Emsley P, Murshudov GN. Modelling covalent linkages in 
> CCP4. Acta Crystallogr D Struct Biol. 2021;77(Pt 
> 6):712-26.doi:10.1107/S2059798321001753.
>
> 3. Nicholls RA, Wojdyr M, Joosten RP, Catapano L, Long F, Fischer M, Emsley 
> P, Murshudov GN. The missing link: covalent linkages in structural models. 
> Acta Crystallogr D Struct Biol. 2021;77(Pt 
> 6):727-45.doi:10.1107/S2059798321003934.
>
> [Head of Macromolecular X-ray Crystallography](https://ki.se/en/mbb/psf-mx) | 
> [Protein Science Facility](https://ki.se/en/mbb/protein-science-facility)
>
> [Medical Biochemistry and 
> Biophysics](https://ki.se/en/mbb/department-of-medical-biochemistry-and-biophysics)
>
> 171 65 Solna | Solnavägen 9
>
> +46 8 524 868 43 | +46 73 322 93 27
>
> martin.mo...@ki.se | [ki.se](https://ki.se/)
>
> __
>
> Karolinska Institutet – a medical university
>
> När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI 
> kommer att behandla dina personuppgifter. [Här finns information om hur KI 
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> here](https://ki.se/en/staff/data-protection-policy).
>
> ---
>
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To unsubscribe from the CCP4BB list, click the followin

Re: [ccp4bb] Maps on mobile phones.

[Jon Cooper]

Thank you to those who replied a week or two ago about this. In the end, I put 
a revised version here:

http://minimapai.de/

I'm not sure if that (econo) domain name is a play on words or an aide memoire 
;-?

Anyway, with practice, it seems to keep working for ~100 or more residues,at a 
time, which might even be useful to somebody ;-?

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent with [ProtonMail](https://protonmail.com/) secure email.

--- Original Message ---
On Monday, March 28th, 2022 at 16:33, Jared Sampson 
 wrote:

> Hi Phoebe -
>
> Your email got me wondering about this as well, so over the weekend I 
> downloaded BioViewer (simple and relatively intuitive, few customizable 
> options), and iMolview (more complex user interface, with more 
> information—e.g. sequence, chain IDs—and more granular control of 
> representation) on iOS. Not sure if there is an Android version for either of 
> those but if you're working with iPads, they might be worth a closer look.
>
> Cheers,
> Jared
>
> On Sun, Mar 27, 2022 at 4:00 PM Phoebe A. Rice  wrote:
>
>> Oo that looks handy!
>>
>> And it reminds me to ask the community: if you wanted to do outreach to high 
>> schoolers and get them to, say, look at a DNA structure, is there a 
>> PyMol-like program that works on tablets? I see PyMol for ipad has been 
>> discontinued.
>>
>> Thanks,
>>
>> Phoebe
>>
>> From: CCP4 bulletin board  on behalf of Paul Emsley 
>> 
>> Reply-To: Paul Emsley 
>> Date: Sunday, March 27, 2022 at 11:11 AM
>> To: "CCP4BB@JISCMAIL.AC.UK" 
>> Subject: Re: [ccp4bb] Maps on mobile phones.
>>
>> On 27/03/2022 00:17, Jon Cooper wrote:
>>
>>> Hello, I have been trying to put together a thing for viewing small blocks 
>>> of CCP4 electron density maps with a mobile web browser. If anyone is 
>>> interested, the current state of it is here:
>>>
>>> http://ic50.org/jbctest14.html
>>
>> Have you seen/heard about uglymol? The name is an insult but the project is 
>> interesting.
>>
>> https://github.com/uglymol/uglymol
>>
>>> Sorry, the link is not https yet, but nothing gets uploaded to the server! 
>>> It seems to work OK on Android and iPhone and the maps (note: only maps; it 
>>> doesn't do MTZ's, sorry) look similar when viewed in Coot (taken as the 
>>> gold standard ;-),
>>
>> For the record, I've never much liked the contouring of Coot - too many 
>> close lines and tiny triangles. I've wanted to change it for a long time, 
>> but it's never been the most important thing to fix.
>>
>>> but I have a few questions about the contouring algorithm that I have used. 
>>> It is "surfacenets.js" from here:
>>>
>>> https://github.com/mikolalysenko/isosurface
>>>
>>> and a paper describing it is here:
>>>
>>> https://www.merl.com/publications/docs/TR99-24.pdf
>>>
>>> Unfortunately, my maths is not good enough to tell if it matters if you 
>>> give it fractional coordinates, rather than orthogonal. I simply give it 
>>> the electron density values on the CCP4 map grid coordinates, which will be 
>>> on non-orthogonal axes for unit cells with non-90 degree angles. It seems 
>>> to give qualitatively similar results to Coot in these cases, so I am 
>>> cautiously optimistic, but not sure.
>>
>> uglymol makes the transformation that you need - so does CootVR for that 
>> matter
>>
>> https://github.com/hamishtodd1/hamishtodd1.github.io/tree/master/cvr
>>
>> Here's Chris Hassall playing with it:
>>
>> https://www.youtube.com/watch?v=-wfopgdN8o4
>>
>> Just to be clear, this is running inside Firefox.
>>
>> (It looks like he discovered a contouring bug when he zooms out)
>>
>>> Another thing is that the results of the contouring are sent out in groups 
>>> of 3 points which are the vertices of triangles forming the surface. Hence, 
>>> I orthogonalize them and get three.js to draw them as just that - 
>>> triangles. My worry is that, since the triangles all have edges in common, 
>>> nearly all of the contour lines (except the ones at the edges of the map 
>>> box) get drawn twice, or at least are sent to three.js twice for drawing, 
>>> which doesn't seem terribly efficient?!
>>
>> Coot used to remove double drawing. The large speed up in contouring in the 
>> 0.9 series is a result of removing that test and just drawing the lines 
>> twice.
>>
>>> 

