Re: [ccp4bb] how to create a figure of a blob

[Harry Powell]

Hi

I was wondering if moorhen might be useful for this?

Harry

> On 18 Jul 2024, at 18:35, Paul Emsley  wrote:
> 
> On 7/18/24 15:33, Andrea Smith wrote:
>> 
>> 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?
>> 
>> [...]
>> 
>> Is printscreen from Coot my only option?
>> 
> Density figures from Coot 1 can look, if I may be so bold, pretty good.  See, 
> for example Catapano et al. (2023):
> 
> https://journals.iucr.org/d/issues/2023/12/00/qe5005/index.html
> 
> 
> 
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Re: [ccp4bb] Error in mosaicity estimation by iMOSFLM

[Harry Powell]

Hi

The simple answer is to estimate your own value (as we always used to do before 
I coded this up about 20 years ago…) by overlaying a prediction over the images 
and determining what value of mosaicity gives the best coverage. It may also be 
worthwhile changing the “mosaic block size” in the “Images” window after you 
have loaded images - for “modern” crystals I find that a value of 5 - 10 
microns here is often useful.

Best wishes

Harry

> On 18 Jul 2024, at 05:01, Arpana Shikha  wrote:
> 
> Dear CCP4 Users,
> 
> I recently updated the CCP4 package from version 8 to 9. I am getting an 
> error while data processing using iMOSFLM (please see the attached picture). 
> The program is not able to estimate the mosaicity. I had never faced such 
> errors for any data. I am using Linux CentOS Fedora 8.
> 
> I am looking forward to having any solutions to fix this issue. Let me know 
> if you need any more information about this.
> 
> With best regards,
> Arpana
> 
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Re: [ccp4bb] message yesterday on the CCP4BB

[Harry Powell]

Hi

Pandora’s box comes to mind…

Harry

> On 10 Jul 2024, at 07:14, Grant Hansman 
>  wrote:
> 
> Hi,
>  
> I sent a message yesterday on the CCP4BB (below). I received so many 
> enquires. Can I edit or stop this message as I no longer need help. The 
> community was so helpful!
>  
> Best,
> Grant
>  
>  
> Subject:
> 
> 
> Looking for a student and/or help with finalizing new virus spike structures
> 
> From:
> 
> 
> Grant Hansman g.hans...@griffith.edu.au
> 
> Reply-To:
> 
> 
> Grant Hansman g.hans...@griffith.edu.au
> 
> Date:
> 
> 
> Tue, 9 Jul 2024 05:52:35 +0100
> 
> Content-Type:
> 
> 
> text/plain
> 
> Parts/Attachments:
> 
> 
> 
> text/plain (17 lines)
> 
> 
> 
> Reply
> 
> Help needed ASAP.
>  
> I am just setting up my new laboratory in Australia (alone at the moment) and 
> already have at least 5 new X-ray structures that need checking and a bit 
> more refinement. High resolution and should not be too much work.
>  
> Therefore, I am looking for a student with experience and/or any help with 
> finalizing the structures (will provide all details to those interested). 
>  
> Happy to add as a co-first author to any manuscripts, as all the wet lab, 
> data collection, and refinements were done by myself ;)
>  
> Cheers. 
>  
>  
>  
> Dr Grant Hansman | Senior Research Fellow
>  
> Institute for Glycomics
> Griffith University | Gold Coast campus | QLD 4222 | Institute for Glycomics 
> (G25) Room 2.56
> T +61 7 5552 9552 | E g.hans...@griffith.edu.au
>  
> griffith.edu.au/institute-glycomics
> 
> Griffith University - CRICOS Provider Number 00233E
> PRIVILEGED - PRIVATE AND CONFIDENTIAL
> This email and any files transmitted with it are intended solely for the use 
> of the addressee(s) and may contain information which is confidential or 
> privileged. If you receive this email and you are not the addressee or 
> responsible for delivery of the email to the addressee(s), please disregard 
> the contents of the email, delete the mail and notify the author immediately.
> 
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Re: [ccp4bb] PDBE - HTTP Status 404?

[Harry Powell]

Ok, it seems to be back again. Maybe the servers had a hangover after 
yesterday’s celebrations…

Harry

> On 5 Jul 2024, at 11:43, Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi folks
> 
> https://www.ebi.ac.uk/pdbe
> 
> HTTP Status 404 - Not Found 
> 
> ??
> 
> Harry
> 
> 
> 
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[ccp4bb] PDBE - HTTP Status 404?

[Harry Powell]

Hi folks

https://www.ebi.ac.uk/pdbe

HTTP Status 404 - Not Found 

??

Harry



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Re: [ccp4bb] CCP4 Cloud Server Structure Prediction Task Unavailable

[Harry Powell]

Hi

You probably need to try again later...

It looks to me as if the CCP4 Cloud server (for “remote”) is down for some 
reason - I just tried to run it and I get a pop-up that says “CCP4 Cloud 
Maintenance”, that includes the text “failed to connect”.

I think that the “structure prediction” task is not available for CCP4 Cloud 
Desktop unless you have AlphaFold set up to run locally on your machine; for 
most users, this is not very likely.

Generally, though, I’ve found that using CCP4 Cloud is by far the easiest way 
to run AlphaFold predictions (rather than for downloading previously predicted 
models from the DB).

Harry

> On 26 Jun 2024, at 06:00, YASH MISRA PHD222012  
> wrote:
> 
> Dear all,
> 
> Can someone help me with this?
> 
> Until yesterday it was working fine but today when I tried running this task 
> I am getting the following error. I tried accessing this task via. 
> https://cloud.ccp4.ac.uk/ using my Windows system as well as LInux but to no 
> avail. 
> 
> 
> 
> I also tried using the CCP4 Cloud Desktop but it showed me the following 
> error:
> 
> 
> 
> I am not sure which software to install for the latter.
> 
> Any assistance would be appreciated.
> 
> Thank you.
> 
> Kind regards
> 
> Yash Misra
> Ph.D. Scholar
> Dr. R. Natesh Lab
> School of Biology
> Indian Institute of Science Education and Research- Thiruvananthapuram
> Kerala
> INDIA
>  
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[ccp4bb] PDBE website down - scheduled "maintenance" or not?

[Harry Powell]

Hi folks

I’m just having issues seeing the PDBe website - does anyone know if this is 
scheduled or if there is another issue?

Harry


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Re: [ccp4bb] List of 3-letter codes of modified amino acids

[Harry Powell]

Hi folks

“Can of worms” is how this could be described!

From various different sources (many thanks Paul, Mitch, Robbie) I have now 
managed to obtain (inter alia) lists of 31, 189, 863 and 916 modified amino 
acids - and there are other, longer (and possibly shorter and equimetric [is 
that even a word?] lists that I could create if I want to be more 
comprehensive! It’s certainly _possible_ that some of the members of an 
individual list are duplicates, but for my current purposes these should 
suffice nearly all the time (and for those cases where the list falls short, I 
would expect people to raise the issue directly with me…)

Once more, I knew this would be the place to ask!

Harry

> On 24 Jun 2024, at 13:40, Robbie Joosten  wrote:
> 
> Hi Harry,
> 
> A BSc student in our lab just had a look at this. Here is the list of 
> mappings pdb-redo uses: 
> https://github.com/PDB-REDO/pdb-redo-main/blob/trunk/tools/pdb-redo-data.cif 
> (second to last loop).
> 
> Cheers,
> Robbie
> 
> pdb-redo-main/tools/pdb-redo-data.cif at trunk · PDB-REDO/pdb-redo-main
> core pdb-redo script, tools and data files. Contribute to 
> PDB-REDO/pdb-redo-main development by creating an account on GitHub.
> github.com
> 
> From: CCP4 bulletin board  on behalf of Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk>
> Sent: Monday, June 24, 2024 2:03 PM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: [ccp4bb] List of 3-letter codes of modified amino acids
>  
> Hi
> 
> An internet search doesn’t yield an obvious list of these (I did find a paper 
> DOI:10.1016/j.jmgm.2006.08.004 that says there are 293, but the link included 
> appears to be dead - http://deposit.pdb.org/hetdictionary.txt).
> 
> I’m almost convinced that this has been asked here previously (if not 
> recently), but a quick search through ccp4bb postings has not revealed it to 
> me.
> 
> Can anyone help?
> 
> Harry
> 
> 
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[ccp4bb] List of 3-letter codes of modified amino acids

[Harry Powell]

Hi

An internet search doesn’t yield an obvious list of these (I did find a paper 
DOI:10.1016/j.jmgm.2006.08.004 that says there are 293, but the link included 
appears to be dead - http://deposit.pdb.org/hetdictionary.txt).

I’m almost convinced that this has been asked here previously (if not 
recently), but a quick search through ccp4bb postings has not revealed it to me.

Can anyone help?

Harry


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Re: [ccp4bb] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography

[Harry Powell]

Hi

Presumably Wladek would know about this - I believe that he is an occasional 
visitor to this BB!

Harry

> On 13 Jun 2024, at 10:40, Martin Malý  wrote:
> 
> Dear John,
> Thank you for the link. It would be great if https://proteindiffraction.org/ 
> (IRRMC) was rescued. I preferred this website but they stopped receiving new 
> data sets - or at least they do not reply to my emails for more than a year. 
> I am worried that the website will disappear and also all the uploaded data 
> sets will be gone...
> Cheers,
> Martin
> 
> On 12/06/2024 20:44, John R Helliwell wrote:
>> Dear Colleagues,
>> Our article on this topic, which I imagine will be of keen interest, 
>> published this afternoon, is available open access from this weblink:-
>> 
>> https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html
>> 
>> Best wishes,
>> John
>> Emeritus Professor John R Helliwell DSc
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> 
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Re: [ccp4bb] Computational crystallography in 2024

[Harry Powell]

Hi Lucas 

This one?

https://www.iucr.org/resources/commissions/crystallographic-computing/schools/kyoto-2008-crystallographic-computing-school

IUCr’s Commission on Crystallographic Computing still holds these - next one 
(probably) in Alberta!

Harry

> On 16 May 2024, at 01:51, Lucas Bleicher  wrote:
> 
> Dear all,
> 
> I've been outside of the field for a few years (I have very fond memories of 
> the 2008 Crystallographic Computing School, but did a lot of different stuff 
> since then), but I'd love to come back and figured this would be the best 
> place to ask - what are the go-to resources today for those who want to write 
> code for crystallography? I remember back then the people involved in Phenix 
> were developing open source libraries at the time. I'm aware Biopython does 
> some stuff regarding coordinates, but as far as I'm aware not what I would 
> need to, for example, writing simple code that would read a PDB and mtz and 
> calculate real space fit for an aminoacid, or generating symmetry neighbours 
> from a asymmetrical unit PDB and its space group. How are people doing things 
> like that in 2024? 
> 
> Cheers, 
> 
> Lucas Bleicher 
> 
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Re: [ccp4bb] a dinosaur asks ... PDB format query

[Harry Powell]

Hi Robbie

I’m not actually using PDB files of proteins - I’m using the PDB format files 
in PDBeChem, because at the moment I’m interested in doing stuff with 
ligands/substrates/etc. The charges I’ve seen so far seem to be not quite what 
I’d expect, but I’m prepared to work around that.

Harry

> On 15 May 2024, at 16:24, Robbie Joosten  wrote:
> 
> Hi Harry,
> 
> It might be better now, but there used to positively charged aspartates in 
> the PDB. You have a better chance taking charges out of the CCD for your 
> atoms of interest. I'm not saying all charges in the CCD are correct, but 
> they are much more reliable. If you find errors, please report them to the 
> proper authority. See it, say it, sorted.
> 
> Cheers,
> Robbie
> 
> On 15 May 2024 14:41, Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hi 
> 
> This is very, very useful and hits on the four-letter name problem that I am 
> encountering - thank you. Saves me trying to produce a new design for a 
> circular object with an axle… 
> 
> For the files that I am trying to use, columns 77-78 are present (actually, 
> columns 79-80 are there so I can read the atomic charge as well, which is 
> useful for my purposes) so I’m hoping that this will be reliable. 
> 
> Harry 
> 
> 
>> On 15 May 2024, at 12:38, Marcin Wojdyr  wrote: 
>> 
>>> 
>>>> • Alignment of one-letter atom name such as C starts at column 14, while 
>>>> two-letter atom name such as FE starts at column 13. 
>>> 
>>> indicating a rule does exist. 
>> 
>> There are programs that don't read/write the element from columns 
>> 77-78, so this rule still matters, but using it is less reliable, as 
>> Robbie wrote. After I wrote a function that reads pdb files for gemmi, 
>> over the next few years I received feedback about cases in which the 
>> element columns are absent and the element determined from the atom 
>> name is incorrect. The problem is primarily with 4-character atom 
>> names that can't be aligned, because they use all the four columns 
>> anyway. I added such comments to the code [1] when trying to get it 
>> right: 
>> 
>> // Atom names HXXX are ambiguous, but Hg, He, Hf, Ho and Hs (almost) 
>> // never have 4-character names, so H is assumed. 
>> 
>> // Similarly Deuterium (DXXX), but here alternatives are Dy, Db and Ds. 
>> // Only Dysprosium is present in the PDB - in a single entry as of 2022. 
>> 
>> // Old versions of the PDB format had hydrogen names such as "1HB ". 
>> // Some MD files use similar names for other elements ("1C4A" -> C). 
>> 
>> // ... or it can be "C210" 
>> 
>> [1] 
>> https://github.com/project-gemmi/gemmi/blob/148f37b7c6561c3a255a6a4dd75d6bae888e/include/gemmi/pdb.hpp#L302
>>  
> 
>  
> 
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Re: [ccp4bb] a dinosaur asks ... PDB format query

[Harry Powell]

Hi

This is very, very useful and hits on the four-letter name problem that I am 
encountering - thank you. Saves me trying to produce a new design for a 
circular object with an axle…

For the files that I am trying to use, columns 77-78 are present (actually, 
columns 79-80 are there so I can read the atomic charge as well, which is 
useful for my purposes) so I’m hoping that this will be reliable. 

Harry


> On 15 May 2024, at 12:38, Marcin Wojdyr  wrote:
> 
>> 
>>> • Alignment of one-letter atom name such as C starts at column 14, while 
>>> two-letter atom name such as FE starts at column 13.
>> 
>> indicating a rule does exist.
> 
> There are programs that don't read/write the element from columns
> 77-78, so this rule still matters, but using it is less reliable, as
> Robbie wrote. After I wrote a function that reads pdb files for gemmi,
> over the next few years I received feedback about cases in which the
> element columns are absent and the element determined from the atom
> name is incorrect. The problem is primarily with 4-character atom
> names that can't be aligned, because they use all the four columns
> anyway. I added such comments to the code [1] when trying to get it
> right:
> 
>  // Atom names HXXX are ambiguous, but Hg, He, Hf, Ho and Hs (almost)
>  // never have 4-character names, so H is assumed.
> 
>  // Similarly Deuterium (DXXX), but here alternatives are Dy, Db and Ds.
>  // Only Dysprosium is present in the PDB - in a single entry as of 2022.
> 
>  // Old versions of the PDB format had hydrogen names such as "1HB ".
>  // Some MD files use similar names for other elements ("1C4A" -> C).
> 
>  // ... or it can be "C210"
> 
> [1] 
> https://github.com/project-gemmi/gemmi/blob/148f37b7c6561c3a255a6a4dd75d6bae888e/include/gemmi/pdb.hpp#L302



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Re: [ccp4bb] a dinosaur asks ... PDB format query

[Harry Powell]

Sorry - just read that 

>  • Alignment of one-letter atom name such as C starts at column 14, while 
> two-letter atom name such as FE starts at column 13.

indicating a rule does exist.

Harry 

> On 15 May 2024, at 11:54, Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi Ezra
> 
> Thanks for this. 
> 
> In other words, would it be true to say that there are no actual rules about 
> what appears in columns 13-16 because “it's a rose by any other name”?
> 
> Harry
> 
>> On 15 May 2024, at 11:38, Ezra Peisach  wrote:
>> 
>> If you take a look at 
>> https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
>> 
>> you will see the following:
>> 
>> 77 - 78LString(2)element  Element symbol, right-justified.
>> 
>> Going by atom name will get you in trouble.  As you stated calcium vs 
>> Calpha.  The element symbol comes from the chemical component dictionary.
>> 
>> 
>> Ezra
>> 
>> 
>> 
>> On 5/15/24 6:28 AM, Harry Powell wrote:
>>> Hi folks
>>> 
>>> I’m sure that this has been answered many times before (I’m sure that when 
>>> I was young I even read it here…), and I *know* that we should all be using 
>>> mmCIF, but I’m using PDB format files generated by a popular Python module 
>>> and I wanted to check the output against a definitive format definition (if 
>>> that’s not tautology).
>>> 
>>> I noticed this because I was encouraged to try Moorhen and found that a HEM 
>>> (apparently written by this module) did not have the atoms connected with 
>>> bonds in the display.
>>> 
>>> I’m particularly interested in metal atoms here, and want to be 100% sure 
>>> that I’ve found a calcium, say, and not a C-alpha.
>>> 
>>> Q: Is it necessary to check columns 77-78 if I really want to be sure?
>>> 
>>> I’ve read the following, but can’t see anything obvious in “official” PDB 
>>> documentation that what it says here is actually defined anywhere:
>>> 
>>>> Atom names are composed of an atomic (element) symbol right-justified in 
>>>> columns 13-14, and trailing identifying characters left-justified in 
>>>> columns 15-16. A single-character element symbol should not appear in 
>>>> column 13 unless the atom name has four characters (for example, see 
>>>> Hydrogen Atoms). Many programs simply left-justify all atom names starting 
>>>> in column 13. The difference can be seen clearly in a short segment of 
>>>> hemoglobin (entry 3hhb):
>>>> 
>>>> Correct:
>>>> HETATM 1071 FE   HEM A   1   8.128   7.371 -15.022 24.00 16.74 
>>>>  FE
>>>> HETATM 1072  CHA HEM A   1   8.617   7.879 -18.361  6.00 17.74 
>>>>   C
>>>> HETATM 1073  CHB HEM A   1  10.356  10.005 -14.319  6.00 18.92 
>>>>   C
>>>> HETATM 1074  CHC HEM A   1   8.307   6.456 -11.669  6.00 11.00 
>>>>   C
>>>> HETATM 1075  CHD HEM A   1   6.928   4.145 -15.725  6.00 13.25 
>>>>   C
>>>> 
>>>> Incorrect:
>>>> HETATM 1071 FE   HEM A   1   8.128   7.371 -15.022 24.00 16.74 
>>>>  FE
>>>> HETATM 1072 CHA  HEM A   1   8.617   7.879 -18.361  6.00 17.74 
>>>>   C
>>>> HETATM 1073 CHB  HEM A   1  10.356  10.005 -14.319  6.00 18.92 
>>>>   C
>>>> HETATM 1074 CHC  HEM A   1   8.307   6.456 -11.669  6.00 11.00 
>>>>   C
>>>> HETATM 1075 CHD  HEM A   1   6.928   4.145 -15.725  6.00 13.25 
>>>>   C
>>> I’m sure that someone here will say “why don’t you look at *, it’s 
>>> obvious”, in which case - many thanks!
>>> 
>>> help
>>> 
>>> Harry
>>> 
>>> 
>>> 
>>> 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] a dinosaur asks ... PDB format query

[Harry Powell]

Hi Ezra

Thanks for this. 

In other words, would it be true to say that there are no actual rules about 
what appears in columns 13-16 because “it's a rose by any other name”?

Harry

> On 15 May 2024, at 11:38, Ezra Peisach  wrote:
> 
> If you take a look at 
> https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
> 
> you will see the following:
> 
> 77 - 78LString(2)element  Element symbol, right-justified.
> 
> Going by atom name will get you in trouble.  As you stated calcium vs Calpha. 
>  The element symbol comes from the chemical component dictionary.
> 
> 
> Ezra
> 
> 
> 
> On 5/15/24 6:28 AM, Harry Powell wrote:
>> Hi folks
>> 
>> I’m sure that this has been answered many times before (I’m sure that when I 
>> was young I even read it here…), and I *know* that we should all be using 
>> mmCIF, but I’m using PDB format files generated by a popular Python module 
>> and I wanted to check the output against a definitive format definition (if 
>> that’s not tautology).
>> 
>> I noticed this because I was encouraged to try Moorhen and found that a HEM 
>> (apparently written by this module) did not have the atoms connected with 
>> bonds in the display.
>> 
>> I’m particularly interested in metal atoms here, and want to be 100% sure 
>> that I’ve found a calcium, say, and not a C-alpha.
>> 
>> Q: Is it necessary to check columns 77-78 if I really want to be sure?
>> 
>> I’ve read the following, but can’t see anything obvious in “official” PDB 
>> documentation that what it says here is actually defined anywhere:
>> 
>>> Atom names are composed of an atomic (element) symbol right-justified in 
>>> columns 13-14, and trailing identifying characters left-justified in 
>>> columns 15-16. A single-character element symbol should not appear in 
>>> column 13 unless the atom name has four characters (for example, see 
>>> Hydrogen Atoms). Many programs simply left-justify all atom names starting 
>>> in column 13. The difference can be seen clearly in a short segment of 
>>> hemoglobin (entry 3hhb):
>>> 
>>> Correct:
>>> HETATM 1071 FE   HEM A   1   8.128   7.371 -15.022 24.00 16.74  
>>> FE
>>> HETATM 1072  CHA HEM A   1   8.617   7.879 -18.361  6.00 17.74  
>>>  C
>>> HETATM 1073  CHB HEM A   1  10.356  10.005 -14.319  6.00 18.92  
>>>  C
>>> HETATM 1074  CHC HEM A   1   8.307   6.456 -11.669  6.00 11.00  
>>>  C
>>> HETATM 1075  CHD HEM A   1   6.928   4.145 -15.725  6.00 13.25  
>>>  C
>>> 
>>> Incorrect:
>>> HETATM 1071 FE   HEM A   1   8.128   7.371 -15.022 24.00 16.74  
>>> FE
>>> HETATM 1072 CHA  HEM A   1   8.617   7.879 -18.361  6.00 17.74  
>>>  C
>>> HETATM 1073 CHB  HEM A   1  10.356  10.005 -14.319  6.00 18.92  
>>>  C
>>> HETATM 1074 CHC  HEM A   1   8.307   6.456 -11.669  6.00 11.00  
>>>  C
>>> HETATM 1075 CHD  HEM A   1   6.928   4.145 -15.725  6.00 13.25  
>>>  C
>> I’m sure that someone here will say “why don’t you look at *, it’s 
>> obvious”, in which case - many thanks!
>> 
>> help
>> 
>> Harry
>> 
>> 
>> 
>> 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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[ccp4bb] a dinosaur asks ... PDB format query

[Harry Powell]

Hi folks

I’m sure that this has been answered many times before (I’m sure that when I 
was young I even read it here…), and I *know* that we should all be using 
mmCIF, but I’m using PDB format files generated by a popular Python module and 
I wanted to check the output against a definitive format definition (if that’s 
not tautology).

I noticed this because I was encouraged to try Moorhen and found that a HEM 
(apparently written by this module) did not have the atoms connected with bonds 
in the display. 

I’m particularly interested in metal atoms here, and want to be 100% sure that 
I’ve found a calcium, say, and not a C-alpha.

Q: Is it necessary to check columns 77-78 if I really want to be sure?

I’ve read the following, but can’t see anything obvious in “official” PDB 
documentation that what it says here is actually defined anywhere:

> Atom names are composed of an atomic (element) symbol right-justified in 
> columns 13-14, and trailing identifying characters left-justified in columns 
> 15-16. A single-character element symbol should not appear in column 13 
> unless the atom name has four characters (for example, see Hydrogen Atoms). 
> Many programs simply left-justify all atom names starting in column 13. The 
> difference can be seen clearly in a short segment of hemoglobin (entry 3hhb):
> 
> Correct:
> HETATM 1071 FE   HEM A   1   8.128   7.371 -15.022 24.00 16.74  FE
> HETATM 1072  CHA HEM A   1   8.617   7.879 -18.361  6.00 17.74   C
> HETATM 1073  CHB HEM A   1  10.356  10.005 -14.319  6.00 18.92   C
> HETATM 1074  CHC HEM A   1   8.307   6.456 -11.669  6.00 11.00   C
> HETATM 1075  CHD HEM A   1   6.928   4.145 -15.725  6.00 13.25   C
> 
> Incorrect:
> HETATM 1071 FE   HEM A   1   8.128   7.371 -15.022 24.00 16.74  FE
> HETATM 1072 CHA  HEM A   1   8.617   7.879 -18.361  6.00 17.74   C
> HETATM 1073 CHB  HEM A   1  10.356  10.005 -14.319  6.00 18.92   C
> HETATM 1074 CHC  HEM A   1   8.307   6.456 -11.669  6.00 11.00   C
> HETATM 1075 CHD  HEM A   1   6.928   4.145 -15.725  6.00 13.25   C

I’m sure that someone here will say “why don’t you look at *, it’s 
obvious”, in which case - many thanks!

help

Harry



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Re: [ccp4bb] AlphaFold3 Transparency and Reproducibility

[Harry Powell]

Do Nature do embarrassment?

H

> On 14 May 2024, at 10:54, Frank von Delft 
> <bcb385fe5582-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> What we really need is a tweet from Nature, declaring their embarrassment at 
> having been suckered into becoming DeepMind's advertising arm.  
> 
> 
> On 14/05/2024 01:56, Paul Adams wrote:
>> 
>> The letter may have had (or helped have) an impact already:
>> 
>> On X today from Pushmeet Kohli @ DeepMind
>> 
>> "We love the excitement & results from the community on AlphaFold 3 and are 
>> doubling the AF Server daily job limit to 20. Happy to also share that we're 
>> working on releasing the AF3 model (incl weights) for academic use, which 
>> doesn’t depend on our research infra, within 6 months".
>> 
>> 
>>> On May 13, 2024, at 11:11 AM, Wankowicz, Stephanie 
>>> <d0e1738c7100-dmarc-requ...@jiscmail.ac.uk> wrote:
>>> 
>>> If it does what it claims – incredibly impressive. The issue we have is 
>>> there is no way to verify or validate the claims it is making. 
>>> 
>>> The letter is a call and start of a conversation about how the 
>>> ever-changing landscape of communication and publication of science should 
>>> be.
>>> 
>>> -Stephanie Wankowicz
>>> From: CCP4 bulletin board  on behalf of Krieger, 
>>> James M 
>>> Sent: Monday, May 13, 2024 10:22 AM
>>> To: CCP4BB@JISCMAIL.AC.UK 
>>> Subject: Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility
>>>  
>>> This Message Is From an External Sender 
>>> This message came from outside your organization. 
>>> It definitely is impressive but it also has clear limitations
>>> 
>>>> On 13 May 2024, at 15:22, Sylvia Fanucchi 
>>>> <d0c4e77ae410-dmarc-requ...@jiscmail.ac.uk> wrote:
>>>> 
>>>> 
>>>> 
>>>> You don't often get email from 
>>>> d0c4e77ae410-dmarc-requ...@jiscmail.ac.uk. Learn why this is important
>>>> 
>>>> Is it just me who is really impressed by it? Am I missing something?
>>>> 
>>>> Get Outlook for Android
>>>> From: CCP4 bulletin board  on behalf of Rafael 
>>>> Marques 
>>>> Sent: Monday, May 13, 2024 3:13:16 PM
>>>> To: CCP4BB@JISCMAIL.AC.UK 
>>>> Subject: Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility
>>>>  
>>>> I tried it yesterday and I was really shocked by how fast it is. When I 
>>>> was preparing to submit my second job, the first one was already finished, 
>>>> which made me think that I was definitely doing something wrong. Probably 
>>>> I was...
>>>> 
>>>> Best wishes 
>>>> 
>>>> Rafael Marques 
>>>> 
>>>> 
>>>> On 13 May 2024 09:53, Harry Powell 
>>>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>>>> Hi folks 
>>>> 
>>>> This arrived in my inbox this morning, and I believe that it may provoke 
>>>> some discussion…
>>>> 
>>>> Wikipedia tells me: στέργει γὰρ οὐδεὶς ἄγγελον κακῶν ἐπῶν 
>>>> 
>>>> Best wishes! 
>>>> 
>>>> Harry 
>>>> 
>>>> >From: Stephanie Wankowicz  
>>>> >Sent: Saturday, May 11, 2024 3:31 PM 
>>>> >To: James Fraser ; Pedro Beltrao 
>>>> > ; Benjamin Cravatt ; Roland 
>>>> > Dunbrack ; Anthony Gitter 
>>>> > ; Kresten Lindorff-Larsen ; 
>>>> > Sergey Ovchinnikov ; Polizzi, Nicholas F. 
>>>> > ; Brian Shoichet 
>>>> > 
>>>> >Subject: AlphaFold3 Transparency and Reproducibility 
>>>> > 
>>>> > 
>>>> >This email from mullane.stepha...@gmail.com originates from outside 
>>>> > Imperial. Do not click on links and attachments unless you recognise the 
>>>> > sender. If you trust the sender, add them to your safe senders list 
>>>> > <https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email 
>>>> > stamping for this address. 
>>>> > 
>>>> >Hello, 
>>>> > 
>>>> > 
>>>> >As many of you, we were incredibly disappointed with the lack of code 
>>>> > or even executables accompanying the publication of AlphaFold3 in 
>>>> > Nature. Alpha

Re: [ccp4bb] Experimental phasing Selenomethionine data collection etc. tips

[Harry Powell]

Hi

With this in mind, I have found the easiest way to generate AlphaFold models 
(for those not in the DB) is actually in CCP4 Cloud-remote - makes MR using AF 
models a real doddle. 

See the Tutorials (in particular on MR) available with CCP4 Cloud.

Harry

> On 14 May 2024, at 09:20, Randy John Read  wrote:
> 
> Dear Marco,
> 
> You don’t mention here or in the earlier thread whether you tried AlphaFold 
> models and, if you did, how you prepared them for MR. I’m happy to hear of 
> any case where we still need experimental phasing methods to solve new 
> protein structures, but we’ve seen very few examples where AlphaFold models 
> didn’t work!
> 
> I’m probably not the only one who would be delighted to take a look at the 
> problem to see what we can learn from it, if AlphaFold models really aren’t 
> working.
> 
> Now, back to your question: to prepare for a SAD phasing experiments one 
> place I would look would be Tom Terwilliger’s recent papers on planning and 
> analysing SAD experiments (https://doi.org/10.1107/S2059798315019269, 
> https://doi.org/10.1107/S2059798315019403) as well as other information on 
> this from the Phenix website, including the YouTube tutorials.
> 
> Best wishes,
> 
> Randy Read
> 
>> On 14 May 2024, at 01:17, Marco Bravo 
>>  wrote:
>> 
>> Hello all,
>> I have a data collection trip next week and plan to collect data on 
>> selenomethionine derivative crystals at the al831 beamline. Are there any 
>> resources, tips, tutorials, literature etc. That you can recommend to help 
>> me prepare for these experiments. Also is there a way to plug in the 
>> experimental data into ccp4 cloud to do the automatic structure solution? Do 
>> I need native and derivative data to solve the structure? Last trip I 
>> collected a seemingly 2.8 angstrom resolution data on a crystal of the 
>> native protein but could not get a solution depsite extensive molecular 
>> replacement attempts. It seems that assigning a space group for the crystals 
>> has been troublesome as well. here is my last thread I posted about the 
>> issue for reference.
>> 
>> https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind2402&L=CCP4BB&O=D&X=CCE6DFA19FA3D40346&Y=mbrav005%40ucr.edu&P=112302
>> 
>> 
>> 
>> 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 http://www.jiscmail.ac.uk/CCP4BB, a 
>> mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions are 
>> available at https://www.jiscmail.ac.uk/policyandsecurity/
> 
> -
> 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:
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> 
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[ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

[Harry Powell]

Hi folks

This arrived in my inbox this morning, and I believe that it may provoke some 
discussion…

Wikipedia tells me: στέργει γὰρ οὐδεὶς ἄγγελον κακῶν ἐπῶν

Best wishes!

Harry

>From: Stephanie Wankowicz  
>Sent: Saturday, May 11, 2024 3:31 PM
>To: James Fraser ; Pedro Beltrao 
> ; Benjamin Cravatt ; Roland 
> Dunbrack ; Anthony Gitter 
> ; Kresten Lindorff-Larsen ; 
> Sergey Ovchinnikov ; Polizzi, Nicholas F. 
> ; Brian Shoichet 
>Subject: AlphaFold3 Transparency and Reproducibility
> 
> 
>This email from mullane.stepha...@gmail.com originates from outside 
> Imperial. Do not click on links and attachments unless you recognise the 
> sender. If you trust the sender, add them to your safe senders list 
>  to disable email stamping 
> for this address. 
> 
>Hello,
> 
> 
>As many of you, we were incredibly disappointed with the lack of code or 
> even executables accompanying the publication of AlphaFold3 in Nature. 
> AlphaFold3 was released without the means to test and use the software in a 
> high-throughput manner. This does not align with the principles of scientific 
> research, which rely on the ability of the community to evaluate, use, and 
> build upon existing work. 
> 
> 
> 
>We have written a letter, which will be posted on Zenodo and submitted as 
> a Letter to the Editor in the coming days.
> 
> 
> 
>Please see the entire letter here. 
> 
>  If you want to endorse this letter, please fill out your name, affiliation, 
> and email in the form. 
> 
> 
> 
>Additionally, a PDF version of the letter can be found here 
> .
>  
> 
> 
> 
>Thank you, 
> 
> 
> 
>Stephanie Wankowicz, UCSF
> 
>Pedro Beltrao, ETH
>Benjamin Cravatt, Scripps
>Roland Dunbrack, FCCC
>Anthony Gitter, UW Madison
>Kresten Lindorff-Larsen, Copenhagen
>Sergey Ovchinnikov, MIT
>Nicholas Polizzi, DFCI/HMS
>Brian Shoichet, UCSF
>James Fraser, UCSF
> 
> 



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[ccp4bb] replacement for Scientific Linux

[Harry Powell]

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


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Re: [ccp4bb] Microscope camera

[Harry Powell]

Hi Pat

Depends on how much you want to spend.

I’d start with a web search for “webcam astrophotography”, which should show 
options on how to remove a webcam’s lens and mount the cam (not the kens, of 
course!) on another optical instrument.

Back in the day, I had a Philips webcam that had a screw-out lens - this device 
was used by amateur astronomers as a cheap way into astrophorography. Philips 
no longer seem to make webcams, but (from what I remember) this was 
plug-and-play, and used the drivers on my Mac.

You could go for a mirrorless interchangeable lens camera - Nikon actually have 
their own webcam utility to turn your DSLR/mirrorless into a suitable device, 
and this would be most likely to use the SLR mount. E-Bay have Nikon bodies 
starting at around $200 today.

Harry



> On 24 Apr 2024, at 22:15, Patrick Loll  wrote:
> 
> Greetings, hive mind,
> 
> We have an old (but still useful) Nikon SMZ stereomicroscope that we use for 
> mounting crystals. I’d like to attach a digital camera to the phototube, both 
> to capture crystal images for archival purposes, and also to live-stream as a 
> teaching tool. 
> 
> I’d be grateful for any suggestions for an inexpensive option here. 
> 
> When this camera was new we used it with an SLR that captured images on 
> *film* (this is where the students gasp). We’ve since gone through one 
> digital camera that probably still works, but the interface and software have 
> become obsolescent. Meanwhile, the microscope keeps on truckin’; interesting 
> to reflect on the relative lifetimes of analog vs. digital tools…
> 
> Thanks in advance for any suggestions,
> 
> Pat
> 
> 
> ---
> Patrick J. Loll, Ph. D.  (he, him, his)
> Professor of Biochemistry & Molecular Biology
> Drexel University College of Medicine
> Room 10-102 New College Building
> 245 N. 15th St., Mailstop 497
> Philadelphia, PA  19102  USA
> 
> (215) 762-7706
> pjl...@gmail.com
> pj...@drexel.edu
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Rescale merged data?

[Harry Powell]

Hi Clemens

I’m “quite”* surprised. Do the authors of these programs offer any explanation 
as to why the scaling programs (given that these are the ones that usually 
provide F/I information for subsequent programs) bother to calculate sigmas if 
they’re going to be ignored?

Harry

* for “quite” surprised, read “you could have knocked me down with a feather”.


> On Thu, Apr 18, 2024 at 09:22:04AM +0100, Harry Powell wrote:
>> Only comment is that (surely) any decent refinement program these days
>> would down-weight any reflections with negligible I/sig(I) (for example,
>> those in the “unobserved” high resolution regions) so that they do not
>> contribute (significantly) to the refinement.
> 
> Not all refinement programs use sigmas as far as we know.



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Re: [ccp4bb] Rescale merged data?

[Harry Powell]

Hi

Only comment is that (surely) any decent refinement program these days would 
down-weight any reflections with negligible I/sig(I) (for example, those in the 
“unobserved” high resolution regions) so that they do not contribute 
(significantly) to the refinement. Or am I wrong (I don’t mind being wrong, and 
since I am a little rusty in these mattrers I would be very happy to be 
educated)?

Doesn’t Aimless produce a table with the cumulative statistics at various 
resolution limits? So you don’t even need to re-scale & merge to get the stats 
to whatever your chosen high resolution limit is (I’d choose CC -1/2 = 0.30, as 
Doeke suggests)? Do HKL or XSCALE do the same (sorry, I haven’t looked at their 
output for quite some time)?

Just my two ha’porth

Harry

> On 17 Apr 2024, at 21:35, Hekstra, Doeke Romke  
> wrote:
> 
> Hi Matt,
>  
> I appreciate disagreement and comments from colleagues. My two cents are that 
> it seems unnecessary to repeat scaling and merging, or any earlier step. If 
> you want to remove structure factor amplitudes or merged intensities from the 
> MTZ file you can do so using MTZUTILS or similar functionality in CCP4 
> (https://www.ccp4.ac.uk/html/mtzutils.html#generalresolution). For 
> refinement, you can specify the desired resolution range in your favorite 
> refinement program.
>  
> My personal convention is to use CC1/2 = 0.30 as the point to which retain 
> data and  = 2 as the nominal resolution of the dataset. If you have 
> the HKL2000 scaling log, you should be able to retrieve this information. I 
> frankly wish we’d just deposit all data in the PDB rather than truncate based 
> on some criterion or another.
>  
> Best, Doeke
>  
> From: Matt Mcleod  
> Sent: Wednesday, April 17, 2024 4:12 PM
> To: Hekstra, Doeke Romke 
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Rescale merged data?
>  
> Sure thing.
>  
> A former student left somewhere between 30-50 datasets but they scaled the 
> data to the detector corners (or maybe edge) in HKL2000.  There are many of 
> the high-resolution bins with no reflections in them.  He then went forward 
> and merged this data, presumably in HKL2000 again and did his model 
> building/refinement.   We now need to re-refine the models against this data 
> for publication but we need a more suitable resolution cutoff for the data. 
>  
> Rather than go back and index/integrate all the data and then rescale the 
> data to a more appropriate place (then merge), I was wondering if there was a 
> way to take the merged reflections as either .sca or .mtz (from 
> scalepacktomtz output) and then rescale to a more appropriate resolution.  It 
> doesn't seem like the student left unmerged data.  
>  
> So, nothing fancy (aniostropy etc), there is just a lot of data that needs to 
> be adjusted and I am trying to avoid reprocessing all the frames again.
>  
> Matt
>  
> On Wed, 17 Apr 2024 at 15:59, Hekstra, Doeke Romke 
>  wrote:
> Hi Matt,
> 
> It would be helpful if you could describe your case in more detail. Do you 
> want to change the resolution cutoff after scaling? Do you want to keep more 
> data? Fewer? Or do you mean something different such as truncation to 
> generate amplitudes, application of anisotropic resolution cutoffs,  or 
> outlier rejection? Are you referring to data that were scaled in HKL2000?
> 
> Best, Doeke
> 
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Matt McLeod
> Sent: Wednesday, April 17, 2024 3:04 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Rescale merged data?
> 
> Hi all,
> 
> I am looking at a old students data and it looks like they didn't properly 
> cut off the data during scaling.  All of the files I have appear to be the 
> merged .sca (or mtz after converting with scalepacktomtz) - is there a way to 
> retruncate the data after merging or do I have to reprocess the data?
> 
> Thanks,
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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>  
> -- 
> Matthew Jordan McLeod, PhD
> Post-Doctoral Fellow - Cornell University
> 
> 
> 
> 
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Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

[Harry Powell]

Hi Fred

There *used* to be CCP14 (for small molecules and powders), but this lost 
funding many years ago.

In the UK, I’d contact the National Crystallography Service at Southampton to 
see if they have any pointers to bulletin boards - I have a vague recollection 
of one but can’t remember the details. Simon Coles is in charge there and may 
be able to help.

John Warren (now at Manchester) used to be very active on the BB I remember 
existing - he may be able to help directly with things like this.

As for your particular question, someone here may be familiar with SHELXL .ins 
files and be able to answer you directly - 30 years ago I *would* have been 
able to spot problems in these files at a glance, but lack of practice means 
that I doubt I could do the same these days!

best wishes

Harry

> On 12 Mar 2024, at 09:00, Fred Vellieux  wrote:
> 
> Hi folks,
> 
> I have a simple question: is there an electronic bulletin board for 
> small-molecule crystallography? I have checked the list of CCP projects and 
> there is no CCP-project for small molecule crystallography in the list.
> 
> I am trying to run SHELXL, and it fails with the cryptic message "** BAD ATOM 
> OR UNKNOWN INSTRUCTION **".
> 
> The alternative for me would be of course to use software meant for 
> macromolecular cystallography (that I know) on small molecule diffraction 
> data. And using the small molecule coordinate files transformed to a suitable 
> format. I don't know if this is feasible or even advised. Probably not.
> 
> Thanks,
> 
> Fred.
> 
> -- 
> MedChem, 1st F. Medicine, Charles University
> BIOCEV, Vestec, Czech Republic
> 
> 
> 
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Re: [ccp4bb] Superimposition save as PDB for ccp4 refmac question

[Harry Powell]

Hi Marco

You could always try the CCP4 tools (since this is the CCP4 BB…) “superpose” or 
“gesamt” to superpose (or is it “superimpose”? discuss…).

Harry

> On 28 Feb 2024, at 00:53, Marco Bravo  wrote:
> 
> Hello all,
> Does anyone know how to save a superimposed pymol or chimerax session as a 
> PDB file in correct format so that I can used it for ccp4 refmac? I am trying 
> to superimpose a protein with DNA bound onto the same protein from a 
> different species without the DNA. I just want the DNA from the protein-DNA 
> complex to be superimposed onto the apo protein structure. I have done the 
> superimposition and got rid of the protein from the original protein-DNA 
> complex and now have the DNA with the apo protein structure. When I try to 
> use this new PDB filer for refmac or even MR I get this error.  Refmac:  
> Input coordinate file is not complete. Does anyone know how to properly do 
> this ? 
> 
> Thank you
> 
> 
> 
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Re: [ccp4bb] [ccp4bb] mmCIF files from PDB format for AlphaFill

[Harry Powell]

Hi folks

I’ve made considerable progress in getting to the bottom of this problem. From 
what I can gather, AlphaFold writes “modelCIF”, which is not quite the same as 
“mmCIF”, and just saying “CIF” is not unambiguous. So I guess I should have 
been more aware of this when posting my original question.