[ccp4bb] Maps on mobile phones.

[Jon Cooper]

Hello, I have been trying to put together a thing for viewing small blocks of 
CCP4 electron density maps with a mobile web browser. If anyone is interested, 
the current state of it is here:

http://ic50.org/jbctest14.html

Sorry, the link is not https yet, but nothing gets uploaded to the server! It 
seems to work OK on Android and iPhone and the maps (note: only maps; it 
doesn't do MTZ's, sorry) look similar when viewed in Coot (taken as the gold 
standard ;-), but I have a few questions about the contouring algorithm that I 
have used. It is "surfacenets.js" from here:

https://github.com/mikolalysenko/isosurface

and a paper describing it is here:

https://www.merl.com/publications/docs/TR99-24.pdf

Unfortunately, my maths is not good enough to tell if it matters if you give it 
fractional coordinates, rather than orthogonal. I simply give it the electron 
density values on the CCP4 map grid coordinates, which will be on 
non-orthogonal axes for unit cells with non-90 degree angles. It seems to give 
qualitatively similar results to Coot in these cases, so I am cautiously 
optimistic, but not sure.

Another thing is that the results of the contouring are sent out in groups of 3 
points which are the vertices of triangles forming the surface. Hence, I 
orthogonalize them and get three.js to draw them as just that - triangles. My 
worry is that, since the triangles all have edges in common, nearly all of the 
contour lines (except the ones at the edges of the map box) get drawn twice, or 
at least are sent to three.js twicefor drawing, which doesn't seem terribly 
efficient?! Is there a nicer way of doing this? I think it might be better to 
have FRODO-style contouring just on the 2D sections of the map, rather than 
having lots of diagonal lines?? Anyway, my 5 YO phone takes about 3 seconds to 
step from one residue to the next, so it seems not too bad, although not ideal!

Finally, its been asked before, but is there a nice way in CCP4i2 to output 
maps that cover the coordinates of the structure, rather than the asymmetric 
unit? Saving maps in Coot gives the asymmetric unit, too, although using Export 
Map Fragment seems the best option. I know about doing this in the old gui with 
mapmask, or using phenix, so just wondering if I've missed a way of doing this 
in i2, etc? I know that suitably extended CCP4 maps are available from the PDBe 
EBI.

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

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Re: [ccp4bb] CSYMMATCH for help

[Jon Cooper]

I don't know for sure, but I think the -origin-hand thing would be for heavy 
atom work where both enantiomers of the solution can fit the data. Cheers, 
Jon.C.