With regard to the programs mentioned (note these are not all my analyses, so 
please don’t shoot the messenger!) - 

* Pymol produces a file which is some way from “standard” and would need work 
to make it usable (so something for Schroedinger to work on, perhaps).

* Coot *almost* produces a file that can be used  (authors aware).

* Gemmi is also close, but no cigar  (authors aware).

* I’d guess that Maxit was last revised many years before modelCIF was 
introduced so I don’t think this would be a fruitful path to follow (the build 
failed on my newly installed Linux because it was an unrecognised system, and 
the most recent binary was built in 2008).

Many thanks to everyone who took the time to read and answer my question!

Harry



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Re: [ccp4bb] [ccp4bb] mmCIF files from PDB format for AlphaFill

[Harry Powell]

Hi Nick

doesn’t look encouraging - 

> ~/maxit/maxit-v8.120-prod-bin-linux/bin/maxit-v8.01-O -i 1A9W_A.pdb -o 1
> Initial filter libaray failed

No need to worry - since the pdb2cif from the pdb-redo team works, and they’re 
the ones who produce AlphaFill, they can always help out if (when) things go 
wrong!

best wishes and thanks again 

Harry

> On 23 Feb 2024, at 14:00, Nicholas Clark 
> <b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi Harry,
> 
> Unfortunately, I did not see that the latest binary update was from 2008. I 
> do not have access to any newer binaries for Linux, as I'm on MacOS. 
> 
> Maybe you can use the MineProt software from the quote I mentioned previously 
> to (in a roundabout way) accomplish the CIF file generation?
> 
> "“Huiwenke:
> 
> MineProt (https://github.com/huiwenke/MineProt) can be used to curate 
> AlphaFold predictions, where PDBs are converted into CIFs using MAXIT 
> (https://sw-tools.rcsb.org/apps/MAXIT/index.html). The generated CIF files 
> support Mol* visualization and downstream analysis such as AlphaFill 
> (https://github.com/PDB-REDO/alphafill).
> Another possible option is to use MAXIT directly, while it needs several 
> additional steps to make generated CIF files support older versions of Mol*. 
> Please refer to 
> https://github.com/huiwenke/MineProt/blob/master/web/api/pdb2alphacif/index.php.”";
> 
> Best,
> 
> Nick
> 
> 
> 
> -- Forwarded message -
> From: Nicholas Clark 
> Date: Fri, Feb 23, 2024 at 8:03 AM
> Subject: Re: [ccp4bb] mmCIF files from PDB format for AlphaFill
> To: Harry Powell 
> Cc: Harry Powell 
> 
> 
> Hi Harry,
> 
> MAXIT binaries are located here:
> 
> https://sw-tools.rcsb.org/apps/MAXIT/binary.html
> 
> Best,
> 
> Nick
> 
> 
> 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
> 
> Cell: 716-830-1908
> 
> 
> On Fri, Feb 23, 2024 at 7:58 AM Harry Powell  
> wrote:
> Hi Nick
> 
> Thanks for responding, but see my earlier reply to Avinash - the build 
> doesn’t like my brand-new, hot off the production line Linux and the location 
> of pre-built exes is not obvious.
> 
> best wishes
> 
> Harry
> 
> > On 23 Feb 2024, at 12:43, Nicholas Clark 
> > <b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote:
> > 
> > Hi Harry,
> > 
> > Have you tried MAXIT from the PDB? It can be installed locally:
> > 
> > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsw-tools.rcsb.org%2Fapps%2FMAXIT%2Findex.html&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C2f0b5620024b4430110208dc346f20b3%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442899115806976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=W3%2BzEKkB1%2BpJznVNIUjTDqMcww3v3YxylxULJCOLgf4%3D&reserved=0
> > 
> > Best,
> > 
> > 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
> > 
> > Cell: 716-830-1908
> > 
> > 
> > On Fri, Feb 23, 2024 at 7:36 AM Harry Powell 
> > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> > Hi Martin, Marcin, Arturo, Avinash
> > 
> > First off, I’m **NOT** saying that there’s anything wrong with the CIF 
> > files produced by these routes - just that AlphaFill doesn’t like them (it 
> > *does* like CIFs from AlphaFold - 
> > 
> > > alphafill process alphafold.cif filled.cif
> > > 1DKE =--- 
> > >  14%
> > 
> > But (while Alphafold models are wonderful, have put us all out of jobs, 
> > etc, etc) they are just a starting point for my project and, for this 
> > purpose, no good in themselves.
> > 
> > Martin, Marcin - gemmi would be a good way to go, but - 
> > 
> > > >>> import gemmi
> > > >>> structure = gemmi.read_structure('old.pdb')
> > > >>> structure.make_mmcif_document().write_file('new.cif')
> > > 
> > > alphafill process new.cif filled.cif
> > > Structure file does not seem to contain polymers, perhaps 
> > > pdbx_poly_seq_scheme is missing?
> > 
> > > gemm

Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

[Harry Powell]

Many thanks to all that replied.

Ida’s suggestion of pdb2cif from the PDB-REDO people is the only one that’s 
worked to date (“worked” in this context means produces a CIF that AlphaFill 
accepts without complaining - can’t imagine why).

Now off to play with my voids…

As they say, standards are wonderful - that’s why there are so many of them.

Have a great weekend

Harry

> On 23 Feb 2024, at 12:46, Ida de Vries  wrote:
> 
> Dear Harry, 
> 
> You could also try to use pdb2cif from the cif-tools: 
> https://github.com/PDB-REDO/cif-tools. The only strict requirement for a PDB 
> formatted file is that it has a HEADER at the first line. After installation, 
> running from the command line is as simple as: pdb2cif file.pdb . 
> 
> Best regards, 
> 
> Ida
> 
> On 23-02-2024 13:43, Nicholas Clark wrote:
>> Hi Harry,
>> 
>> Have you tried MAXIT from the PDB? It can be installed locally:
>> 
>> https://sw-tools.rcsb.org/apps/MAXIT/index.html
>> 
>> Best,
>> 
>> 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
>> 
>> Cell: 716-830-1908
>> 
>> 
>> On Fri, Feb 23, 2024 at 7:36 AM Harry Powell 
>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>> Hi Martin, Marcin, Arturo, Avinash
>> 
>> First off, I’m **NOT** saying that there’s anything wrong with the CIF files 
>> produced by these routes - just that AlphaFill doesn’t like them (it *does* 
>> like CIFs from AlphaFold - 
>> 
>> > alphafill process alphafold.cif filled.cif
>> > 1DKE =---  
>> > 14%
>> 
>> But (while Alphafold models are wonderful, have put us all out of jobs, etc, 
>> etc) they are just a starting point for my project and, for this purpose, no 
>> good in themselves.
>> 
>> Martin, Marcin - gemmi would be a good way to go, but - 
>> 
>> > >>> import gemmi
>> > >>> structure = gemmi.read_structure('old.pdb')
>> > >>> structure.make_mmcif_document().write_file('new.cif')
>> > 
>> > alphafill process new.cif filled.cif
>> > Structure file does not seem to contain polymers, perhaps 
>> > pdbx_poly_seq_scheme is missing?
>> 
>> > gemmi convert old.pdb gemmi.cif
>> > alphafill process gemmi.cif filled.cif
>> > Structure file does not seem to contain polymers, perhaps 
>> > pdbx_poly_seq_scheme is missing?
>> 
>> :-(
>> 
>> Arturo - I’ve never scripted PyMol, but saving as CIF from the graphics 
>> interface - 
>> 
>> > alphafill process pymol.cif filled.cif
>> > Structure file does not seem to contain polymers, perhaps 
>> > pdbx_poly_seq_scheme is missing?
>> 
>> 
>> Avinash - Maxit *might* work, but I fell at the first hurdle - although the 
>> help page says 
>> 
>> > Note: It is highly recommended to utilize binary distribution,
>> 
>> it’s not obvious where to get this. So I download and try to build from 
>> source, and get (after unpacking and setting ENVs) - 
>> 
>> > make
>> > Warning: this seems to be an unsupported operating system.
>> >  
>> > Supported systems are:
>> >   SunOS .. version 4.1.x and 5.2 or higher
>> >   Linux .. any version 
>> >   SGI IRIX ... version 5.3-6.4
>> > make: *** [Makefile:32: compile] Error 1
>> 
>> which is odd, because this is a new Linux system installed this week
>> 
>> > [hpowell@ld-mjeste3 maxit-v11.100-prod-src]$ more /etc/redhat-release
>> > Rocky Linux release 9.3 (Blue Onyx)
>> 
>> best wishes all
>> 
>> Harry
>> 
>> 
>> 
>> > 
>> > On 23 Feb 2024, at 11:55, Martin Malý  wrote:
>> > 
>> > Dear Harry,
>> > 
>> > You can try to read your PDB file and save it as mmCIF using gemmi:
>> > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgemmi.readthedocs.io%2Fen%2Flatest%2Fmol.html%23reading&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C211237fcc56e48de6bda08dc346bc149%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442885643631876%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=kPhUsO0dv9gty%2F08hhxQw5IlXdJGu%2BkXlxyLUKYNLm4%3D&reserved=0
>> > https://n

Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

[Harry Powell]

Hi Martin, Marcin, Arturo, Avinash

First off, I’m **NOT** saying that there’s anything wrong with the CIF files 
produced by these routes - just that AlphaFill doesn’t like them (it *does* 
like CIFs from AlphaFold - 
 
> alphafill process alphafold.cif filled.cif
> 1DKE =---  14%

But (while Alphafold models are wonderful, have put us all out of jobs, etc, 
etc) they are just a starting point for my project and, for this purpose, no 
good in themselves.

Martin, Marcin - gemmi would be a good way to go, but - 

> >>> import gemmi
> >>> structure = gemmi.read_structure('old.pdb')
> >>> structure.make_mmcif_document().write_file('new.cif')
> 
> alphafill process new.cif filled.cif
> Structure file does not seem to contain polymers, perhaps 
> pdbx_poly_seq_scheme is missing?

> gemmi convert old.pdb gemmi.cif
> alphafill process gemmi.cif filled.cif
> Structure file does not seem to contain polymers, perhaps 
> pdbx_poly_seq_scheme is missing?

:-(

Arturo - I’ve never scripted PyMol, but saving as CIF from the graphics 
interface - 

> alphafill process pymol.cif filled.cif
> Structure file does not seem to contain polymers, perhaps 
> pdbx_poly_seq_scheme is missing?


Avinash - Maxit *might* work, but I fell at the first hurdle - although the 
help page says 

> Note: It is highly recommended to utilize binary distribution,

it’s not obvious where to get this. So I download and try to build from source, 
and get (after unpacking and setting ENVs) - 

> make
> Warning: this seems to be an unsupported operating system.
>  
> Supported systems are:
>   SunOS .. version 4.1.x and 5.2 or higher
>   Linux .. any version 
>   SGI IRIX ... version 5.3-6.4
> make: *** [Makefile:32: compile] Error 1

which is odd, because this is a new Linux system installed this week

> [hpowell@ld-mjeste3 maxit-v11.100-prod-src]$ more /etc/redhat-release
> Rocky Linux release 9.3 (Blue Onyx)

best wishes all

Harry



> 
> On 23 Feb 2024, at 11:55, Martin Malý  wrote:
> 
> Dear Harry,
> 
> You can try to read your PDB file and save it as mmCIF using gemmi:
> https://gemmi.readthedocs.io/en/latest/mol.html#reading
> https://gemmi.readthedocs.io/en/latest/mol.html#id3
> 
> Best wishes,
> Martin
> 
> 
>> Hi folks
>> 
>> I am in the situation of having coordinates of apoproteins (i.e. polypeptide 
>> chains without prosthetic groups) in PDB format - but I need them in mmCIF 
>> format so I can run them through a locally built copy of AlphaFill.
>> 
>> I need something I can install locally, so web services are a no-no.
>> 
>> I’ve tried obabel and Coot to convert the PDB to mmCIF, but AlphaFill 
>> doesn’t like the files produced. Before I spend time searching through 
>> available options on the interweb, does anyone know of a utility that can 
>> provide me with suitable mmCIFs? Note that I *only* have the coordinates 
>> because they come from modelling.
>> 
>> I’m assuming that I’ve run obabel and Coot correctly!
>> 
>> obabel:
>> 
>>> alphafill process protein_obabel.cif  filled.cif
>>> Structure file does not seem to contain polymers, perhaps 
>>> pdbx_poly_seq_scheme is missing?
>> 
>> Coot:
>> 
>>> alphafill process protein_A-coot-0.cif filled.cif 
>>> Error reading file ‘protein_A-coot-0.cif'
>>>  >> parse error at line 2: This file does not seem to be an mmCIF file
>> 
>> Harry
>> 
>> 
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Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

[Harry Powell]

Hi Marta

Thanks for this.

Unfortunately, I can’t use a web resource for this - I have to do it locally 
(partly because I’m providing a web service, and it’s better not to blame other 
providers when my service fails).

I’d be likely to be doing this > 1000 times a day (every day from now until I 
retire ;-)); I’ve found with other web resources that this can trigger DDOS 
protection systems (e.g. being temporarily banned…).

best wishes

Harry

> On 23 Feb 2024, at 11:41, Marta Martínez  wrote:
> 
> Hi Harry
> 
> I use this link: https://mmcif.pdbj.org/converter/
> 
> to convert pdb to mmCIF .  Hope, it was usuful for your modelled coodinates.
> 
> Regards
> 
> Marta
> 
> 
> 
> El 2024-02-23 12:32, Harry Powell escribió:
> 
>> Hi folks
>> 
>> I am in the situation of having coordinates of apoproteins (i.e. polypeptide 
>> chains without prosthetic groups) in PDB format - but I need them in mmCIF 
>> format so I can run them through a locally built copy of AlphaFill.
>> 
>> I need something I can install locally, so web services are a no-no.
>> 
>> I’ve tried obabel and Coot to convert the PDB to mmCIF, but AlphaFill 
>> doesn’t like the files produced. Before I spend time searching through 
>> available options on the interweb, does anyone know of a utility that can 
>> provide me with suitable mmCIFs? Note that I *only* have the coordinates 
>> because they come from modelling.
>> 
>> I’m assuming that I’ve run obabel and Coot correctly!
>> 
>> obabel:
>> 
>>> alphafill process protein_obabel.cif  filled.cif
>>> Structure file does not seem to contain polymers, perhaps 
>>> pdbx_poly_seq_scheme is missing?
>> 
>> Coot:
>> 
>>> alphafill process protein_A-coot-0.cif filled.cif 
>>> Error reading file ‘protein_A-coot-0.cif'
>>>  >> parse error at line 2: This file does not seem to be an mmCIF file
>> 
>> Harry
>> 
>> 
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[ccp4bb] mmCIF files from PDB format for AlphaFill

[Harry Powell]

Hi folks

I am in the situation of having coordinates of apoproteins (i.e. polypeptide 
chains without prosthetic groups) in PDB format - but I need them in mmCIF 
format so I can run them through a locally built copy of AlphaFill.

I need something I can install locally, so web services are a no-no.

I’ve tried obabel and Coot to convert the PDB to mmCIF, but AlphaFill doesn’t 
like the files produced. Before I spend time searching through available 
options on the interweb, does anyone know of a utility that can provide me with 
suitable mmCIFs? Note that I *only* have the coordinates because they come from 
modelling.

I’m assuming that I’ve run obabel and Coot correctly!

obabel:

> alphafill process protein_obabel.cif  filled.cif
> Structure file does not seem to contain polymers, perhaps 
> pdbx_poly_seq_scheme is missing?

Coot:

> alphafill process protein_A-coot-0.cif filled.cif 
> Error reading file ‘protein_A-coot-0.cif'
>  >> parse error at line 2: This file does not seem to be an mmCIF file

Harry


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Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

[Harry Powell]

Hi Graeme (I may well have mentioned this when we shared an office) et al

I’ll add something from my small-molecule crystallography days, when we used 
point detectors - so this would be pre-1996 which was the last time I used one 
of these machines.

I don’t remember which structure it was (feel free to go through the CSD to 
check on my behalf, but many structures were not deposited in those days and 
languish in a PhD thesis!); I had a dataset with three 90º angles, but the 
processing statistics (and overall cell volume) indicated quite plainly that it 
was monoclinic (probably P21). I re-refined the unit cell as if it were 
triclinic and the “best” 90 degree angle with the smallest ESD was the one that 
corresponded to the monoclinic beta; the two 90º angles refined away from their 
true value more.

A result of that experiment was that (since then) I never assumed that the 
values of the angles from the data processing showed unambiguously that I had a 
high symmetry solution. I believe that Pointless arose after a 
hexagonal/C-centred orthorhombic ambiguity arose (but my memory could be faulty 
here).

Best wishes

Harry

> On 23 Feb 2024, at 09:58, Winter, Graeme (DLSLtd,RAL,LSCI) 
> <6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi Huw
> 
> (first: thank to Phil for picking this up; it caused much confusion)
> 
> While I get where you are coming from, it is still from a mathematical 
> standpoint correct to consider e.g. a tetragonal crystal as monoclinic - P21 
> is a subgroup of P43212 (say) so strictly it is possible and correct - if 
> experimentally unlikely - to have the situation we are discussing here occur. 
> 
> Also, under merging data to investigate twinning is a current bb topic.
> 
> Telling users to “fiddle the parameters” so that the strict test is satisfied 
> feels like a non-ideal answer: a warning when importing such data could be 
> legitimate e.g. “hmm I note a = b and al=be=ga=90 _exactly_ this is unusual, 
> I hope you know what you are doing” rather than a flat out error.
> 
> Literally I got involved as I had a dials user ask me how to do this 
> parameter fiddling in a more niche case and I thought that was a suboptimal 
> solution to an artificial problem :-) 
> 
> On a personal note, I think it is important that the tools we develop still 
> allow people to explore problems rather than railroading them down one true 
> route which is the only allowed way to look at a problem: we learn a lot by 
> exploring odd corners as here. 
> 
> Best wishes Graeme
> 
>> On 23 Feb 2024, at 09:49, Huw Jenkins  wrote:
>> 
>> [You don't often get email from h.t.jenk...@me.com. Learn why this is 
>> important at https://aka.ms/LearnAboutSenderIdentification ]
>> 
>> Hi Graeme,
>> 
>>> On 21 Feb 2024, at 16:52, Winter, Graeme (DLSLtd,RAL,LSCI) 
>>> <6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:
>>> 
>>> Processing a data set in lower than necessary symmetry e.g. tetragonal as 
>>> monoclinic you _cannot_ import the merged MTZ file into i2 because it is 
>>> impossible to have 90 degree angles for P21
>> 
>> I had a look at the code in CCP4i2 that generates the errors in the 
>> screenshots you posted. The first one is only generated if two cell 
>> parameters are *exactly* equal and the second is generated when beta is 
>> between 89. and 90.0001 degrees.
>> 
>> I think these tests should only fail if the data were processed assuming 
>> higher symmetry so that unit cell parameters were restrained and then the 
>> space group changed to a lower symmetry one. Isn't the correct approach when 
>> the true symmetry is lower than originally assumed to repeat the data 
>> processing without applying constraints imposed by the higher symmetry - 
>> because, for example, cell parameters refined assuming cell length/angle 
>> constraints may not predict the reflection positions as well as if these 
>> restraints were not applied, reflections assumed to be symmetry equivalent 
>> when they weren't may lead to suboptimal scaling etc etc?
>> 
>> 
>> Huw
> 
> 
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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Difficult Molecular replacement

[Harry Powell]

Hi Marco

Further to Pedro’s comment, one way to avoid missing data in cusps is to use a 
multi-sweep strategy for data collection (as championed by the good folk at 
Global Phasing over many years). Many of the problems encountered in structure 
solution can be traced back to a sub-optimal data collection.

You don’t say which beamline at ALS you used, but if it’s got a kappa or 
similar fitted the beamline staff should be able to help.

best wishes

Harry

> On 20 Feb 2024, at 09:20, Pedro Matias  wrote:
> 
> Hi Marco,
> 
> Further to Zhen's comment, that can also happen if you have a cusp containing 
> one of the reciprocal lattice axes. The SG may be P212121 but one of the 21 
> is never located due to the missing data.



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Re: [ccp4bb] RMSD per residue graph for multiple aligned PDB files

[Harry Powell]

AFAIK the CCP4 tools “superpose” and “gesamt” both give tables of per-residue 
RMSD

Harry

> On 5 Jan 2024, at 10:49, Tomas Malinauskas  
> wrote:
> 
> Dear All,
> 
> I apologize for asking a somewhat off-topic question.
> 
> I have multiple aligned PDB files loaded in PyMOL, each representing
> different conformations of the same protein. I'm interested in
> creating a graph displaying RMSD per residue, similar to those shown
> at 
> https://www.ks.uiuc.edu/Training/Tutorials/science/aars/aars_html.bak/node22.html
> or 
> https://www.compchems.com/how-to-compute-the-rmsf-using-gromacs/#the-gmx-rmsf-command.
> 
> I'm wondering if anyone has a script available that can calculate RMSD
> per residue and write the data to a text file for graph generation. If
> so, would they be able to share it with everyone?
> 
> Thank you for your help.
> 
> Best wishes,
> Tomas
> 
> 
> 
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Re: [ccp4bb] what is isomorphous?

[Harry Powell]

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)
>> 
>> 
>> 
>> 
>> 
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> 
> 
> 
> -- 
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
> 
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> 
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Re: [ccp4bb] RMSF calculation in pymol

[Harry Powell]

Hi

Not PyMol, but relevant to the ccp4BB - why not try “gesamt” for this?

e.g. for the nmr structure 1q01 - 

> gesamt pdb1q01.ent -s '/1/A' pdb1q01.ent -s '/2/A' pdb1q01.ent -s '/3/A' 
> -r0=1.5 -sigma=1.0 -o 1q01_cluster.cif -o-cf -a align.seq

gives me an alignment of the first three models in the file

Harry


> On 14 Dec 2023, at 21:55, Krieger, James M  wrote:
> 
> I don’t have one for pymol, but there is a function in prody for it.
> 
> Best wishes 
> James 
> 
>> On 14 Dec 2023, at 21:41, Srivastava, Dhiraj  
>> wrote:
>> 
>> 
>> Hi All
>> sorry for off topic question. does anyone have script for rmsf 
>> calculation of multistate pdb file in pymol? There used to be a script 
>> rmsf_states  written by Robert Campbell but with newer version of pymol, 
>> it's not working. 
>> 
>> Thank you
>> Dhiraj
>> 
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Re: [ccp4bb] What could these crystals be?

[Harry Powell]

Hi

I can’t see any (obvious) suggestions in the current list of answers to try 
room temperature diffraction before introducing cryoprotectants and cryocooling 
your crystals (but I might just have missed it). 

Often, just the act of changing the conditions that your crystals sit in will 
destroy internal order and stop them being crystals. Cooling the crystals to 
cryogenic temperatures can also destroy crystallinity (that’s why people spend 
so much time and effort in optimising cryoprotectant strategies).

Over the last couple of days, people on ccp4bb have suggested in-situ data 
collection, i.e. with the crystals sitting in the plate they grew in - this is 
a great way to avoid any physical damage. There may well be a facility 
relatively close to you that you could get access to in order to try this. As 
pointed out by some of the correspondents in the “Fragile Crystals” thread, 
some places will also grow your crystals for you on site, using your 
conditions. Unfortunately, I don’t know where “yahoo” is, so I can’t make a 
suggestion as to which might be closer/easier for you to access!

best wishes

Harry

> On 24 Nov 2023, at 08:59, careinaedgo...@yahoo.com 
> <02531c126adf-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> 
> I wanted to thank everyone for their suggestions and ideas regarding the 
> eyeball shaped crystals that I got at the beginning of the month.
> I can confirm that these crystals do indeed contain protein and DNA which is 
> good news. 
> I have tried a number of different buffers and salts since then. I have also 
> tried seeding but nothing I have tried has changed the morphology of the 
> crystals. They remain thin, flat and eyeball/pumpkin seed shaped.
> It is not difficult to make the crystals, they form quite easily under quite 
> a few conditions. The difficulty is in the diffraction. By changing the 
> buffer conditions we can now see some very weak diffraction (previously there 
> was no diffraction at all).
> Are there any suggestions as to how to improve diffraction of these crystals? 
> I did try different cryoprotectants, parabar, glycerol, PEG but no 
> difference. I think perhaps the problem is heterogeneity considering my 
> sample contains both protein and DNA. 
> Any suggestions or thoughts are welcome.
> Thank you
> Careina 
> 
> On Wednesday, November 8, 2023 at 06:18:46 PM GMT+2, careinaedgo...@yahoo.com 
> <02531c126adf-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> 
> 
> The reservior solution is 0.2 M NaCl2, 0.1 M HEPES pH 7.5, and 25% 3350 PEG
> 
> Protein buffer is 300 mM NaCl, 20 mM HEPES pH 7.5, 3mM TCEP
> 
> The drop contains 1.5ul protein-DNA complex and 1.5 ul reservior solution 
> 
> 
> On Wednesday, November 8, 2023 at 05:12:25 PM GMT+2, 
> stephen.c...@rc-harwell.ac.uk  wrote:
> 
> 
> Hi Careina,
> 
> Without knowing what's in your protein buffer or crystallisation condition 
> it's hard to comment.
> 
> Best wishes,
> Steve
> 
> Dr Stephen Carr
> Research Complex at Harwell (RCaH)
> Rutherford Appleton Laboratory
> Harwell Oxford
> Didcot
> Oxon OX11 0FA
> United Kingdom
> Email stephen.c...@rc-harwell.ac.uk
> tel 01235 567717
> From: CCP4 bulletin board  on behalf of 
> careinaedgo...@yahoo.com <02531c126adf-dmarc-requ...@jiscmail.ac.uk>
> Sent: 08 November 2023 15:00
> To: ccp4bb 
> Subject: [ccp4bb] What could these crystals be?
>  
> 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 but they do not 
> diffract at all. Any ideas as to what could cause this?
> Careina
> 
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Re: [ccp4bb] Fragile Crystals

[Harry Powell]

Hi

Well worth contacting your favourite (or favorite…) synchrotron about in-plate 
data collection - I’d imagine that APS has something in-place (there was a 
report way back in the depths of time [2015, when I still worked in the field…] 
about a prototype on ID-19?), and that might be easier to get samples to (from 
Birmingham) than one of the European facilities.

Harry

> On 23 Nov 2023, at 09:31, Jose A. MARQUEZ  wrote:
> 
> Dear Elizabeth,
> 
> In situ data collection is a good approach to try in your case. You could use 
> the CrystalDirect technology for automated crystal harvesting that is more 
> gentle to crystals than manual harvesting. This is  available both at EMBL 
> Grenoble and EMBL Hamburg facilities, which offer integrated crystallography 
> services in collaboration with the ESRF and Petra III synchrotrons. 
> 
> doi:10.3791/62491. 
> doi:10.1016/j.crmeth.2021.100102. 
> doi:10.1107/s0907444912031459.
> 
> Best wishes
> 
> Josan
> _ 
> Jose A. Marquez, Senior Scientist 
> Head of the Crystallization Facility 
> European Molecular Biology Laboratory, Grenoble. 
> Delivery address: EMBL, 71, Avenue des Martyrs 
> 38000 Grenoble, France 
> Postal address: EMBL, 71, Avenue des Martyrs 
> CS 90181 38042 Grenoble Cedex 9, France 
> Phone +33 (0)476 20 74 25 
> Fax. +33 (0)476 20 71 99 
> 
> 
> https://www.embl.org/groups/marquez/
>  
> 
> https://www.embl.org/services-facilities/grenoble/high-throughput-crystallisation/
>  
> 
> https://htxlab.embl.org/
>  
> _
> 
> On 11/22/2023 5:44 PM, Blake, Morgan Elizabeth wrote:
>> Hello!
>> 
>> I am a PhD student working on a crystallography project to wrap up my 
>> dissertation research. I have purified a complex of two proteins, and I can 
>> consistently grow crystals in 10% PEG3350, 0.2M KSCN, 0.1M BIS-TRIS propane 
>> pH 7.5. These crystals have sharp edges and can grow to a large size 
>> (greater than 0.5 mm), but the crystals seem to be very fragile. When we 
>> open the drops to harvest the crystals, we have little time to harvest the 
>> crystals before they crack. When we move the crystals to a cryoprotectant, 
>> over time they start fracturing. We've tried using different percentages of 
>> glycerol, ethylene glycol, PEG400, and oil for cryoprotectants with no 
>> success. Needless to say, the crystals do not diffract well, with spot 
>> patterns that look very streaky/mosaic, which I presume is due to the 
>> defects that we see in harvesting/handling. We have screened for alternate 
>> crystallization conditions, but we seem to get the same morphology in other 
>> conditions. Does anyone have suggestions for additives we could use 
>> post-crystallization to help stabilize our crystals?
>> 
>> Thanks for your advice!
>> 
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[ccp4bb] HH-Suite, HHBLits, HHSearch query

[Harry Powell]

Hi folks

I was wondering if anyone on ccp4bb could give me a hand with some queries I 
have about HHBlits and HHSearch?

The “issues” page on github (https://github.com/soedinglab/hh-suite/issues) 
seems to be completely moribund and no-one has answered any queries for quite 
some time - this may be associated with the project losing funding (which is a 
huge loss to the community at large).

Harry


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Re: [ccp4bb] Video link for RSC meeting on "British X-ray Crystallographers."

[Harry Powell]

Hi Jon

many thanks for this!

For those interested in Peter Morris, there was an interview with him in 
Chemical and Engineering News at the end of September - 


https://cen.acs.org/people/CEN-talks-with-Peter-J-T-Morris-science-historian/101/i32

Harry

> On 9 Nov 2023, at 22:57, Jon Cooper 
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> 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
>  
> My thanks for Professor Stephen Neidle for recording his talk without an 
> audience in the following week and to Kathryn Espino of RSC Networks for 
> uploading them to YouTube.
> 
> Best wishes,
>  
> Peter Morris
> 
> Best wishes, Jon Cooper.
> jon.b.coo...@protonmail.com
> 
> Sent with Proton Mail secure email.
> 
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Re: [ccp4bb] radiation damage and image discard

[Harry Powell]

Hi

I’ve never actually used it in anger (one should never be angry when processing 
data…), but doesn’t AutoProc, developed by the good folks at Global Phasing do 
a lot of these analyses? Clemens, Claus etc may have something pertinent to say.

Harry

> On 30 Oct 2023, at 13:23, Jorge Iulek  wrote:
> 
> Dear all,
> 
>   I have found many fundamental studies on image processing and 
> refinement indexes concerning the decision on cutting resolution for a 
> dataset, always meant to get better models, the final objective. Paired 
> refinement has been a procedure mostly indicated.
>   I have been searching studies alike concerning, in these days of 
> thousands of collected images and strong x ray beams, the cutting (or 
> truncation) of the (sequentially due to rotation method) recorded images in a 
> dataset due to radiation damage. Once again, I understand the idea is to 
> always produce better models.
>   On one hand, the more images one uses, the higher the multiplicity, 
> what (higher multiplicity) leads to better averaged intensity (provided 
> scaling makes a good job), on the other hand, the more images one uses, lower 
> intensity (due to the radiation damage) equivalent reflections come into play 
> for scaling, etc. How to balance this? I have seen a case in which truncating 
> images with some radiation damage led to worse CC(1/2) and  (at the 
> same high resolution shell, multiplicities around 12.3 and then 5.7), but 
> this might not be the general finding. In a word, are there indicators of the 
> point where to truncate more precisely the images such that the dataset will 
> lead to a better model? I understand tracing a sharp borderline might not be 
> trivial, but even a blurred borderline might help, specially in the moment of 
> image processing.
>   I find that in 
> https://ccp4i2.gitlab.io/rstdocs/tasks/aimless_pipe/scaling_and_merging.html#estimation-of-resolution
>  there is a suggestion to try refinement with both truncating and not 
> truncating.
>   Sure other factors come into play here, like diffraction anisotropy, 
> crystal internal symmetry, etc., but to start one might consider just the 
> radiation damage due to exposure to x rays. Yes, further on, it would be nice 
> the talk evolves to those cases when we see peaks and valleys along the 
> rotation due to crystal anisotropy, whose average height goes on diminishing.
>   Comments and indications to papers and material to study are welcome. 
> Thanks.
>   Yours,
> 
> Jorge
> 
> 
> 
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Re: [ccp4bb] Assistant Professor in Structural Biology, University of Nebraska-Lincoln

[Harry Powell]

On the general topic of tenure, I read an interesting article in the news organ 
of the American Chemical Society (Chemical and Engineering News) about the 
future of tenure in the US recently - it’s available free-to-view (C&EN allows 
viewing one article a month without being a paid subscriber) - 

> https://cen.acs.org/careers/great-tenure-debate-again/101/i29

If you have a free 10 -15 minutes…

Harry 

> On 16 Oct 2023, at 08:15, Tim Gruene  wrote:
> 
> On Sun, 15 Oct 2023 19:44:45 +
> "Hekstra, Doeke Romke"  wrote:
> 
>> Mark is, of course, right that this practice is nearly universal,
> 
> 'universal' to the universe of the US ;-) in Austria, one typically
> gets 14 salaries per year, in Germany, the salary year usually has 12
> months, following the calendar, including 1 month holidays 
> 
> Cheers,
> Tim
> 
> -- 
> --
> 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
> 
> 
> 
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Re: [ccp4bb] Issues in diffraction image export compatible to iMosflm

[Harry Powell]

Hi

If you’re not in a hurry, I should be able to take a look and see what needs to 
be done (I’m a little busy right now, but I do know more than a ittle about 
Mosflm and image formats). Otherwise I’d contact Mathias Meyer directly at 
Rigaku Oxford Diffraction, who should be able to point you in the right 
direction.

Best wishes

Harry

> On 10 Oct 2023, at 06:17, Vyankatesh Rajmane  wrote:
> 
> Dear all,
> We have collected diffraction data on a Rigaku FR-X machine with a 
> HyPix-6000HE detector. The images are in .rod_img format. We are trying to 
> export the data in iMosflm compatible format using the options available in 
> CrysAlisPro RED software provided by Rigaku. But the images generated show 
> vertical strips instead of diffraction spots which gives error in processing. 
> Can anyone suggest a method to convert the .rod_img images in iMosflm 
> compatible format. Thank you!  
> 
> -- 
>  Vyankatesh Rajmane
> E-mail: vyankates...@gmail.com
> 
> 
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Re: [ccp4bb] naturally obsessed - the movie

[Harry Powell]

Okay, I’ve found a DVD with it on…

Harry

> On 3 Oct 2023, at 14:51, Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Good idea, but amazon.com.be tells me - 
> 
> "Actuellement indisponible. 
> Nous ne savons pas quand cet article sera de nouveau approvisionné ni s'il le 
> sera.”
> 
> and amazon.co.uk - 
> 
> "Currently unavailable. 
> We don't know when or if this item will be back in stock.”
> 
> and amazon.com - 
> 
> "This item cannot be shipped to your selected delivery location. Please 
> choose a different delivery location.” (I’m in the UK).
> 
> :-(
> 
> I’ll continue looking for it. My emails from 2011 indicate that I was lent a 
> physical copy, and ISTR that when it came round to returning it, I was told 
> to keep it… so it should be somewhere in my “archives"
> 
> Harry
> 
>> On 3 Oct 2023, at 14:22, F.Xavier Gomis-Rüth  wrote:
>> 
>> You can purchase it from Amazon.
>> 
>> On 3/10/23 15:21, Burak Veli Kabasakal wrote:
>>> Dear all,
>>> 
>>> Sorry I realized the movie is only 10 mins covering the beginning - thanks 
>>> for people who warned me. I think I was also using the online link to 
>>> access the full movie. Unfortunately it is no longer available. But I will 
>>> continue to search if I have the full version.
>>> 
>>> Best regards,
>>> 
>>> Burak
>>> 
>>> Hughes, Jonathan , 3 Eki 2023 Sal, 
>>> 15:57 tarihinde şunu yazdı:
>>> excellent – but the mp4 seems to cut out at about 10 min...
>>> 
>>> j
>>> 
>>> 
>>> --
>>> 
>>> Jon Hughes
>>> 
>>> 
>>> Von: CCP4 bulletin board  Im Auftrag von Burak Veli 
>>> Kabasakal
>>> Gesendet: Dienstag, 3. Oktober 2023 13:04
>>> An: CCP4BB@JISCMAIL.AC.UK
>>> Betreff: Re: [ccp4bb] naturally obsessed - the movie
>>> 
>>> 
>>> Dear Chris and all,
>>> 
>>> 
>>> I had seen this movie when I was a graduate student at UC Davis, then my 
>>> PhD advisor at Imperial College, James Murray had shown it to our group. 
>>> Now, I show this movie to my research students. It is really a must-see 
>>> movie for people who are doing PhD or planning to do PhD, especially in 
>>> structural biology.
>>> 
>>> 
>>> I have an mp4 copy, I can share it via a google drive link:  
>>> https://drive.google.com/drive/folders/1HqoDIi5QyH8im_Ya8me8eDC6e7huY6d0?usp=sharing
>>>  
>>> 
>>> 
>>> Best regards,
>>> 
>>> 
>>> Burak
>>> 
>>> 
>>> Chris Ulens , 3 Eki 2023 Sal, 13:02 tarihinde şunu 
>>> yazdı:
>>> 
>>> Dear members of the ccp4bb,
>>> 
>>> I have a somewhat unusual question. For many years I have shown the movie 
>>> “Naturally Obsessed - the making of a scientist” for educative purposes in 
>>> my classes at the faculty of medicine in KU Leuven. I just noticed that the 
>>> movie is no longer freely downloadable. 
>>> https://pbsinternational.org/programs/naturally-obsessed/ PBS responded to 
>>> me that they no longer have the distribution rights. Could anyone   
>>> point me toward a downloadable movie or perhaps a DVD 
>>> so I can show it in my class this semester?
>>> 
>>> 
>>> Thank you very much in advance.
>>> 
>>> Chris
>>> 
>>> 
>>> ———
>>> 
>>> Prof. Chris Ulens
>>> 
>>> Laboratory of Structural Neurobiology
>>> 
>>> Department of Cellular and Molecular Medicine
>>> 
>>> Facuty of Medicine
>>> 
>>> Herestraat 49, PB901
>>> 
>>> 3000 Leuven
>>> 
>>> Belgium
>>> 
>>> 
>>> 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
>>> 
>>> 
>>> 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] naturally obsessed - the movie

[Harry Powell]

Good idea, but amazon.com.be tells me - 

"Actuellement indisponible. 
Nous ne savons pas quand cet article sera de nouveau approvisionné ni s'il le 
sera.”

and amazon.co.uk - 

"Currently unavailable. 
We don't know when or if this item will be back in stock.”

and amazon.com - 

"This item cannot be shipped to your selected delivery location. Please choose 
a different delivery location.” (I’m in the UK).

:-(

I’ll continue looking for it. My emails from 2011 indicate that I was lent a 
physical copy, and ISTR that when it came round to returning it, I was told to 
keep it… so it should be somewhere in my “archives"

Harry

> On 3 Oct 2023, at 14:22, F.Xavier Gomis-Rüth  wrote:
> 
> You can purchase it from Amazon.
> 
> On 3/10/23 15:21, Burak Veli Kabasakal wrote:
>> Dear all,
>> 
>> Sorry I realized the movie is only 10 mins covering the beginning - thanks 
>> for people who warned me. I think I was also using the online link to access 
>> the full movie. Unfortunately it is no longer available. But I will continue 
>> to search if I have the full version.
>> 
>> Best regards,
>> 
>> Burak
>> 
>> Hughes, Jonathan , 3 Eki 2023 Sal, 15:57 
>> tarihinde şunu yazdı:
>> excellent – but the mp4 seems to cut out at about 10 min...
>> 
>> j
>> 
>>  
>> --
>> 
>> Jon Hughes
>> 
>>  
>> Von: CCP4 bulletin board  Im Auftrag von Burak Veli 
>> Kabasakal
>> Gesendet: Dienstag, 3. Oktober 2023 13:04
>> An: CCP4BB@JISCMAIL.AC.UK
>> Betreff: Re: [ccp4bb] naturally obsessed - the movie
>> 
>>  
>> Dear Chris and all,
>> 
>>  
>> I had seen this movie when I was a graduate student at UC Davis, then my PhD 
>> advisor at Imperial College, James Murray had shown it to our group. Now, I 
>> show this movie to my research students. It is really a must-see movie for 
>> people who are doing PhD or planning to do PhD, especially in structural 
>> biology.
>> 
>>  
>> I have an mp4 copy, I can share it via a google drive link:  
>> https://drive.google.com/drive/folders/1HqoDIi5QyH8im_Ya8me8eDC6e7huY6d0?usp=sharing
>>  
>> 
>>  
>> Best regards,
>> 
>>  
>> Burak
>> 
>>  
>> Chris Ulens , 3 Eki 2023 Sal, 13:02 tarihinde şunu 
>> yazdı:
>> 
>> Dear members of the ccp4bb,
>> 
>> I have a somewhat unusual question. For many years I have shown the movie 
>> “Naturally Obsessed - the making of a scientist” for educative purposes in 
>> my classes at the faculty of medicine in KU Leuven. I just noticed that the 
>> movie is no longer freely downloadable. 
>> https://pbsinternational.org/programs/naturally-obsessed/ PBS responded to 
>> me that they no longer have the distribution rights. Could anyone
>>point me toward a downloadable movie or perhaps a DVD so 
>> I can show it in my class this semester?
>> 
>>  
>> Thank you very much in advance.
>> 
>> Chris
>> 
>>  
>> ———
>> 
>> Prof. Chris Ulens
>> 
>> Laboratory of Structural Neurobiology
>> 
>> Department of Cellular and Molecular Medicine
>> 
>> Facuty of Medicine
>> 
>> Herestraat 49, PB901
>> 
>> 3000 Leuven
>> 
>> Belgium
>> 
>>  
>> 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
>> 
>> 
>> 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] naturally obsessed - the movie

[Harry Powell]

Hi Chris

I seem to remember arranging a showing or two of it at the 2011 IUCr meeting in 
Madrid (Frances Bernstein asked my about doing this, to give credit where it’s 
due). I have a vague memory of having obtained the DVD but couldn’t swear to it 
now. I’ll have a look through my bits and bobs to see if I can find it.

Do you have a deadline?

Harry

> On 3 Oct 2023, at 11:02, Chris Ulens  wrote:
> 
> Dear members of the ccp4bb,
> I have a somewhat unusual question. For many years I have shown the movie 
> “Naturally Obsessed - the making of a scientist” for educative purposes in my 
> classes at the faculty of medicine in KU Leuven. I just noticed that the 
> movie is no longer freely downloadable. 
> https://pbsinternational.org/programs/naturally-obsessed/ PBS responded to me 
> that they no longer have the distribution rights. Could anyone point me 
> toward a downloadable movie or perhaps a DVD so I can show it in my class 
> this semester?
> 
> Thank you very much in advance.
> Chris
> 
> ———
> Prof. Chris Ulens
> Laboratory of Structural Neurobiology
> Department of Cellular and Molecular Medicine
> Facuty of Medicine
> Herestraat 49, PB901
> 3000 Leuven
> Belgium
> 
> 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] Intractable outliers in wwPDB validation report

[Harry Powell]

Hi

I think It may be worthwhile submitting your model and data to PDB-REDO to see 
if (inter alia) you have applied any unconscious bias to your building that has 
resulted in these outliers, or over- or under-interpreted the data. It’s quick 
and easy to submit and requires remarkably little effort on your part - another 
tool to your collection.