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 Original Message 
On 18 Mar 2022, 04:02, 付兴科_201928000807036 wrote:

> Dear Colleagues,
>
> In cysmmatch of CCP4, there is a keyworded input，“-origin-hand”. The 
> resolution with "-origin-hand" is very different from the resolution without 
> "-origin-hand". What's the mean of "origin shif" ? How does it work?
> The reference page is .
>
> I'm looking forward to your reply.
>
> Regards
>
> Best wishes,
>
> Fu Xingke
>
> Institute of Physics CAS
>
> ---
>
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Re: [ccp4bb] Unable to reduce the values of R-work and R-free

[Jon Cooper]

One practical point: I had the same experience recently with a structure that 
had been worked on by others previously. Refmac was automatically picking up a 
data column from some earlier work, unknown to me, rather than the observed 
data from XDS and the R-factors were sticking at the values you have. So, 
stating the very obvious, sorry, it would be worth double-checking which data 
are being used as the refinement target.

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 Original Message 
On 7 Mar 2022, 08:39, Mudassar Ali Khan wrote:

> Dear all,
>
> I am trying to solve an x-ray structure of a protein for which the structure 
> is not available. I have performed data reduction using XDS followed by 
> Aimless (output file attached herewith). Molecular replacement was performed 
> using Phaser MR (CCP4i) with modelled structure followed by rigid body and 
> restrained refinement. In coot, the electron density is fitting well with the 
> structure, however, I am not able to reduce the R-work and R-free beyond 0.43 
> and 0.46 respectively.
>
> I have also tried the same with Phenix, but the R-work and R-free were almost 
> the same as obtained from ccp4i.
> Any suggestion to reduce R-work and R-free will be greatly appreciated.
>
> Thanks!
>
> Regards,
> Mudassar Ali Khan
> Graduate student
> KS-101, Varma Lab
> Advanced Centre for Treatment Education and Research in Cancer (ACTREC)
> Navi-Mumbai, India
>
> ---
>
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Re: [ccp4bb] Ligand occupancy refinement

[Jon Cooper]

Hello, the ligand needs to be treated as one occupancy group since refining 
individual occupancies would be a case of refining too many parameters, unless 
it was a very fragmentary compound!! It is one keyword in refmac, but I can't 
remember for phenix, sorry! Ta jc

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 Original Message 
On 3 Mar 2022, 14:15, Akanksha Tomar wrote:

> Hi everyone,
>
> I am trying to refine the occupancy of a bound ligand. After fixing the 
> protein model and water I fitted the ligand into it. Currently, I am using 
> Phenix Refine with occupancy refinement for individual atoms switched on. 
> After the refinement, the overall occupancy of the ligand is 0.7 and the RSCC 
> value is 0.86. The resolution of the structure is 2.1 Å.
>
> Now the problem is that the program has assigned different occupancies to 
> different atoms of the ligand. For some cases, it has assigned 0 occupancies 
> to atoms for which there is a clear positive peak.
>
> Why it has been done so and is it acceptable?
>
> Any help would be greatly appreciated.
>
> Thank you.
>
> --
>
> Best Regards,
> Akanksha Tomar
> Pre-Doctoral Fellow,
> C\o Dr. Arockiasamy Arulandu,
> Membrane Protein Biology Group,
> International Center for Genetic Engineering and Biotechnology,
> New Delhi, India
>
> ---
>
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Re: [ccp4bb] SHELXD for help

[Jon Cooper]

The diagonal elements of the scale matrix are 1/a, 1/b and 1/c for orthogonal 
cells. It converts orthogonal coordinates to fractional. There should be more 
info on the rcsb.org website or in the ccp4 documentation e.g. for pdbset. 
Cheers, Jon.C.