Harry

> On 25 Sep 2023, at 07:00, Guillaume Gaullier  
> wrote:
> 
> A good example of such expected outliers can be found in structures of 
> nucleosomes: the validation report always flags almost all DNA bases as 
> geometry outliers. But we have no end of evidence that these structures are 
> correct: for instance, the many ensemble and single-molecule FRET studies of 
> nucleosomes that relied on said structures to design their labeling scheme 
> and to formulate testable hypotheses.
> 
> If your map insists on putting some residues in an uncomfortable 
> conformation, it’s possible that this is indeed what is going on in the 
> protein and not necessarily a modeling error.
> 
> Cheers,
> 
> Guillaume
> 
>> On 23 Sep 2023, at 21:50, Eleanor Dodson 
>> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> 
>> Well - some outliers are infix able! There are various reasons - floppy 
>> residues like arg or lys 
>> In multiple positions; strain due to protein folding constraints, etc.
>> 
>> I use the validation report to check for obvious modelling errors but if you 
>> can’t find any, you have to just submit the results of your experiment... 
>> 
>> On Sat, 23 Sep 2023 at 02:29, Nitin Kulhar 
>> <9dfccc771c91-dmarc-requ...@jiscmail.ac.uk> 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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>> 
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> 
> 
> 
> 
> 
> 
> 
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Re: [ccp4bb] the structures of Nucleic acid

[Harry Powell]

Hi

I am also reminded that I was involved in the data collection but not structure 
solution of a DNA cyclic octamer from a single wavelength dataset collected to 
atomic resolution (on image plate…), which was solved after locating a Ba 
(which turned out to be one of several with partial occupancy); the structure 
solution was actually carried out in the laboratory of one G.M. Sheldrick, 
using software that I think may have never been released to the public.

See 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC20809/

for details...

Harry

> On 19 Sep 2023, at 20:53, Diana Tomchick  
> wrote:
> 
> I have also found that there is significant anomalous signal from strontium 
> near the Se K-edge, which is useful if one uses strontium chloride instead of 
> potassium chloride (or in addition to KCl) during crystal growth.
> 
> Diana
> 
> **
> Diana R. Tomchick
> Professor
> Departments of Biophysics and Biochemistry
> UT Southwestern Medical Center
> 5323 Harry Hines Blvd.
> Rm. ND10.214A
> Dallas, TX 75390-8816
> diana.tomch...@utsouthwestern.edu
> (214) 645-6383 (phone)
> (214) 645-6353 (fax)
> 
> 
> 
>> On Sep 19, 2023, at 1:32 PM, Wagner, Armin (DLSLtd,RAL,LSCI) 
>>  wrote:
>> 
>> 
>> EXTERNAL MAIL
>> 
>> Dear Fu Xingke,
>>  
>> Indeed P-SAD is quite attractive but requires high resolution as the number 
>> of anomalous scatterers (1 P per nucleotide) is rather large, but the unit 
>> cells are typically quite small, resulting in a rather small number of 
>> anomalous differences per scatterer. Based on the very nice publication from 
>> Tom Terwilliger et al. ( https://doi.org/10.1107/S2059798315019269) we wrote 
>> a little web app to predict the success for S-SAD phasing at the 
>> long-wavelength beamline I23 at Diamond. 
>> https://www.diamond.ac.uk/Instruments/Mx/I23/resolution-requirement-phasing-app.html
>> While the predictions are pretty reliable for S-SAD, there is a (not heavily 
>> tested) option to also submit DNA or RNA sequences, which can give you a 
>> hint on what you are against, or what resolution you should aim for. 
>> Unfortunately, we have not had many successful examples to far, but 
>> basically all the P-SAD projects which were predicted not to work at the 
>> resolutions the crystals diffracted to didn’t solve, so we are very 
>> interested in projects which are predicted to work to fine tune this also 
>> for P-SAD as there will be continuous need for experimental phasing in 
>> particular for non-canonical RNA/DNA structures.
>>  
>> 5-Br-U is a good alternative and works well, but we have also managed to 
>> solve RNA/DNA by K-SAD or Co-SAD (https://doi.org/10.1093/nar/gkaa439) and 
>> Ca could be attractive as a potential anomalous scatter as well.
>>  
>> Best regards,
>>  
>> Armin
>>  
>>  
>>  
>>  
>> From: CCP4 bulletin board  on behalf of Mark J. van 
>> Raaij 
>> Date: Tuesday, 19 September 2023 at 12:31
>> To: CCP4BB@JISCMAIL.AC.UK 
>> Subject: Re: [ccp4bb] the structures of Nucleic acid
>> 
>> This just appeared and may be relevant:
>> https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad726/7272628
>>  
>> Critical Reviews and Perspectives
>> When will RNA get its AlphaFold moment? 
>> Mark van Raaij
>> Dpto de Estructura de Macromoleculas, lab 20B
>> Centro Nacional de Biotecnologia - CSIC
>> calle Darwin 3
>> E-28049 Madrid, Spain
>> tel. +34 91 585 4616 (internal 432092)
>> 
>> 
>> 
>> On 18 Sep 2023, at 18:07, William G. Scott 
>> <2844d921eb97-dmarc-requ...@jiscmail.ac.uk> wrote:
>>  
>> The phosphorus absorption edge is about 5.8Å.
>> 
>> I've had much better luck with 5-Br-U for anomalous phasing.
>> 
>> Molecular replacement with sub-structural fragments can also work:
>> 
>> 
>> 
>> Yours sincerely,
>> 
>> William G. Scott
>> Professor, Department of Chemistry and Biochemistry
>> and The Center for the Molecular Biology of RNA
>> University of California at Santa Cruz
>> Santa Cruz, California 95064  
>> USA
>> 
>> 
>> On Sep 18, 2023, at 2:43 AM, Eleanor Dodson 
>> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> I am afraid most scientists will use the most straightforward technique! 
>> If SAD is available the PHOSPHATE backbone of DNA will provide sufficient 
>> signal to allow SAD to work, and you get an unambiguous answer to whether it 
>> is A-DNA or B or Z...
>> MR will usually work of course as well
>> Eleanor
>> 
>> 
>> On Mon, 18 Sept 2023 at 09:18, Natesh Ramanathan  
>> wrote:
>> Dear Fu Xingke,
>> 
>> Depends on what Nucleic Acid you are talking of.  If it is RNA, you 
>> can expect some sequence to tertiary structure correspondence so you might 
>> be able to try more MR as compared to DNA.   DNA may have double helical 
>> architecture but less sequence to tertiary structure correspondence, and 
>> hence DNA is less likely to hav

Re: [ccp4bb] the structures of Nucleic acid

[Harry Powell]

Hi folks

just my two ha’porth.

Back in the mid 1990s, when MAD was becoming common and tunable beamlines were 
being installed at every synchrotron you could shake a stick at, I was involved 
in several successful projects involving 5-Br-U in oligo-DNA crystallography. 
In my (very, very) naïve hands at the time it worked like magic (I remember my 
shock at seeing the base stacking in the first map I calculated for one of the 
structures) - and this was using data collected on image plates with each image 
spanning rather more than 1 degree - so not how it would be done now.

Since just about everything to do with data collection and processing and 
structure solution has improved by leaps and bounds since then, I would back 
Br-SAD to yield a structure.

If anyone’s interested, they can see my contribution regarding this at the 1997 
CCP4 Study Weekend proceedings (this was prior to them appearing in Acta D), 
available at - 

https://legacy.ccp4.ac.uk/courses/proceedings/1997/h_powell/main.html

Contributions at the same meeting by others whose names will be instantly 
recognizable may well be more use than mine…

Best wishes

Harry

> On 19 Sep 2023, at 19:32, Wagner, Armin (DLSLtd,RAL,LSCI) 
>  wrote:
> 
> 5-Br-U is a good alternative and works well, but we have also managed to 
> solve RNA/DNA by K-SAD or Co-SAD (https://doi.org/10.1093/nar/gkaa439) and Ca 
> could be attractive as a potential anomalous scatter as well.
>  
> Best regards,
>  
> Armin
>  
>  
>  
>  
> From: CCP4 bulletin board  on behalf of Mark J. van 
> Raaij 
> Date: Tuesday, 19 September 2023 at 12:31
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: Re: [ccp4bb] the structures of Nucleic acid
> 
> This just appeared and may be relevant:
> https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad726/7272628
>  
> Critical Reviews and Perspectives
> When will RNA get its AlphaFold moment? 
> Mark van Raaij
> Dpto de Estructura de Macromoleculas, lab 20B
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. +34 91 585 4616 (internal 432092)
> 
> 
> 
> On 18 Sep 2023, at 18:07, William G. Scott 
> <2844d921eb97-dmarc-requ...@jiscmail.ac.uk> wrote:
>  
> The phosphorus absorption edge is about 5.8Å.
> 
> I've had much better luck with 5-Br-U for anomalous phasing.
> 
> Molecular replacement with sub-structural fragments can also work:
> 
> 
> 
> Yours sincerely,
> 
> William G. Scott
> Professor, Department of Chemistry and Biochemistry
> and The Center for the Molecular Biology of RNA
> University of California at Santa Cruz
> Santa Cruz, California 95064  
> USA
> 
> 
> On Sep 18, 2023, at 2:43 AM, Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> I am afraid most scientists will use the most straightforward technique! 
> If SAD is available the PHOSPHATE backbone of DNA will provide sufficient 
> signal to allow SAD to work, and you get an unambiguous answer to whether it 
> is A-DNA or B or Z...
> MR will usually work of course as well
> Eleanor
> 
> 
> On Mon, 18 Sept 2023 at 09:18, Natesh Ramanathan  
> wrote:
> Dear Fu Xingke,
> 
> Depends on what Nucleic Acid you are talking of.  If it is RNA, you 
> can expect some sequence to tertiary structure correspondence so you might be 
> able to try more MR as compared to DNA.   DNA may have double helical 
> architecture but less sequence to tertiary structure correspondence, and 
> hence DNA is less likely to have a 3D structure like RNA specific structure 
> for a sequence.
> 
> SAD has become a straight forward method to avoid all these problems 
> to get ab-initio structure.  So many go for it directly.
> 
> Hope that helps.
> Best wishes,
> Natesh
> 
> On Mon, 18 Sept 2023 at 13:36, fuxingke  wrote:
> Dear Colleagues,
> 
> Reacently, I find the structures of Nucleic acid are solved by 
> single-wavelength anomalous diffraction(SAD). So, why molecular replacement 
> (MR) not?
> 
> Regards
> 
> 
> 
> Best wishes,
> 
> Fu Xingke
> 
> Institute of Physics CAS
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
> 
> 
> -- 
> --
> "Live Simply and do Serious Things .. "
> - Dorothy Mary Crowfoot Hodgkin OM, FRS
> 
> "In Science truth always wins"
> - Max Ferdinand Perutz OM FRS
> --
> Dr. Ramanathan Natesh
> Associate Professor, 
> School of Biology and Center for High-Performance Computing (CHPC),
> Founding and Current President of Cryo Electron Microscopy and 3 Dimensional 
> Image Processing Society of India (CEM3DIPSI),
> Indian Institute of Science Education and Research Thiruvananthapuram 
> (IISER-TVM),
> Maruthamala P.O., Vithura,
> Thiruvananthapuram,  695551, Kerala, Indi

Re: [ccp4bb] Determining Second Lattice

[Harry Powell]

Hi Matt

Call me old-fashioned but I’d use Mosflm for this. The multiple lattice 
autoindexing is easy to run and easy to interpret.

Harry

> On 30 Aug 2023, at 16:20, Matt McLeod  wrote:
> 
> Hi all,
> 
> I have a lot of large datasets that I want to screen to determine if there 
> are one or two lattices in the diffraction.  I was wondering if there was a 
> simple and quick way to do so.
> 
> Currently, I am processing with DIALS and getting to the indexing where the 
> percent indexed indicates if there is potentially a second lattice - and then 
> visually inspected when there is a significant number of rejection.
> 
> I have autoprocess log files ie aimless.log, autoindex.log, fast_dp.log that 
> were generated at the beamline but I cannot see a similar metric suggesting 
> second lattices. 
> 
> Any insight would be appreciated!
> Matt
> 
> 
> 
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Re: [ccp4bb] mmciif pdb file editor.

[Harry Powell]

Hi

There is no particular special editor from PDB (or from anywhere else, as far 
as I know) for doing this - mmCIF is basically a simple text file with a 
defined set of contents. It frees you from the tyranny of fixed-width columns 
that your have in the historic PDB file.

I’d just use whatever text editor you have on your system - so on LInux or Mac, 
something like vim, emacs, nano, on Windows Notepad. No need for anything 
special.

But I’d also be wary about screwing up the file completely with your edits - 
it’s easy to turn a compliant file into something invalid. 

Harry

> On 30 Aug 2023, at 14:05, Krishnan Raman  wrote:
> 
> How do I edit mmcif files from pdb?  Is there a editor for download from pdb 
> website? Thanks krish
>  
>  
> 
> 
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Re: [ccp4bb] ILLUSTRATE in PYMOL

[Harry Powell]

Hi

Since this is the ccp4 bulletin board, it’s always worth mentioning CCP4MG for 
producing images & movies of macromolecules. Comes with the package, and you 
can get help from the author directly if you have any issues.

Harry

> On 17 Aug 2023, at 02:09, khaja faisal tarique  
> wrote:
> 
> Thanks everyone for their valuable feedback. It helped a lot.
> 
> Best
> 
> Faisal
> 
> On Tue, 15 Aug 2023, 19:19 khaja faisal tarique, 
>  wrote:
> Hi everyone
> 
> Is there any way to make surface representation of a protein structure 
> similar to the 'Illustrate: Non-photorealistic Biomolecular Illustration' 
> (https://ccsb.scripps.edu/illustrate/) using scripts in Pymol ? It will be 
> really helpful if someone can share this with me.
> 
> Thanks
> 
> Faisal
> 
> 
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Re: [ccp4bb] An unknown but strong positive electron density in my crystal

[Harry Powell]

Hi

> Has anyone seen similar density to this before and/or can suggest how to 
> model this positive density? Many thanks.

Romulan bird of prey?

Harry

> 
> Regards,
> 
> Yue Li
> 
> 
> 
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Re: [ccp4bb] Cannot select any recommended SG for the protein BsAlaDH

[Harry Powell]

Apropos Phil’s last point - 

> 
> 4.  On the model front, go find an AlphaFold model, they have worked for me 
> multiple times in molecular replacement so far.

If there is no extant Alphafold model, it may be worthwhile creating your own 
via colabfold (duckduckgo it like I did…). Only takes a short time...

best wishes

Harry

> On 2 Aug 2023, at 20:20, Phil Jeffrey  wrote:
> 
> 1.  Completeness is primarily an issue with using the right point group and 
> crystal system, not the actual space group (e.g. in primitive point group mmm 
> the space groups P222, P2221, P21212, P212121 should all have essentially the 
> same completeness).
> 2.  If "refinalize" in CrysAlisPro doesn't let you choose the right point 
> group and system, then you should process the data with another program.  
> XDS, MOSFLM, DIALS, autoPROC etc might work, and I have to believe they'd be 
> better at scaling your data.
> 3.  If you can export the unscaled data from CrysAlisPro you might be able to 
> feed it into POINTLESS and AIMLESS for scaling
> 
> 4.  On the model front, go find an AlphaFold model, they have worked for me 
> multiple times in molecular replacement so far.
> 
> Phil Jeffrey
> Princeton
> 
> 
> 
> On 8/2/23 3:00 PM, CENGIZ KAAN FERAH wrote:
>> Hello,
>> So I'm trying to get the data processed that I gathered from XRD for the 
>> protein BsAlaDH. Unfortunately from the method that I know of on CrysAlisPro 
>> I cannot select the recommended space group for the protein. This results in 
>> the data not being complete. Still I can get good unit cells and the 
>> degrees. Another problem is that this protein has no structure published on 
>> PDB. And the homolog proteins do not have high similarities. By that way I 
>> cannot really find a suitable space group. Can someone give me a hand on 
>> this issue.
>> Thank you.
>> 
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[ccp4bb] Macs, XQuartz, ccp4i2, Coot, iMosflm....

[Harry Powell]

Hi folks

I note that the installation pages for ccp4i2 tell me that I need _exactly_ 
version 2.8.0 of XQuartz so that things like Coot, iMosflm, etc will work. The 
problem with that is that my TrueType fonts seem to have disappeared from 
XEmacs and I’m left with the spidery bit-mapped fonts (I installed XQuartz 
2.8.0 - 2021-03-21 - First release with native Apple Silicon support, which is 
one the many “exactly 2.8.0” available).

Are there any cures for this (I’m actually running on an Intel box, not Apple 
Silicon) that let me continue to run my choice of tools “ancient and modern” 
with a pleasing appearance?

Harry



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Re: [ccp4bb] Patenting ligand binding?

[Harry Powell]

I’m left wondering which aspects of the patent application are novel and 
haven’t already been published elsewhere in the list of references (which 
include a number of Tamir’s other papers).

Others will know - can you patent something that you have already published in 
a paper? I try to steer clear of lawyers and the law...

Harry

> On 28 Jul 2023, at 12:36, John R Helliwell  wrote:
> 
> Dear Graeme,
> Yes indeed, interesting.
> There are clearly aspects of microED of proteins which might be documented as 
> non-obvious otherwise it wouldn’t have been a bit stuck ie without the 
> widespread community take up until recent years. 
> In terms of a concept patent, which this might be interpreted as, an 
> interesting one in my experience was the Kodak Storage Phosphor patent which 
> held up Fuji for a considerable time in its commercialisation of its image 
> plates even though Fuji had several specific know how patents. 
> In terms of cost of patenting, especially worldwide, this is a major 
> stumbling block at least at Univ Manchester who have a keen eye for whether 
> it might be deemed worth it. 
> Thanks for sharing.
> Greetings,
> John 
> 
> Emeritus Professor John R Helliwell DSc
> 
> 
> 
> 
>> On 28 Jul 2023, at 08:46, Winter, Graeme (DLSLtd,RAL,LSCI) 
>> <6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>>  Interesting
>> 
>> https://www.freepatentsonline.com/20230228695.pdf
>> 
>> Patent for use of electron diffraction to assess ligand binding
>> 
>> Stumbled across this because the patent application cites my work - felt 
>> that this would be of interest to the community
>> 
>> … discuss?
>> 
>> Graeme
>> 
>>  
>> -- 
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Re: [ccp4bb] On the production of a two domain protein

[Harry Powell]

Hi Armando

At the risk of appearing flippant, why not submit the sequence of the 
full-length protein to something like Alphafold (readily available to all via 
ColabFold (see 
https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb)?
 

I suspect that each of the two domains may be modelled well (provided your 
sequence is less than 2000 residues, I think) and correspond to what you have 
found experimentally, but the region between the two would have poorer 
statistics (PAE matrix would show low values and lDDT would be lower between 
the two domains).

An alternative would be to use one of the traditional homology modelling tools 
like Phyre2 in “intensive" mode (which is designed for multi domain proteins), 
but the results would probably not be as good (you can make of that what you 
will); the advantage of Phyre2 is that it’s very, very easy to run (submitting 
a job would take less time than it’s taken me to type this sentence), and has 
very helpful user support (see 
http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index)

It would at least give you something to think about before spending time in the 
lab.

Harry

> On 26 Jul 2023, at 09:14, Armando Albert  wrote:
> 
> Dear all, 
> We are trying to characterize a protein consisting of two domains. We have 
> successfully produced, purified and crystallized both domains independently. 
> However, we are unable to overexposes a soluble form of  the full-length 
> protein. Can anyone provide a strategy to merge back the independent domains 
> into a single protein chain or to modify the construct to succeed in the 
> overproduction of the full-length protein? 
> Armando
> 
> 
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Re: [ccp4bb] 1990s-style stereo viewer

[Harry Powell]

Hi Jon

Thanks for this, but as Wim and Adrian have pointed out - I can’t have been 
referring to a PS300 (maybe it was one of the ESV series, I don’t know. I might 
have remembered if I’d actually had any useful phases and done any building… by 
the time that happened we’d moved onto SGI machines) because they had the 
set-up your pictures are of. 

However,  these pics may still be of use to me.

Thanks everyone who has replied to this - I knew this would be the right place 
to ask!

Harry

> On 25 Jul 2023, at 00:23, Jon Cooper 
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> I have attached some pictures of the PS300 setup from the Birkbeck Image 
> Collection. I can make out a bit of the stereo glasses behind the dial box 
> and is that the control box on top? 
> 
> Best wishes, Jon Cooper.
> jon.b.coo...@protonmail.com
> 
> Sent with Proton Mail secure email.
> 
> --- Original Message ---
> On Monday, July 24th, 2023 at 17:38, Goldman, Adrian 
>  wrote:
> 
> 
>> Yes but this is just classic side by side stereo. I had one until quite 
>> recently. My memory of the ps300 is that it was fullscreen, not side by side 
>> with the display synced as another poster said.
>> 
>> I also feel that the ps300 didn’t flicker because it was a raster display so 
>> no matter how many lines it still displayed at 30 or 60 hz. Don’t remember. 
>> The ps2, on the other hand drew each vectors line by line - and my god that 
>> flickered awfully with “complex” objects.
>> 
>> Adrian
>> 
>> Sent from my iPhone
>> 
>>> On 24 Jul 2023, at 18:53, Harry Powell 
>>> 193323b1e616-dmarc-requ...@jiscmail.ac.uk wrote:
>>> 
>>> Hi Alastair
>>> 
>>> YES! Those are the ones.
>>> 
>>> Many thanks
>>> 
>>> Harry
>>> 
>>>> On 24 Jul 2023, at 16:46, Alastair MC EWEN alast...@igbmc.fr wrote:
>>>> 
>>>> Hi Harry,
>>>> 
>>>> Are these the ones you mean?
>>>> 
>>>> Best,
>>>> Alastair
>>>> 
>>>> ~
>>>> Alastair McEwen, PhD
>>>> Integrated Structural Biology Platform
>>>> IGBMC
>>>> 1 rue Laurent Fries
>>>> 67404 ILLKIRCH - FRANCE
>>>> tel: +33 (0)3 69 48 52 82
>>>> From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK on behalf of Harry Powell 
>>>> 193323b1e616-dmarc-requ...@jiscmail.ac.uk
>>>> Sent: 24 July 2023 16:58:26
>>>> To: CCP4BB@JISCMAIL.AC.UK
>>>> Subject: [ccp4bb] 1990s-style stereo viewer
>>>> 
>>>> Hi folks
>>>> 
>>>> I was wondering if anyone has a photo of the old-style head-mounted stereo 
>>>> viewers that used to be used to see 3D images from wall-eyed stereo pairs? 
>>>> I don’t mean the ones that were used to view the side-by-side stereo 
>>>> images that once appeared in printed journals, but the ones that were used 
>>>> for advanced computer graphics machines like E&S PS300.
>>>> 
>>>> From my somewhat dim memory, they had an adjustable mirror on one side so 
>>>> that the two views could be coalesced (with the adjustment knob on the top 
>>>> of the box).
>>>> 
>>>> More in hope than expectation…
>>>> 
>>>> Harry
>>>> 
>>>> 
>>>> 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 
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>>>> <20230724_174436.jpg>
>>> 
>>> 
>>> 
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>> 
>> 
>> ##

Re: [ccp4bb] 1990s-style stereo viewer

[Harry Powell]

Hi Alastair

YES! Those are the ones.

Many thanks

Harry

> On 24 Jul 2023, at 16:46, Alastair MC EWEN  wrote:
> 
> Hi Harry,
> 
> Are these the ones you mean? 
> 
> Best,
> Alastair
> 
> ~
> Alastair McEwen, PhD
> Integrated Structural Biology Platform
> IGBMC
> 1 rue Laurent Fries
> 67404 ILLKIRCH - FRANCE
> tel: +33 (0)3 69 48 52 82
> From: CCP4 bulletin board  on behalf of Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk>
> Sent: 24 July 2023 16:58:26
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] 1990s-style stereo viewer
>  
> Hi folks
> 
> I was wondering if anyone has a photo of the old-style head-mounted stereo 
> viewers that used to be used to see 3D images from wall-eyed stereo pairs? I 
> don’t mean the ones that were used to view the side-by-side stereo images 
> that once appeared in printed journals, but the ones that were used for 
> advanced computer graphics machines like E&S PS300.
> 
> From my somewhat dim memory, they had an adjustable mirror on one side so 
> that the two views could be coalesced (with the adjustment knob on the top of 
> the box).
> 
> More in hope than expectation…
> 
> Harry
> 
> 
> 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 
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> <20230724_174436.jpg>



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Re: [ccp4bb] 1990s-style stereo viewer

[Harry Powell]

Can’t have been a PS300 in that case!

I’ve since been reminded that they were made of wood (the stereo viewers, not 
the Evans and Sutherland. But I’m probably wrong about that as well…)

Harry

> On 24 Jul 2023, at 16:03, Wim Burmeister  wrote:
> 
> Hi,
> the E&S PS300 already used LCD-based shutter glasses connected with a wire 
> although awfully flickering with a switching frequency in the 8 Hz range!
> Wim
> 
> - Mail original -
> De: "Harry Powell" <193323b1e616-dmarc-requ...@jiscmail.ac.uk>
> À: "CCP4BB" 
> Envoyé: Lundi 24 Juillet 2023 16:58:26
> Objet: [ccp4bb] 1990s-style stereo viewer
> 
> Hi folks
> 
> I was wondering if anyone has a photo of the old-style head-mounted stereo 
> viewers that used to be used to see 3D images from wall-eyed stereo pairs? I 
> don’t mean the ones that were used to view the side-by-side stereo images 
> that once appeared in printed journals, but the ones that were used for 
> advanced computer graphics machines like E&S PS300.
> 
> From my somewhat dim memory, they had an adjustable mirror on one side so 
> that the two views could be coalesced (with the adjustment knob on the top of 
> the box).
> 
> More in hope than expectation…
> 
> Harry
> 
> 
> 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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> -- 
> Wim Burmeister 
> Professor 
> Institut de Biologie Structurale (IBS) CIBB 
> 71 avenue des Martyrs / CS 20192 
> 38044 Grenoble Cedex 9, FRANCE 
> E-mail: [ mailto:wim.burmeis...@ibs.fr | wim.burmeis...@ibs.fr ] 
> Mobile: +33 (0) 7 50 49 19 91 
> [ 
> http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/
>  | website ]
> 
> 
> 
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[ccp4bb] 1990s-style stereo viewer

[Harry Powell]

Hi folks

I was wondering if anyone has a photo of the old-style head-mounted stereo 
viewers that used to be used to see 3D images from wall-eyed stereo pairs? I 
don’t mean the ones that were used to view the side-by-side stereo images that 
once appeared in printed journals, but the ones that were used for advanced 
computer graphics machines like E&S PS300.

From my somewhat dim memory, they had an adjustable mirror on one side so that 
the two views could be coalesced (with the adjustment knob on the top of the 
box).

More in hope than expectation…

Harry


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Re: [ccp4bb] PDB, mmCIF, chain ID

[Harry Powell]

Update on this.

It seems that I was wrong, and time spent reading the manual and various 
tutorials on PDBx/mmCIF would have yielded dividends. Who would have thought 
that (we all know that people write manuals solely for their own benefit ;-))?

However, thanks to all who replied off-board to tell me that the chain ID in 
legacy PDB format in _atom_site.auth_asym_id in the mmCIF, and not in either of 
the two items I mentioned previously.

best wishes and happy Solstice!

Harry

> On 9 Jun 2023, at 15:57, Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi folks
> 
> I’ve noticed that for some structures, the PDB file seems to have the mmCIF 
> entry for the “_atom_site.label_asym_id” as the chain ID, and for other PDB 
> files it has the “_atom_site.label_entity_id”.
> 
> e.g. for 4bpq, for ATOM 1 I see - 
> 
>> CIF: ATOM 1N N  . UNK A 1 1   ? 14.187  19.549  -8.010  1.00 0.00 ? 1   
>> UNK A N  1
>> 
>> PDB: ATOM  1  N   UNK A   1  14.187  19.549  -8.010  1.00  0.00  
>>  N  
>> 
> but for 6p9o for ATOM 1 I see - 
> 
>> CIF: ATOM 1 N N . ARG A 1 64 ? -0.538 27.658 131.675 1.00 39.97 ? 64 ARG 1 N 
>> 1 64 UNP P03300 643 R
>> 
>> PDB: ATOM  1  N   ARG 1  64  -0.538  27.658 131.675  1.00 39.97  
>>  N  
> 
> both have the corresponding loop items in the same order
> 
> loop_
> _atom_site.group_PDB
> _atom_site.id
> _atom_site.type_symbol
> _atom_site.label_atom_id
> _atom_site.label_alt_id
> _atom_site.label_comp_id
> _atom_site.label_asym_id
> _atom_site.label_entity_id
> _atom_site.label_seq_id
> 
> so it shouldn’t be that the items are in a different order (which I think is 
> allowed in STAR formats).
> 
> Any ideas which one is right? Or are they both right? Or both wrong? Or am I 
> wrong about this, and have just mis-read the entries? (the refinement program 
> for 6p9o is given as both REFMAC and “PHENIX” in the CIF - presumably 
> phenix.refine, but I wouldn’t bet my house on it).
> 
> Harry
> 
> 
> 
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Re: [ccp4bb] checkCIF alert

[Harry Powell]

Hi

One small issue with Aaron’s answer - the alert specifically says “Not (SHELXL) 
Weight”, so I suspect that you may not be using SHELXL for your refinement, in 
which case the “OMIT” instructions may not be available or may take a slightly 
different form.

There’s an open-access IUCr paper written by Ton Spek that describes what to do 
when you get PLATON (and other checkCIF) alerts that should probably be your 
first port of call (maybe even before asking a bunch of macromolecular 
crystallographers what a small molecule check means, but some here may argue 
with that!).

> https://journals.iucr.org/e/issues/2020/01/00/su5533/index.html
> 
> https://doi.org/10.1107/S2056989019016244
> 
> checkCIF validation ALERTS: what they mean and how to respond
> 
> Anthony L. Spek

best wishes

Harry

> 
> On 12 Jun 2023, at 10:29, Aaron Finke 
>  wrote:
> 
> Hi Soheil,
> 
> This usually means there are outliers in the reflection list that are 
> affecting the weight parameter S that SHELXL uses. Use the OMIT instruction 
> in your SHELXL .ins file to remove those ten disagreeable reflections, e.g.
> 
> OMIT -1 -1 1
> OMIT 1 0 1
> etc.
> 
> In addition, this tends to include low-angle reflections measured “behind” 
> the beamstop. In your CheckCIF you may have an PLAT919_ALERT that checks for 
> such reflections.
> 
> Best,
> Aaron
> --
> Aaron Finke
> Beamline Scientist, MAX IV
> Lund University
> e-mail: aaron.fi...@maxiv.lu.se
> 
>> On Jun 12, 2023, at 09:51, Soheil Mahmoudi  
>> wrote:
>> 
>> Hi Everyone,
>> 
>> I am preparing a cif file from an inorganic compound measured with X-ray, I 
>> get an unexpected error during chechCIF evaluation as below,
>> 
>> Alert level A,PLAT939_ALERT_3_A Large Value of Not (SHELXL) Weight Optimized 
>> S .1029.36 Check
>> 
>> I check the disagreeable reflection and there is no more than 10.
>> 
>> Please let me know how I can solve or justify this error if you have already 
>> encountered such a problem.
>> 
>> Best Regards
>> 
>> -- 
>> Soheil Mahmoudi MSc,
>> 
>> Department of Inorganic Chemistry,
>> 
>> Faculty of Chemistry,
>> 
>> University of Vienna,
>> 
>> Währinger Straße 42,
>> 
>> 1090 Wien
>> 
>> 
>> 
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[ccp4bb] PDB, mmCIF, chain ID

[Harry Powell]

Hi folks

I’ve noticed that for some structures, the PDB file seems to have the mmCIF 
entry for the “_atom_site.label_asym_id” as the chain ID, and for other PDB 
files it has the “_atom_site.label_entity_id”.

e.g. for 4bpq, for ATOM 1 I see - 

> CIF: ATOM 1N N  . UNK A 1 1   ? 14.187  19.549  -8.010  1.00 0.00 ? 1   
> UNK A N  1
> 
> PDB: ATOM  1  N   UNK A   1  14.187  19.549  -8.010  1.00  0.00   
> N  
> 
but for 6p9o for ATOM 1 I see - 

> CIF: ATOM 1 N N . ARG A 1 64 ? -0.538 27.658 131.675 1.00 39.97 ? 64 ARG 1 N 
> 1 64 UNP P03300 643 R
> 
> PDB: ATOM  1  N   ARG 1  64  -0.538  27.658 131.675  1.00 39.97   
> N  

both have the corresponding loop items in the same order

loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id

so it shouldn’t be that the items are in a different order (which I think is 
allowed in STAR formats).

Any ideas which one is right? Or are they both right? Or both wrong? Or am I 
wrong about this, and have just mis-read the entries? (the refinement program 
for 6p9o is given as both REFMAC and “PHENIX” in the CIF - presumably 
phenix.refine, but I wouldn’t bet my house on it).

Harry



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Re: [ccp4bb] Error in xdsgui: you have to install generate_XDS.INP in your path

[Harry Powell]

Hi David

This is *exactly* what I did when implementing iMosflm’s double-clickable icons 
for Mac, Windows (“proper” Windows, not WSL, CygWin or MSYS) and Linux, many 
years ago…

Since MacOS is based on (may well actually be, I can’t remember…) BSD UNIX, 
loads of shell things (nearly but not quite 100%) that work for Linux will also 
work for Macs (as you suspect).

Harry

> On 5 Jun 2023, at 12:31, David J. Schuller  wrote:
> 
> I am not familiar with Macs, but on Linux the first problem could be easily 
> solved by having the desktop shortcut call a brief shell script rather than 
> the executable. The script would first set up the environment properly, then 
> call the executable.
> 
> 
> ===
>  All Things Serve the Beam
>  ===
>  David J. Schuller
>  modern man in a post-modern world
>  MacCHESS, Cornell University
>  schul...@cornell.edu
> From: CCP4 bulletin board  on behalf of Kay Diederichs 
> 
> Sent: Sunday, June 4, 2023 8:43 AM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: Re: [ccp4bb] Error in xdsgui: you have to install generate_XDS.INP 
> in your path
>  
> Dear Zhen Gong,
> 
> Installation of XDS and associated programs is documented in the 
> "Installation" article in XDSwiki.
> If I google "XDSwiki installation article", it is the first hit.
> 
> Your PATH is probably different when you double-click XDSGUI to start it, 
> compared to what it is on the command line.
> So don 't double-click it! Start XDSGUI from the command line - this way you 
> also see error messages from generate_XDS.INP, and output of POINTLESS and 
> Coot.
> Use the latest versions of the programs.
> 
> Concerning HDF5 processing, read the Installation article. 
> As Graeme said, you need a library, and you need to tell XDS where it is, 
> with a LIB= line in XDS.INP . 
> There are different library versions for Intel Mac and Silicon Mac. 
> if you have a Silicon Mac, I recommend to use the specific Silicon Mac 
> versions of XDS, XDSGUI and the library.
> 
> Hope this helps,
> Kay
> 
> On Sat, 3 Jun 2023 18:24:24 +0100, Zhen Gong  wrote:
> 
> >Dear all,
> >
> >I have encountered this problem in xdsgui: you have to install 
> >generate_XDS.INP in your path. Generate_XDS.INP works fine in command line 
> >but not in the GUI. I saw the same question was raised up by another user 
> >previously on CCP4bb but I was not able to see Key's reply any more. 
> >
> >Thank you very much for your help!
> >
> >Best regards,
> >Zhen
> >
> >
> >
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> >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
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Re: [ccp4bb] British X-ray Crystallographers

[Harry Powell]

Hi Gerard

I’ve mentioned it to the organiser - we shall see how long the Garmen will be 
there!

Harry

> On 24 May 2023, at 10:27, Gerard Bricogne  wrote:
> 
> Dear Jon,
> 
> Quite a line-up indeed.
> 
> Might someone at the RSC correct the typo in Elspeth's surname (in two
> places)? Or is it a plural form ;-) ?
> 
> 
> With best wishes,
> 
>  Gerard
> 
> --
> On Tue, May 23, 2023 at 10:16:54PM +, 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](https://proton.me/) secure email.
>> 
>> 
>> 
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> 
> 
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Re: [ccp4bb] British X-ray Crystallographers

[Harry Powell]

The answer at the moment is - 

> You raise an interesting point. We did a hybrid meeting back in December
> 2021 during the actual pandemic and it was not a happy experience. It was
> also felt by some people that having a hybrid depressed the in-person
> attendance. It was also expensive and the results were not that good. 
> 
> But I agree that many (all?) of the talks will be of lasting value. I will
> think about how we could record it without incurring great expense. 

So (being an optimist, as those who know me well know :-)) I’d say “maybe”.

Harry

> 
> On 24 May 2023, at 10:17, Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi Boaz
> 
> No informaiton on the website about this but I have asked the organiser.
> 
> Harry
> 
>> On 24 May 2023, at 09:58, Boaz Shaanan  wrote:
>> 
>> Indeed! Will it  perhaps be possible to watch the event by zoom? Or will a 
>> recording of it be availabe later on? Any idea?
>> Cheers,
>> Boaz
>> 
>> Boaz Shaanan, Ph.D.
>> Dept. of Life Sciences
>> Ben Gurion University
>> Beer Sheva, Israel
>> 
>> On May 24, 2023 11:26, Harry Powell 
>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>> Hi Jon
>> 
>> “Preaching to the choir”!
>> 
>> Harry
>> 
>>> On 23 May 2023, at 23:16, Jon Cooper 
>>> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> 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:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>> 
>> 
>> 
>> 
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> 
> 
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Re: [ccp4bb] British X-ray Crystallographers

[Harry Powell]

Hi Boaz

No informaiton on the website about this but I have asked the organiser.

Harry

> On 24 May 2023, at 09:58, Boaz Shaanan  wrote:
> 
> Indeed! Will it  perhaps be possible to watch the event by zoom? Or will a 
> recording of it be availabe later on? Any idea?
> Cheers,
> Boaz
> 
> Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben Gurion University
> Beer Sheva, Israel
> 
> On May 24, 2023 11:26, Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hi Jon
> 
> “Preaching to the choir”!
> 
> Harry
> 
> > On 23 May 2023, at 23:16, Jon Cooper 
> > <488a26d62010-dmarc-requ...@jiscmail.ac.uk> 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:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> > 
> 
> 
> 
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Re: [ccp4bb] British X-ray Crystallographers

[Harry Powell]

Hi Jon

“Preaching to the choir”!

Harry

> On 23 May 2023, at 23:16, Jon Cooper 
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> 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:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 



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Re: [ccp4bb] choosing an NMR structure from PDB

[Harry Powell]

Hi folks

many thanks for the replies - all very helpful. 

I can see that my example of P01132 might have been taken as a protein that I 
have a real current interest in - unfortunately, it isn’t (pace! to anyone who 
is working on malaria), it was just the first example I found that had no 
structures other than NMR (for any of the 60,000 odd other UniProts in the PDB 
which have both NMR and X-ray structures, I’ll leave it up to you to decide 
which I would choose!).

As David points out, PDBe-KB is incredibly useful for finding things like this 
(and in fact what I tend to use as a first port of call), and the sorting is 
useful - though (moving away from my original question to the wonderful world 
of X-ray) I find that it’s still necessary to engage brain when looking at the 
results (e.g. for P38398, 4y2g (2.5Å, Rwork 0.215, Rfree 0.252) is #1 but 1t15 
(1.85Å, Rwork 0.206, Rfree 0.222) is at #6 - why? looking at the PDB-REDO 
entries is educational), so it’s challenging to write scripts that will scrape 
the whole DB and give the “best” model for each.

Harry


> Hi Harry,
> 
> A useful starting point when looking for the 'best' [insert criteria here] 
> structure in the PDB for a specific protein is to visit the PDBe-KB 
> aggregated views pages (https://pdbekb.org). These pages group PDB data based 
> upon UniProt accession and the 'structures' tab on these pages shows all the 
> available PDB entries containing this protein, as well as other resources 
> that provide structural data for this protein (including some 'new-fangled 
> predicted models'). For your UniProt ID, the relevant page is 
> https://www.ebi.ac.uk/pdbe/pdbe-kb/proteins/P01132/structures.
> 
> The list of of PDB entries is sorted to have the 'best' structure at the top 
> - in this case, weighted by a combination of UniProt coverage, resolution 
> (for X-ray/EM) and validation. It also displays information on resolution (if 
> applicable), any bound ligands etc. to give this context to help in choosing 
> a suitable structure.
> 
> As you mention, for your example these are all NMR entries containing similar 
> sized fragments of the full length UniProt sequence, so the ordering is 
> predominantly using validation data to sort these. Unfortunately, in your 
> case the most recent entry was before mandatory deposition of chemical 
> shifts, so you do not have the option of experimental validation which is now 
> available for recently deposited NMR entries. Therefore these are all ordered 
> based on geometric validation.
> 
> So, although there is no concrete answer to your question, the above process 
> should help in filtering the options.
> 
> Kind Regards,
> David

> On 3 May 2023, at 13:51, Randy John Read  wrote:
> 
> Hi Harry,
> 
> My advice would be to use one of those new-fangled predicted models. You can 
> find a model in the AlphaFold database at the EBI 
> (https://alphafold.ebi.ac.uk/entry/P01132). If you look at it, there are 
> parts (likely corresponding to the constructs that were crystallised) that 
> look confidently predicted, connected by poorly-predicted loops. If you take 
> the PDB file and the PAE matrix, you can run process_predicted_model either 
> from Phenix or CCP4, which will give you individual files for the confident 
> parts of the full prediction that are likely to have the correct relative 
> orientations. (If you want to use the models for molecular replacement, 
> you’ll find that the least-confident parts are downweighted by being assigned 
> high B-factors, which is much better than having the best parts of the 
> models, with pLDDT near 100, downweighted the most by interpreting pLDDT as a 
> B-factor.) I would bet that these models will be more accurate than typical 
> NMR models.
> 
> Best wishes,
> 
> Randy

> Hi Harry
>  
> First off I would look at quality metrics. For the structures from the same 
> paper you will need to check what the differences are in the paper and choose 
> what’s closest to what you have need (experimental conditions etc) assuming 
> they all have similar quality
>  
> As a secondary priority you will want to look at number of restraints (and 
> especially in the region of interest)
>  
> Note I would expect the more modern structures from cyana and aria to better 
> due to improved methodologies
>  
> Regards
> Gary

> Hi, here is my small contribution.
> 
> The answer to your question depends quite dramatically on the intended use. 
> If you want the "best" structure you might want to see how many restraints 
> per residue were used and if high-resolution restraints as RDCs had been used.
> Recall that NMR structures are build using monomer libraries that are 
> seriously different

[ccp4bb] choosing an NMR structure from PDB

[Harry Powell]

Hi folks

I was wondering.