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 Original Message 
On 1 Mar 2022, 11:16, Dom Bellini - MRC LMB wrote:

> Hi Fu,
>
> "The SCALEn (n = 1, 2, or 3) records present the transformation from the 
> orthogonal coordinates as contained in the entry to fractional 
> crystallographic coordinates." (please see here 
> https://www.wwpdb.org/documentation/file-format-content/format33/sect8.html)
>
> "The self-correlation coefficient for the anomalous signal should be above 
> 25% for a significant signal." (for example see here 
> https://www.ccp4.ac.uk/schools/Japan-2014/lectures/shelxcde_tutorial.pdf or
> here 
> (https://www.ccp4.ac.uk/schools/APS-2010/tutorials/shelx/tutorial_shelx_chicago2009.pdf).
>
> I hope this should help you or at least point you towards the right 
> directions.
>
> BW,
>
> D
>
> On 01/03/2022 10:06, fu wrote:
>
>> Dear Colleagues,
>>
>> I have two question.
>>
>> The first question is, in SHELXD, they use XPREP to calculate the 
>> correlation coefficient(CCano) between the signed anomalous differences at 
>> different wavelengths? What’s the meaning? And how to calculate it? The 
>> reference is 《Schneider, T.R. & Sheldrick, G.M. (2002). "Substructure 
>> Solution with SHELXD", Acta Crystallogr. D58, 1772-1779》
>>
>> Second, what is the "SCALE1 SCALE2 SCALE3" in following picture?
>>
>> Best wishes,
>>
>> Fu Xingke
>>
>> Institute of Physics CAS
>>
>> 从 Windows 版[邮件](https://go.microsoft.com/fwlink/?LinkId=550986)发送
>>
>> ---
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> --
> Dom Bellini, Xray Crystallography Facility (1S205)
> MRC Laboratory of Molecular Biology
> Francis Crick Avenue
> Cambridge Biomedical Campus
> Cambridge CB2 0QH
> Phone 01223 267839
>
> ---
>
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Re: [ccp4bb] Negative density

[Jon Cooper]

I thought it was tryptophan but the nitrogen and extra bond are in the wrong 
places so it must be a ligand and, if so, have you tried refining the 
occupancy? Cheers, Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 22 Feb 2022, 05:34, S wrote:

> Hi All,
>
> I am getting this negative density in the centre of the ring. Could you 
> please help me with this?
>
> Resolution: 1.7A
> 2FoFc - 1.5
> FoFc - 3.0
>
> Thanks in advance.
> Regards,
> Renu
>
> ---
>
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Re: [ccp4bb] Help with interpreting Tyrosine modification

[Jon Cooper]

Hello, yes, that's right. We've all seen guanidinium groups parallel with 
aromatic rings and shielding them from solvent. I think it might approach that 
sort of arrangement in this case. Cheers, Jon.C.

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 Original Message 
On 1 Feb 2022, 16:52, Krieger, James M wrote:

> Probably arginine and tyrosine do like each other a fair bit. They can form 
> both cation-pi interactions and hydrogen bonds.
> Best wishes
> James
>
>> On 1 Feb 2022, at 16:41, Jon Cooper 
>> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hello, I did wonder if it might be an alternative conformation for the 
>> quanidinium group of that nearby arginine. Being such high resolution, quite 
>> low occupancy groups would show up, I think, but it may just be too far away 
>> and I don't know how much tyrosine and arginine like each other!
>>
>> Sent from ProtonMail mobile
>>
>>  Original Message 
>> On 1 Feb 2022, 09:28, Misba Ahmad < misba.ah...@gmail.com> wrote:
>>
>>> Thank you for your suggestions.
>>> As this is a high resolution structure (1.1Å) I have been refining it with 
>>> anisotropic B-factors.
>>> Placing a propionate or modelling a phosphate at this position blows up 
>>> during the refinement.
>>> I will inform you if I am successful in figuring this out.
>>>
>>> Best
>>> Misbha
>>>
>>> On Sat, Jan 29, 2022 at 7:01 PM SHEPARD William 
>>>  wrote:
>>>
>>>> Dear Misba,
>>>>
>>>> Perhaps it's a silly question, but have you tried to model in propionate? 
>>>> The carboxylate group could make H-bonds to both the Arginine sidechain 
>>>> and the the tyrosine OH group. Propionate should show no anomalous signal.
>>>>
>>>> Just my 2-bits worth.
>>>>
>>>> Cheers,
>>>> Bill
>>>>
>>>> - Original Message -
>>>> From: "Gerard Bricogne" 
>>>> To: CCP4BB@JISCMAIL.AC.UK
>>>> Sent: Saturday, 29 January, 2022 18:34:26
>>>> Subject: Re: [ccp4bb] Help with interpreting Tyrosine modification
>>>>
>>>> Dear Misba,
>>>>
>>>> Thank you for your reply and for the very clear picture. I hope you
>>>> will be able to share the result once the mystery is solved.
>>>>
>>>> With best wishes,
>>>>
>>>> Gerard.
>>>>
>>>> --
>>>> On Sat, Jan 29, 2022 at 03:32:30PM +0100, Misba Ahmad wrote:
>>>>> Dear Gerard,
>>>>> The data were collected at 0.966Å and I can see the anomalous peaks for As
>>>>> at Cysteines which are modified and I have correctly modelled those (see
>>>>> image below). However, at this Tyr, I don't see an anomalous signal.
>>>>>
>>>>> [image: 4.png]
>>>>>
>>>>> On Sat, Jan 29, 2022 at 3:06 PM Gerard Bricogne 
>>>>> wrote:
>>>>>
>>>>> > Dear Misba,
>>>>> >
>>>>> > A wild guess: have you considered the possibility that this extra
>>>>> > density could be a cacodylate adduct? Cacodylate is well known to react
>>>>> > with
>>>>> > thiols - see
>>>>> >
>>>>> >
>>>>> > [https://febs.onlinelibrary.wiley.com/doi/pdfdirect/10.1016/0014-5793(72)80224-2](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffebs.onlinelibrary.wiley.com%2Fdoi%2Fpdfdirect%2F10.1016%2F0014-5793(72)80224-2&data=04%7C01%7Ckriegerj%40PITT.EDU%7C3bfe6a715d964db88a1c08d9e5a1740e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637793305180888406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=quySIsk%2BnzbHh5o3bYoOGbiXsx1ItJGTt3y6aI2oc5M%3D&reserved=0)
>>>>> >
>>>>> > Here the chemistry is different but you never know. If your data are
>>>>> > redundant enough that you have good anomalous completeness, and were
>>>>> > collected above the As K-edge (11.8667 keV), it might be a good idea to
>>>>> > compute an anomalous difference Fourier and check for the presence of a
>>>>> > peak
>>>>> > at the same location as the highest one in your ordinary difference map.
>>>>> >
>>>>> > Only a wild guess, though ... .
>>>>> >
>>>>> >
>>>

Re: [ccp4bb] Help with interpreting Tyrosine modification

[Jon Cooper]

Hello, I did wonder if it might be an alternative conformation for the 
quanidinium group of that nearby arginine. Being such high resolution, quite 
low occupancy groups would show up, I think, but it may just be too far away 
and I don't know how much tyrosine and arginine like each other!

Sent from ProtonMail mobile

 Original Message 
On 1 Feb 2022, 09:28, Misba Ahmad wrote:

> Thank you for your suggestions.
> As this is a high resolution structure (1.1Å) I have been refining it with 
> anisotropic B-factors.
> Placing a propionate or modelling a phosphate at this position blows up 
> during the refinement.
> I will inform you if I am successful in figuring this out.
>
> Best
> Misbha
>
> On Sat, Jan 29, 2022 at 7:01 PM SHEPARD William 
>  wrote:
>
>> Dear Misba,
>>
>> Perhaps it's a silly question, but have you tried to model in propionate? 
>> The carboxylate group could make H-bonds to both the Arginine sidechain and 
>> the the tyrosine OH group. Propionate should show no anomalous signal.
>>
>> Just my 2-bits worth.
>>
>> Cheers,
>> Bill
>>
>> - Original Message -
>> From: "Gerard Bricogne" 
>> To: CCP4BB@JISCMAIL.AC.UK
>> Sent: Saturday, 29 January, 2022 18:34:26
>> Subject: Re: [ccp4bb] Help with interpreting Tyrosine modification
>>
>> Dear Misba,
>>
>> Thank you for your reply and for the very clear picture. I hope you
>> will be able to share the result once the mystery is solved.
>>
>> With best wishes,
>>
>> Gerard.
>>
>> --
>> On Sat, Jan 29, 2022 at 03:32:30PM +0100, Misba Ahmad wrote:
>>> Dear Gerard,
>>> The data were collected at 0.966Å and I can see the anomalous peaks for As
>>> at Cysteines which are modified and I have correctly modelled those (see
>>> image below). However, at this Tyr, I don't see an anomalous signal.
>>>
>>> [image: 4.png]
>>>
>>> On Sat, Jan 29, 2022 at 3:06 PM Gerard Bricogne 
>>> wrote:
>>>
>>> > Dear Misba,
>>> >
>>> > A wild guess: have you considered the possibility that this extra
>>> > density could be a cacodylate adduct? Cacodylate is well known to react
>>> > with
>>> > thiols - see
>>> >
>>> >
>>> > https://febs.onlinelibrary.wiley.com/doi/pdfdirect/10.1016/0014-5793(72)80224-2
>>> >
>>> > Here the chemistry is different but you never know. If your data are
>>> > redundant enough that you have good anomalous completeness, and were
>>> > collected above the As K-edge (11.8667 keV), it might be a good idea to
>>> > compute an anomalous difference Fourier and check for the presence of a
>>> > peak
>>> > at the same location as the highest one in your ordinary difference map.
>>> >
>>> > Only a wild guess, though ... .
>>> >
>>> >
>>> > With best wishes,
>>> >
>>> > Gerard.
>>> >
>>> > --
>>> > On Sat, Jan 29, 2022 at 12:18:58PM +0100, Misba Ahmad wrote:
>>> > > Placing a water molecule satisfies most of the density and forms nice
>>> > > H-bonds but there is still some residual density left (8.6 and 5.6 
>>> > > rmsd).
>>> > >
>>> > > Best
>>> > > Misbha
>>> > > [image: 3.png]
>>> > >
>>> > >
>>> > > On Sat, Jan 29, 2022 at 11:05 AM Klaus Futterer 
>>> > > wrote:
>>> > >
>>> > > > Looks more like water molecules. Phosphorylation would give a much
>>> > bigger
>>> > > > peak, and shape of density does not fit either. I don't think this is 
>>> > > > a
>>> > > > covalent modification. Model some water molecules and see what the
>>> > > > distances are and what difference density is left.
>>> > > >
>>> > > >
>>> > > > Klaus
>>> > > >
>>> > > >
>>> > > > ===
>>> > > > Klaus Fütterer, PhD
>>> > > > Reader in Structural Biology
>>> > > >
>>> > > >
>>> > > > School of Biosciences
>>> > > > LES College Email:
>>> > > > k.futte...@bham.ac.uk
>>> > > > University of Birmingham Phone: +44 - 121 - 414
>>> > > > 5895
>>> > > > Birmingham, B15 2TT, UK (voice mail messages
>>> > > > will forward to my email inbox)
>>> > > >
>>> > > > My normal working hours are Mon - Fri 8.30 - 5.30 pm.
>>> > > >
>>> > > >
>>> > > > ===
>>> > > > --
>>> > > > *From:* CCP4 bulletin board  on behalf of
>>> > > > misba.ah...@gmail.com 
>>> > > > *Sent:* 29 January 2022 09:45:24
>>> > > > *To:* CCP4BB@JISCMAIL.AC.UK
>>> > > > *Subject:* Re: [ccp4bb] Help with interpreting Tyrosine modification
>>> > > >
>>> > > > Hi Tom,
>>> > > > The protein was expressed in E Coli.
>>> > > >
>>> > > > Best
>>> > > > Misbha
>>> > > >
>>> > > > On Sat, 29 Jan 2022, 10:18 Peat, Tom (Manufacturing, Clayton) <
>>> > > > tom.p...@csiro.au> wrote:
>>> > > >
>>> > > >> Hello Misba,
>>> > > >>
>>> > > >> Doesn't quite look like a phosphate, maybe O-sulfation?
>>> > > >> Maybe just as important as the buffer and crystallisation conditions
>>> > > >> would be how it was expressed? Insect cells?
>>> > > >>
>>> > > >> Best of luck, tom
>>> > > >>
>>> > > >> Tom Peat, PhD
>>> > > >>
>>> > > >> Biomedical Program, CSIRO
>>> > > >> tom.p...@csiro.au
>>> > > >>
>>>