If there is a UniProt entry (for example, P01132, but there are plenty of 
others) for which I want the “best” (whatever that might mean) representative 
_experimental_ structure (i.e. not one of these new-fangled predicted models 
that some folk say have removed the need for actually doing experiments), but 
there are only NMR models - how do I choose?

I don’t mean “which model from the ensemble do I choose” - that’s a different 
question.

For P01132, for example, I could choose (from the PDB) 1A3P, 1EGF, 1EPG, 1EPH, 
1EPI, 1EPJ, 1GK5 or 3EGF. Note that some of these are from the same paper, so 
may be in different conditions (e.g. pH). All except the first (1A3P) cover the 
same bit of sequence.

Specifically, what should I look for in the downloadable files (mmCIF, for 
example) from the PDB?

Thoughts?

Harry


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Re: [ccp4bb] COOT crash in ccp4i2 - Error in wrapper coot_rebuild 0.0

[Harry Powell]

I hadn’t noticed until just now, but this also happens on Linux machines at 
SLAC - 

> Distributor ID:   Debian
> Description:  Debian GNU/Linux 10 (buster)
> Release:  10
> Codename: buster

:-(

Harry


> On 29 Mar 2023, at 15:02, Joseph Cockburn  wrote:
> 
> Dear BB,
> Quite a few of my students are having problems when they use COOT through 
> CCP4i2. COOT crashes, and throws the following error:
>  
> “- ERROR - Ccoot_rebuild:56 Error in wrapper coot_rebuild 0.0:: External 
> process exited”
>  
> (see attached screenshot).
> These are undergrad students who have installed the latest version of CCP4i2 
> onto their own machines. They are working through a tutorial on molecular 
> replacement, model rebuilding and refinement. They get this error when they 
> run COOT after REFMAC. This fault has occurred on both mac and windows 
> machines.
> Does anyone know how to fix this?
> Kind regards,
> Joe
>  
>  
> --
> Dr Joseph J B Cockburn DPhil
> Program Leader, Biochemistry and Medical Biochemistry
> Group Leader and Lecturer in X-ray Crystallography
> The Astbury Centre for Structural and Molecular Biology
> School of Molecular and Cellular Biology
> Faculty of Biological Sciences
> University of Leeds
> Leeds LS2 9JT
> UK
> +44 (0)113 3430758
>  
> Sometimes I need to send emails in the evenings or at weekends, but I don’t 
> expect a reply outside of your normal working hours.
>  
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 
> 



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[ccp4bb] Fwd: Crystallographic Computing School

[Harry Powell]

Dear all

Those of you who are travelling to Melbourne for the IUCr Congress and General 
Assembly in August may be interested in this (which finishes in time to get to 
the opening ceremony of the main Congress). 

To get an idea of the content of the workshop, you may wish to look at tetails 
of previous events held by the IUCr Commission for Crystallographic Computing 
which are are available here - 

> https://www.iucr.org/resources/commissions/computing/schools

Harry


> Begin forwarded message:
> 
> From: "Lutz, M.H. (Martin)" 
> Subject: Crystallographic Computing School
> Date: 23 March 2023 at 10:07:01 GMT
> To: "Lutz, M.H. (Martin)" 
> 
> 
> Dear colleagues,
> 
> as programmers and software developers you may be interested in the 
> Crystallographic Computing School. This is a satellite to the IUCr congress 
> and will take place from 19-Aug to 22-Aug-2023 at the Australian synchrotron 
> in Melbourne. We have a list of very interesting topics and great speakers. 
> Registration is now open.
> 
> http://www.cryst.chem.uu.nl/lutz/IUCrSchool2023/ 
> 
> Best wishes,
> Martin
> 
> --
> Martin Lutz
> Structural Biochemistry
> Bijvoet Centre for Biomolecular Research
> Faculty of Science
> Utrecht University
> Universiteitsweg 99
> 3584 CG Utrecht
> The Netherlands
> Tel. [+31] 06-22735980
>  



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Re: [ccp4bb] To Trim or Not to To Trim

[Harry Powell]

Whoops!

A quick glance at the PDB entry indicates I must have been clairvoyant to have 
read it 20 years ago. 

Harry

> On 20 Mar 2023, at 10:35, Harry Powell  wrote:
> 
> And there was Crambin to 0.48Å (I’ll leave it to others to argue whether or 
> not cramin is a protein, since it has “only” 46 amino acids) where (from 
> memory, I haven’t read the paper for at least 20 nyears…) they modelled 
> multiple water networks.
> 
> 3NIR, for reference.
> 
> Harry
> 
> 
>> On 20 Mar 2023, at 10:20, Eleanor Dodson 
>> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Thank you for such a careful analysis of modelling a "true" structure. You 
>> should publish this James.
>> 
>> It shows amongst other things, how R factors depend on our modelling of 
>> solvent which is not represented as individual atoms (And also I think on 
>> how the scales are derived between observation and calculation.)
>> Years ago someone refined vitamin B12 against high resolution (0.6A?) data. 
>> There is about 20-25% solvent volume I think..t was clear in the maps that 
>> there were partially occupied networks of water which extended throughout 
>> the lattice. This is probably true for proteins as well, and must affect the 
>> conformations of surface sidechains? 
>> Eleanor
>> The B12creference ...
>> 
>> Biophys J. 1986 Nov; 50(5): 967–980.
>> doi: 10.1016/S0006-3495(86)83537-8
>> PMCID: PMC1329821
>> PMID: 3790697
>> Water structure in vitamin B12 coenzyme crystals. II. Structural 
>> characteristics of the solvent networks.
>> 
>> H Savage
>> 
>> On Sun, 19 Mar 2023 at 19:37, James Holton  wrote:
>> They say one test is worth a thousand expert opinions, so I tried my hand at 
>> the former.
>> 
>> The question is: what is the right way to treat disordered side chains?:
>> a) omit atoms you cannot see
>> b) build them, and set occupancy to zero
>> c) build them, and "let the B factors take care of it"
>> d) none of the above
>> 
>> The answer, of course, is d).
>> 
>> Oh, c'mon.  Yes, I know one of a,b, or c is what you've been doing your 
>> whole life. I do it too.  But, let's face it: none of these solutions are 
>> perfect.  So, the real question is not which one is "right", but which is 
>> the least wrong?  
>> 
>> We all know what is really going on: the side chain is flapping around. No 
>> doubt it spends most of its time in energetically reasonable but 
>> nevertheless numerous conformations.  There are 41 "Favorable" rotamers for 
>> Lys alone, and it doesn't take that many to spread the density thin enough 
>> to fall below the classical 1-sigma contour level. The atoms are still 
>> there, they are still contributing to the data, and they haven't gone far. 
>> So why don't we "just" model that?  Already, I can hear the cries of 
>> "over-fitting!" and "observations/parameters!", "model bias!", and "think of 
>> the children!"  Believe it or not, none of these are the major issue here. 
>> Allow me to demonstrate:
>> 
>> Consider a simple case where we have a Lys side chain in ten conformers. I 
>> chose from popular rotamers, but evenly spread. That is, all 10 conformers 
>> have an occupancy of 0.10, and there is a 3-3-4 split of chi1 values between 
>> minus, plus and trans.  This will give the maximum contrast of density 
>> between CB and CG.  Let us further require that there is no strain in this 
>> ground-truth. No stretched bonds, no tortured angles, no clashes, etc.  Real 
>> molecules don't occupy such high-energy states unless they absolutely have 
>> to.  Let us further assume that the bulk solvent works the way phenix models 
>> it, which is a probe radius of 1.1 A for both ions and aliphatics and a 
>> shrink radius of 0.9.  But, instead of running one phenix.fmodel job, I ran 
>> ten: one for each conformer (A thru J).  To add some excitement, I moved the 
>> main chain ~0.2 A in a random direction for each conformer. I then took 
>> these ten calculated electron density maps (bulk solvent and all) and added 
>> them together to form the ground truth for the following trials. Before 
>> refinement, I added noise consistent with an I/sigma of 50 and cut the 
>> resolution at 2.0 A. Wilson B is 50:
>> 
>> CCtrue   Rwork%  Rfree%   fo-fc(sigma)   description
>> 0.8943 9.05   10.60  5.9 stump at CB
>> 0.9540 9.29   11.73  6.0 single conformer, zero occu

Re: [ccp4bb] To Trim or Not to To Trim

[Harry Powell]

And there was Crambin to 0.48Å (I’ll leave it to others to argue whether or not 
cramin is a protein, since it has “only” 46 amino acids) where (from memory, I 
haven’t read the paper for at least 20 nyears…) they modelled multiple water 
networks.

3NIR, for reference.

Harry


> On 20 Mar 2023, at 10:20, Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Thank you for such a careful analysis of modelling a "true" structure. You 
> should publish this James.
> 
> It shows amongst other things, how R factors depend on our modelling of 
> solvent which is not represented as individual atoms (And also I think on how 
> the scales are derived between observation and calculation.)
> Years ago someone refined vitamin B12 against high resolution (0.6A?) data. 
> There is about 20-25% solvent volume I think..t was clear in the maps that 
> there were partially occupied networks of water which extended throughout the 
> lattice. This is probably true for proteins as well, and must affect the 
> conformations of surface sidechains? 
> Eleanor
> The B12creference ...
> 
> Biophys J. 1986 Nov; 50(5): 967–980.
> doi: 10.1016/S0006-3495(86)83537-8
> PMCID: PMC1329821
> PMID: 3790697
> Water structure in vitamin B12 coenzyme crystals. II. Structural 
> characteristics of the solvent networks.
> 
> H Savage
> 
> On Sun, 19 Mar 2023 at 19:37, James Holton  wrote:
> They say one test is worth a thousand expert opinions, so I tried my hand at 
> the former.
> 
> The question is: what is the right way to treat disordered side chains?:
> a) omit atoms you cannot see
> b) build them, and set occupancy to zero
> c) build them, and "let the B factors take care of it"
> d) none of the above
> 
> The answer, of course, is d).
> 
> Oh, c'mon.  Yes, I know one of a,b, or c is what you've been doing your whole 
> life. I do it too.  But, let's face it: none of these solutions are perfect.  
> So, the real question is not which one is "right", but which is the least 
> wrong?  
> 
> We all know what is really going on: the side chain is flapping around. No 
> doubt it spends most of its time in energetically reasonable but nevertheless 
> numerous conformations.  There are 41 "Favorable" rotamers for Lys alone, and 
> it doesn't take that many to spread the density thin enough to fall below the 
> classical 1-sigma contour level. The atoms are still there, they are still 
> contributing to the data, and they haven't gone far. So why don't we "just" 
> model that?  Already, I can hear the cries of "over-fitting!" and 
> "observations/parameters!", "model bias!", and "think of the children!"  
> Believe it or not, none of these are the major issue here. Allow me to 
> demonstrate:
> 
> Consider a simple case where we have a Lys side chain in ten conformers. I 
> chose from popular rotamers, but evenly spread. That is, all 10 conformers 
> have an occupancy of 0.10, and there is a 3-3-4 split of chi1 values between 
> minus, plus and trans.  This will give the maximum contrast of density 
> between CB and CG.  Let us further require that there is no strain in this 
> ground-truth. No stretched bonds, no tortured angles, no clashes, etc.  Real 
> molecules don't occupy such high-energy states unless they absolutely have 
> to.  Let us further assume that the bulk solvent works the way phenix models 
> it, which is a probe radius of 1.1 A for both ions and aliphatics and a 
> shrink radius of 0.9.  But, instead of running one phenix.fmodel job, I ran 
> ten: one for each conformer (A thru J).  To add some excitement, I moved the 
> main chain ~0.2 A in a random direction for each conformer. I then took these 
> ten calculated electron density maps (bulk solvent and all) and added them 
> together to form the ground truth for the following trials. Before 
> refinement, I added noise consistent with an I/sigma of 50 and cut the 
> resolution at 2.0 A. Wilson B is 50:
> 
> CCtrue   Rwork%  Rfree%   fo-fc(sigma)   description
> 0.8943 9.05   10.60  5.9 stump at CB
> 0.9540 9.29   11.73  6.0 single conformer, zero occupancy
> 0.947110.35   15.04  5.1 single conformer, full occupancy, 
> refmac5
> 0.9523 9.78   15.61  4.9 single conformer, full occupancy, 
> phenix.refine
>
> So, it would appear that the zero-occupancy choice "wins", but by the 
> narrowest of margins.  Here CCtrue is the Pearson correlation coefficient 
> between the ground-truth right-answer electron density and the 2fofc map 
> resulting from the refinement.  Rwork and Rfree are the usual suspects, and 
> fo-fc indicates the tallest peak in the difference map. Refinement was with 
> refmac unless otherwise indicated. I think we often forget that both phenix 
> and refmac restrain B factor values, not just through bonds but through 
> space, and they use rather different algorithms. Refmac tries to make the 
> histogram of B factors "look right", whereas phenix allows steeper gradien

Re: [ccp4bb] To Trim or Not to To Trim

[Harry Powell]

Hi Jürgen

You might think so, but I’d disagree. Not going too far away from your line of 
reasoning I could also put in a completely fictitious ligand or cofactor and 
assign its occupancies to zero (I really, really knew it was there but I just 
couldn’t find any evidence… :-))

Harry

> On 10 Mar 2023, at 16:58, Jurgen Bosch  wrote:
> 
> Going back to RIP phasing methods :-)
> So Harry in your particular case occupancy of zero would actually reflect 
> reality for those “combusted” atoms.
> 
> Jürgen 
> 
>> On Mar 10, 2023, at 11:56 AM, Harry Powell 
>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Hi folks
>> 
>> One other thing that I haven’t noticed anyone mentioning yet (sorry to those 
>> who have mentioned it!!) is that you may not see your sidechain atoms in 
>> density because they are not there at all, in spite of what you may have had 
>> in the original protein, or even if the atoms were really there in the 
>> crystal _before_ exposure to the beam.
>> 
>> The coordinates are supposed to be what you actually find, not what you hope 
>> is there.
>> 
>> Just my two ha’porth
>> 
>> Harry
>> 
>> 
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Re: [ccp4bb] To Trim or Not to To Trim

[Harry Powell]

Hi folks

One other thing that I haven’t noticed anyone mentioning yet (sorry to those 
who have mentioned it!!) is that you may not see your sidechain atoms in 
density because they are not there at all, in spite of what you may have had in 
the original protein, or even if the atoms were really there in the crystal 
_before_ exposure to the beam.

The coordinates are supposed to be what you actually find, not what you hope is 
there.

Just my two ha’porth

Harry



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Re: [ccp4bb] Structural alignment and classification

[Harry Powell]

Hi Eleanor

According to 

https://www.ccp4.ac.uk/html/gesamt.html

"Gesamt aligns two or more structures…”

and 

https://www.ccp4.ac.uk/html/superpose.html

"superpose aligns and superposes two or more protein structures…”

But the real expert is probably Eugene.

Harry

> On 6 Mar 2023, at 14:55, Eleanor Dodson  wrote:
> 
> Does Superpose or GESAMT align multiple structures? 
> And can either read the NMR format and apply alignment to MODEL 1 ; MODE:L 2 
> etc?
> Eleanor
> 
> On Mon, 6 Mar 2023 at 14:53, Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> Or you could use Gesamt - also in CCP4.
> 
> Harry
> 
> > On 6 Mar 2023, at 13:15, Kay Diederichs  
> > wrote:
> > 
> > Dear Armando,
> > 
> > besides THESEUS, you could use SUPERPOSE (in CCP4) or USalign 
> > (https://zhanggroup.org/US-align/).
> > In my tests, THESEUS sometimes crashed in different ways. USalign is very 
> > robust; SUPERPOSE is fast.
> > 
> > HTH,
> > Kay
> > 
> > On Mon, 6 Mar 2023 08:35:20 +0100, Armando Albert  
> > wrote:
> > 
> >> Dear all, 
> >> I want to align several structures we obtained from a fragment screening 
> >> campaign and cluster them according to RMSD. 
> >> Is MNYFIT still running? What else can I run?
> >> Thank you
> >> Armando
> >> 
> >> 
> >> 
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Re: [ccp4bb] Structural alignment and classification

[Harry Powell]

Or you could use Gesamt - also in CCP4.

Harry

> On 6 Mar 2023, at 13:15, Kay Diederichs  
> wrote:
> 
> Dear Armando,
> 
> besides THESEUS, you could use SUPERPOSE (in CCP4) or USalign 
> (https://zhanggroup.org/US-align/).
> In my tests, THESEUS sometimes crashed in different ways. USalign is very 
> robust; SUPERPOSE is fast.
> 
> HTH,
> Kay
> 
> On Mon, 6 Mar 2023 08:35:20 +0100, Armando Albert  
> wrote:
> 
>> Dear all, 
>> I want to align several structures we obtained from a fragment screening 
>> campaign and cluster them according to RMSD. 
>> Is MNYFIT still running? What else can I run?
>> Thank you
>> Armando
>> 
>> 
>> 
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Re: [ccp4bb] Tools for structure-based multiple sequence alignment

[Harry Powell]

Hi Manoj

If the structures are in the PDB, then PDB-KB may have already done the work 
for you - 

https://www.ebi.ac.uk/pdbe/pdbe-kb/

They run Gesamt on homologous structures for the whole PDB every week (as I 
understand it).

Harry

> On 2 Mar 2023, at 07:45, Manoj N  wrote:
> 
> Dear all,
> We want to generate a structure-based multiple sequence 
> alignment for a large number of homologous structures (>100). 
> 
> What are the available programs (stand-alone or webserver) to do this? 
> 
> Thank you,
> Best wishes,
> Manoj
> 
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[ccp4bb] Bioinformatics post

[Harry Powell]

Hi folks

Please let anyone know who may be interested in working in the heart of South 
Kensington, funded by the Wellcome Trust.

Job Opportunity for Experienced Bioinformatics Software Developer (Phyre and 
Missense3D) See:   
https://www.jobs.ac.uk/job/CXG066/bioinformatics-software-developer-in-protein-structure-and-genetic-variant-modelling
 

 
Both programs are run as web services; Phyre2 is a homology modelling program - 
even in the time of AlphaFold we’re processing > 1000 models a day (project 
supervised by Prof Mike Sternberg). Missense-3D predicts the structural changes 
introduced by an amino acid substitution (project supervised by Dr Alessia 
David).

> http://www.sbg.bio.ic.ac.uk/phyre2/
> http://missense3d.bc.ic.ac.uk/missense3d/

Harry 




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Re: [ccp4bb] Future Diffraction Methods

[Harry Powell]

My (limited) experience of the Diffraction Methods GRC suggests that the most 
valuable part of these meetings is when people get together outside the talks - 
so independent of the session chairs (apart from the people that they invite) 
and of any instructions given to speakers.

Just my two ha’porth

Harry

> On 30 Jan 2023, at 11:54, Frank von Delft  wrote:
> 
> Whether cross-pollination happens depends on the session chairs, and the 
> remit they're given, and the instructions given to the speakers:  if early on 
> everybody sets the tone, to inform as much as advertise, then it could be a 
> rip-roaringly interesting meeting.
> 
> At least, I've never encountered a method that was beyond my or any of my 
> students' comprehension, at least at some high level, provided we were 
> allowed to ask questions about it.
> 
> Frank
> 
> 
> 
> On 30/01/2023 10:40, Gerard Kleywegt wrote:
>> Hi all,
>> 
>> I'm a big believer in cross-pollination between disciplines. I think there 
>> could be room for a multidisciplinary methods meeting (MMM) provided the 
>> right topics are chosen. If these are things that concern NMR-ists, 
>> X-ray-ans and cryo-EM-ers equally you might get the right mix of people in 
>> the room and exchange of ideas and experiences with it. For example, all 
>> three use Maximum Likelihood (ML) methods. All three are or possibly will be 
>> interested in applying Machine Learning (e, ML) methods (e.g., in 
>> cryo-EM these have already been used for automatic particle picking and map 
>> improvement). And they all need to worry about validating models based on 
>> predicted models.
>> 
>> Having said that, I think there is also a need for specialised, 
>> method-specific meetings, but the two types of meeting are not mutually 
>> exclusive.
>> 
>> My 2 öre,
>> 
>> --Gerard
>> 
>> 
>> 
>> On Mon, 30 Jan 2023, Alexandre Ourjoumtsev wrote:
>> 
>>> Hi, everybody, hi, Nukri and Pavel !
>>> 
>>> I fully agree with Pavel that, if the speakers are not exceptional, if they 
>>> are (as usually) concentrated on their specific and narrow problems, 
>>> cross-discipline meetings make us lost quite fast, they are annoying and 
>>> useless. Richard Feynmann had the same experience, according to his books 
>>> :-)
>>> 
>>> At such meetings, people need to have a common point. However, it may be a 
>>> point different from the SUBJECT of the research. This may be common TOOLS. 
>>> And this indeed may lead to new ideas and results, maybe great ones.
>>> 
>>> There is a many-years positive experience of such meetings in Pushchino in 
>>> 80ths (both of you know this place; for other readers of this post - this 
>>> was indeed a great place !). Closer to our community, as I remember, Paul 
>>> Adams and John Spence organized such kind of meetings about 20 years ago in 
>>> US. I guess I know practical results from both these groups of meetings. 
>>> Some Crystallographic Computing Schools also try to act a little bit 
>>> "around the tools".
>>> 
>>> Why do not we think specifically in THIS direction (which is actually what 
>>> Nukri said, right? and somehow not so far from the previous GRC?) ?
>>> This is hard but feasible. But indeed hard :-(
>>> 
>>> Best regards to everybody,
>>> and many thanks to James for raising the problem !
>>> 
>>> Sacha Urzhumtsev
>>> 
>>> - Le 30 Jan 23, à 2:38, Nukri Sanishvili  a écrit :
>>> 
 Hi Pavel,
 Your description of the current status is exactly correct. And that's 
 exactly
 what I am proposing to change or, more accurately, try to change. By 
 seeking
 out and bringing together people who do complementary and collaborative 
 work,
 so they can set an example for others.
 This, of course, isn't meant in place of more narrowly defined topical 
 meetings
 and conferences but to be in addition to those.
 James asked the community if we had new ideas and this is a new-ish 
 approach I
 was suggesting.
 Don't get me wrong - I myself will happily continue my efforts in more 
 narrowly
 defined meetings.
 Best wishes,
 Nukri
>>> 
 On Sun, Jan 29, 2023 at 6:44 PM Pavel Afonine < [ 
 mailto:pafon...@gmail.com |
 pafon...@gmail.com ] > wrote:
>>> 
> Nukri,
>>> 
> IMO, the idea of cross-discipline meetings is great conceptually, at 
> least for
> reasons you pointed out, but utopical in practice. When we attend our
> field-specific meetings we meet colleagues we know, we talk to 
> collaborators
> from the past or find new ones, we have things in common that we can talk 
> about
> to forge something new, we meet authors of papers we were excited to 
> read, and
> so on, and so on.
> I once attended a meeting of some chemistry society, well, which is not 
> too far
> from what we are doing, really, as interpreting atomic models is 
> essentially
> putting your chemistry knowledge into production. And, at that meeting I 

Re: [ccp4bb] binding pockets...

[Harry Powell]

Hi

This was brought to my attention after I posted yesterday, to add to the list I 
sent then - 

pyvol - Python (as a PyMol plug-in, a python module and as a command-line 
Python script) - needs a config file to run - 
https://schlessinger-lab.github.io/pyvol/index.html 

The output is the surface of the pocket as vertices and faces in a file with 
the extension “.obj” (the other programs fill the pocket with dummy atoms). 
Result looks most similar to that from parKVFinder.


Again, many thanks for the input

Harry

> On 12 Jan 2023, at 11:26, Harry Powell  wrote:
> 
> Hi folks
> 
> a round-up of what I’ve found - four examples that I can run from the 
> command-line.
> 
> fpocket - mostly C, C++ - https://github.com/Discngine/fpocket
> 
> ghecom - C - https://pdbj.org/ghecom/
> 
> parKVFinder (replaces KVFinder, also available as a Python module) - Python:C 
> 60:40 - https://github.com/lbc-lnbio/parkvfinder
> 
> p2rank - Groovy, Java (won't run with Java 19 on my High Sierra box, works 
> with Java 17) - https://github.com/rdk/p2rank
> 
> and some screenshots (from QtMG) of the surface of the largest pocket found 
> by each (using default settings) for the polypeptide from chain A of 1A9W (a 
> haemoglobin) I’ve removed all HETATMs from this before running the progs) 
> superimposed over the haem (or heme, if you prefer ;-)) - in the order of the 
> programs given above - 
> 
> 
> 
> Harry




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Re: [ccp4bb] binding pockets...

[Harry Powell]

Hi Mike

Interesting. I haven’t looked at Java stuff for quite some time…

Harry

> On 4 Jan 2023, at 12:53, Mike S  wrote:
> 
> Have you tried P2Rank?  It is quite fast, and there is a standalone version 
> that has command line options to run against all coordinate files in a 
> directory using batch mode.
> 
> https://prankweb.cz/
> https://prankweb.cz/about
> https://github.com/rdk/p2rank
> 
> You can try the web version to see how it performs with one of your 
> favorites.  I like the automatically created pymol scripts as well.  It does 
> occasionally split a larger pocket into smaller ones, similar to the fpocket 
> behavior, but perhaps not quite as frequent.
> 
> -Mike
> 
> On Wed, Jan 4, 2023 at 6:31 AM Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> THX for the replies - 
> 
> > On 3 Jan 2023, at 22:56, Bernhard Rupp  wrote:
> > 
> > There is also a service from our Polish friends:
> > called Spaceball (jokes aside) that calculates the volume of protein 
> > cavities (http://www.ifpan.edu.pl/~chwastyk/spaceball/).
> > and the services in Hamburg are useful for visualization of binding pockets 
> > and channels
> > https://proteins.plus/
> 
> I really want something that I can put iin a script, not a web-page. These 
> both appear to be web interfaces 
> 
> > James Holton - 
> > 
> > PanDDA?
> 
> PanDDA is really for density analysis across putative changed-state datasets 
> - I have many thousands of models to inspect that have no associated 
> experimental datasets
> 
> > Andre Godoy - 
> > 
> > if you mean predicting binding sites, FT map is quite good
> > 
> 
> Unfortunately another web interface - http://ftmap.bu.edu/serverhelp.php
> 
> I’m really after alternatives to programs like:
> 
> pyKVFinder (but that won’t install easily from PYPI on my Mac because 
> my OS is too old - if anyone wants to buy me a new big, fast Mac to replace 
> my old, fast Mac I should be able to install that easily!!) or 
> 
> fpocket (which works okay but is splitting up “obvious" single-site 
> pockets into multiple pockets). 
> 
> Plus they need to be able to run from a script (or from the command-line so 
> it can be scripted) - web interfaces are okay if you have a few examples, but 
> when you’re analysing 1000 - 1500 models a day, clicking buttons gets a 
> little boring!
> 
> Sorry my initial post wasn’t clearer
> 
> Harry
> 
> 
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Re: [ccp4bb] binding pockets...

[Harry Powell]

THX for the replies - 

> On 3 Jan 2023, at 22:56, Bernhard Rupp  wrote:
> 
> There is also a service from our Polish friends:
> called Spaceball (jokes aside) that calculates the volume of protein cavities 
> (http://www.ifpan.edu.pl/~chwastyk/spaceball/).
> and the services in Hamburg are useful for visualization of binding pockets 
> and channels
> https://proteins.plus/

I really want something that I can put iin a script, not a web-page. These both 
appear to be web interfaces 

> James Holton - 
> 
> PanDDA?

PanDDA is really for density analysis across putative changed-state datasets - 
I have many thousands of models to inspect that have no associated experimental 
datasets

> Andre Godoy - 
> 
> if you mean predicting binding sites, FT map is quite good
> 

Unfortunately another web interface - http://ftmap.bu.edu/serverhelp.php

I’m really after alternatives to programs like:

pyKVFinder (but that won’t install easily from PYPI on my Mac because 
my OS is too old - if anyone wants to buy me a new big, fast Mac to replace my 
old, fast Mac I should be able to install that easily!!) or 

fpocket (which works okay but is splitting up “obvious" single-site 
pockets into multiple pockets). 

Plus they need to be able to run from a script (or from the command-line so it 
can be scripted) - web interfaces are okay if you have a few examples, but when 
you’re analysing 1000 - 1500 models a day, clicking buttons gets a little 
boring!

Sorry my initial post wasn’t clearer

Harry


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[ccp4bb] binding pockets...

[Harry Powell]

Hi folks

I was wondering what people’s favourite program is to find binding pockets in 
proteins. I’ve had a look at a couple but each has its own idiosyncrasies.

HNY

Harry


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Re: [ccp4bb] ligands found in ChEBI...

[Harry Powell]

Hi folks

it seems that the “easiest” way to get my coords if I know the ChEBI identifier 
is to do something like this in Python3 (note this snippet has no error 
checking!):

> import sys # only needed to parse the command-line arguments
> chebi = sys.argv[1] # expect ChEBI identifier without the leading “CHEBI:" 
> import pubchempy # have to pip install or conda install, whatever for your 
> environment
> pubchempy.download("SDF", f“ChEBI_{chebi}.sdf", f”CHEBI:{chebi}", "name", 
> record_type="3d", overwrite=True)

and running that with “64119” as the argument gives me a file ChEBI_64119.sdf 
with 3D coords.

Many thanks to all who got me out of my hole!

Harry

> On 6 Dec 2022, at 12:19, Harry Powell  wrote:
> 
> Hi Julie
> 
> Ta.
> 
> Do you know if there’s an API (pref. Python 3.9 or later) for downloading the 
> 3D coordinates from ChemSpider?
> 
> Harry
> 
>> On 6 Dec 2022, at 12:04, Julie Tucker 
>> <20908adb55d7-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Chemspider can also provide you with a .mol file amongst other things.
>> http://www.chemspider.com/Chemical-Structure.2424.html?rid=281bd645-a2c9-4d07-af08-c3148b323194
>> Best wishes
>> Julie
>> 
>> On Tue, 6 Dec 2022 at 11:55, Oliver Smart  wrote:
>> Hi Harry,
>> 
>> The SDF found at ChEBI is a 2D SDF with the coordinates used for the 
>> diagram. I do not think that ChEBI has
>> 3D coordinates. Why not use PubChem instead as this does provide 3D sdf 
>> files?
>> 
>> For your caffeine example:
>> 
>> https://pubchem.ncbi.nlm.nih.gov/compound/64119 
>> 
>> There 
>> 
>> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/2519/record/SDF/?record_type=3d&response_type=save&response_basename=Conformer3D_CID_2519
>>  
>> 
>> Provides a  SDF file.
>> 
>> Hope this helps
>> 
>> Oliver
>> 
>> p.s. I you are stuck with ChEBI identifiers it would be possible to 
>> programatically find the equivalent PubChem CID.
>> 
>> 
>> 
>> 
>>> On 6 Dec 2022, at 11:31, Harry Powell 
>>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>>> 
>>> Hi folks
>>> 
>>> Can anyone help with this?
>>> 
>>> I must have missed something in the documentation, because I don’t 
>>> understand why the .mol and .sdf files downloaded from 
>>> 
>>> https://www.ebi.ac.uk/chebi
>>> 
>>> seem to have aromatic C-C bonds that are 0.825 Å long (it’s a few decades 
>>> now since I solved any small molecule structures, but something around 
>>> 1.395Å rings a faint bell).
>>> 
>>> I need to have ligands that have realistic sizes, and while I’m perfectly 
>>> at ease scaling the models to what I think are sensible sizes, I can’t help 
>>> but think that this isn’t necessary and I’ve missed something somewhere.
>>> 
>>> Here’s an example of a molecule that I used this morning - 
>>> 
>>> 
>>> https://www.ebi.ac.uk/chebi/saveStructure.do?defaultImage=true&chebiId=31332&imageId=0
>>> 
>>> contents of downloaded file - 
>>>> 
>>>> Marvin  01140911122D  
>>>> 
>>>> 15 15  0  0  0  0999 V2000
>>>>  -0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>>  -0.71450.41250. N   0  0  0  0  0  0  0  0  0  0  0  0
>>>>   0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>>   0.71450.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>>   0.   -0.82500. N   0  0  0  0  0  0  0  0  0  0  0  0
>>>>   0.0.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>>   1.49920.66740. N   0  0  0  0  0  0  0  0  0  0  0  0
>>>>   1.4992   -0.66750. N   0  0  0  0  0  0  0  0  0  0  0  0
>>>>   1.98410.0. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>>  -1.4289   -0.82500. O   0  0  0  0  0  0  0  0  0  0  0  0
>>>>   0.00011.65000. O   0  0  0  0  0  0  0  0  0  0  0  0
>>>>   0.0001   -1.65000. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>>   1.75411.45200. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>>  -1.42890.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>>   2.0809   -1.53650. O   0  0  0  0  0  0  0  0  0  0  0  0
>>>> 10  1  2  0  0  0  0
>>>> 1  2  1  0  0  0  0
>>>> 14  

Re: [ccp4bb] ligands found in ChEBI...

[Harry Powell]

Hi Julie

Ta.

Do you know if there’s an API (pref. Python 3.9 or later) for downloading the 
3D coordinates from ChemSpider?

Harry

> On 6 Dec 2022, at 12:04, Julie Tucker 
> <20908adb55d7-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Chemspider can also provide you with a .mol file amongst other things.
> http://www.chemspider.com/Chemical-Structure.2424.html?rid=281bd645-a2c9-4d07-af08-c3148b323194
> Best wishes
> Julie
> 
> On Tue, 6 Dec 2022 at 11:55, Oliver Smart  wrote:
> Hi Harry,
> 
> The SDF found at ChEBI is a 2D SDF with the coordinates used for the diagram. 
> I do not think that ChEBI has
> 3D coordinates. Why not use PubChem instead as this does provide 3D sdf files?
> 
> For your caffeine example:
> 
> https://pubchem.ncbi.nlm.nih.gov/compound/64119 
> 
> There 
> 
> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/2519/record/SDF/?record_type=3d&response_type=save&response_basename=Conformer3D_CID_2519
>  
> 
> Provides a  SDF file.
> 
> Hope this helps
> 
> Oliver
> 
> p.s. I you are stuck with ChEBI identifiers it would be possible to 
> programatically find the equivalent PubChem CID.
> 
> 
> 
> 
>> On 6 Dec 2022, at 11:31, Harry Powell 
>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Hi folks
>> 
>> Can anyone help with this?
>> 
>> I must have missed something in the documentation, because I don’t 
>> understand why the .mol and .sdf files downloaded from 
>> 
>>  https://www.ebi.ac.uk/chebi
>> 
>> seem to have aromatic C-C bonds that are 0.825 Å long (it’s a few decades 
>> now since I solved any small molecule structures, but something around 
>> 1.395Å rings a faint bell).
>> 
>> I need to have ligands that have realistic sizes, and while I’m perfectly at 
>> ease scaling the models to what I think are sensible sizes, I can’t help but 
>> think that this isn’t necessary and I’ve missed something somewhere.
>> 
>> Here’s an example of a molecule that I used this morning - 
>> 
>>  
>> https://www.ebi.ac.uk/chebi/saveStructure.do?defaultImage=true&chebiId=31332&imageId=0
>> 
>> contents of downloaded file - 
>>> 
>>>  Marvin  01140911122D  
>>> 
>>> 15 15  0  0  0  0999 V2000
>>>   -0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -0.71450.41250. N   0  0  0  0  0  0  0  0  0  0  0  0
>>>0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>0.71450.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>0.   -0.82500. N   0  0  0  0  0  0  0  0  0  0  0  0
>>>0.0.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>1.49920.66740. N   0  0  0  0  0  0  0  0  0  0  0  0
>>>1.4992   -0.66750. N   0  0  0  0  0  0  0  0  0  0  0  0
>>>1.98410.0. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -1.4289   -0.82500. O   0  0  0  0  0  0  0  0  0  0  0  0
>>>0.00011.65000. O   0  0  0  0  0  0  0  0  0  0  0  0
>>>0.0001   -1.65000. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>1.75411.45200. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -1.42890.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>2.0809   -1.53650. O   0  0  0  0  0  0  0  0  0  0  0  0
>>> 10  1  2  0  0  0  0
>>>  1  2  1  0  0  0  0
>>> 14  2  1  0  0  0  0
>>>  8  3  1  0  0  0  0
>>>  4  3  2  0  0  0  0
>>>  7  4  1  0  0  0  0
>>>  1  5  1  0  0  0  0
>>>  5  3  1  0  0  0  0
>>> 12  5  1  0  0  0  0
>>>  6  2  1  0  0  0  0
>>>  6  4  1  0  0  0  0
>>> 11  6  2  0  0  0  0
>>>  9  7  1  0  0  0  0
>>> 13  7  1  0  0  0  0
>>>  9  8  2  0  0  0  0
>>> M  END
>>> 
>> 
>> Harry
>> 
>> 
>> 
>> 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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> 
> 
> 
> -- 
> Julie Tuck

Re: [ccp4bb] ligands found in ChEBI...

[Harry Powell]

Hi Oliver

I’d just worked that out when I tried an obviously non-planar molecule (that I 
didn’t include with my breakfast this morning)!

PubChem looks like a useful way forward - many thanks.

Harry

> On 6 Dec 2022, at 11:55, Oliver Smart  wrote:
> 
> Hi Harry,
> 
> The SDF found at ChEBI is a 2D SDF with the coordinates used for the diagram. 
> I do not think that ChEBI has
> 3D coordinates. Why not use PubChem instead as this does provide 3D sdf files?
> 
> For your caffeine example:
> 
> https://pubchem.ncbi.nlm.nih.gov/compound/64119 
> 
> There 
> 
> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/2519/record/SDF/?record_type=3d&response_type=save&response_basename=Conformer3D_CID_2519
>  
> 
> Provides a  SDF file.
> 
> Hope this helps
> 
> Oliver
> 
> p.s. I you are stuck with ChEBI identifiers it would be possible to 
> programatically find the equivalent PubChem CID.
> 
> 
> 
> 
>> On 6 Dec 2022, at 11:31, Harry Powell 
>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Hi folks
>> 
>> Can anyone help with this?
>> 
>> I must have missed something in the documentation, because I don’t 
>> understand why the .mol and .sdf files downloaded from 
>> 
>>  https://www.ebi.ac.uk/chebi
>> 
>> seem to have aromatic C-C bonds that are 0.825 Å long (it’s a few decades 
>> now since I solved any small molecule structures, but something around 
>> 1.395Å rings a faint bell).
>> 
>> I need to have ligands that have realistic sizes, and while I’m perfectly at 
>> ease scaling the models to what I think are sensible sizes, I can’t help but 
>> think that this isn’t necessary and I’ve missed something somewhere.
>> 
>> Here’s an example of a molecule that I used this morning - 
>> 
>>  
>> https://www.ebi.ac.uk/chebi/saveStructure.do?defaultImage=true&chebiId=31332&imageId=0
>> 
>> contents of downloaded file - 
>>> 
>>>  Marvin  01140911122D  
>>> 
>>> 15 15  0  0  0  0999 V2000
>>>   -0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -0.71450.41250. N   0  0  0  0  0  0  0  0  0  0  0  0
>>>0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>0.71450.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>0.   -0.82500. N   0  0  0  0  0  0  0  0  0  0  0  0
>>>0.0.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>1.49920.66740. N   0  0  0  0  0  0  0  0  0  0  0  0
>>>1.4992   -0.66750. N   0  0  0  0  0  0  0  0  0  0  0  0
>>>1.98410.0. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -1.4289   -0.82500. O   0  0  0  0  0  0  0  0  0  0  0  0
>>>0.00011.65000. O   0  0  0  0  0  0  0  0  0  0  0  0
>>>0.0001   -1.65000. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>1.75411.45200. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -1.42890.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>2.0809   -1.53650. O   0  0  0  0  0  0  0  0  0  0  0  0
>>> 10  1  2  0  0  0  0
>>>  1  2  1  0  0  0  0
>>> 14  2  1  0  0  0  0
>>>  8  3  1  0  0  0  0
>>>  4  3  2  0  0  0  0
>>>  7  4  1  0  0  0  0
>>>  1  5  1  0  0  0  0
>>>  5  3  1  0  0  0  0
>>> 12  5  1  0  0  0  0
>>>  6  2  1  0  0  0  0
>>>  6  4  1  0  0  0  0
>>> 11  6  2  0  0  0  0
>>>  9  7  1  0  0  0  0
>>> 13  7  1  0  0  0  0
>>>  9  8  2  0  0  0  0
>>> M  END
>>> 
>> 
>> Harry
>> 
>> 
>> 
>> 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 
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Re: [ccp4bb] ligands found in ChEBI...

[Harry Powell]

Whoops. 

It looks like these entries are not supposed to be 3D models, but 
representations of 2D line drawings (which I noticed when I had a look at an 
obviously non-planar molecule).

Which is a shame, because I was hoping I could use them in 3D modelling…

Sorry for polluting your inboxes!

Harry

> On 6 Dec 2022, at 11:31, Harry Powell  wrote:
> 
> Hi folks
> 
> Can anyone help with this?
> 
> I must have missed something in the documentation, because I don’t understand 
> why the .mol and .sdf files downloaded from 
> 
>   https://www.ebi.ac.uk/chebi
> 
> seem to have aromatic C-C bonds that are 0.825 Å long (it’s a few decades now 
> since I solved any small molecule structures, but something around 1.395Å 
> rings a faint bell).
> 
> I need to have ligands that have realistic sizes, and while I’m perfectly at 
> ease scaling the models to what I think are sensible sizes, I can’t help but 
> think that this isn’t necessary and I’ve missed something somewhere.
> 
> Here’s an example of a molecule that I used this morning - 
> 
>   
> https://www.ebi.ac.uk/chebi/saveStructure.do?defaultImage=true&chebiId=31332&imageId=0
> 
> contents of downloaded file - 
>> 
>>  Marvin  01140911122D  
>> 
>> 15 15  0  0  0  0999 V2000
>>   -0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>   -0.71450.41250. N   0  0  0  0  0  0  0  0  0  0  0  0
>>0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>0.71450.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>0.   -0.82500. N   0  0  0  0  0  0  0  0  0  0  0  0
>>0.0.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
>>1.49920.66740. N   0  0  0  0  0  0  0  0  0  0  0  0
>>1.4992   -0.66750. N   0  0  0  0  0  0  0  0  0  0  0  0
>>1.98410.0. C   0  0  0  0  0  0  0  0  0  0  0  0
>>   -1.4289   -0.82500. O   0  0  0  0  0  0  0  0  0  0  0  0
>>0.00011.65000. O   0  0  0  0  0  0  0  0  0  0  0  0
>>0.0001   -1.65000. C   0  0  0  0  0  0  0  0  0  0  0  0
>>1.75411.45200. C   0  0  0  0  0  0  0  0  0  0  0  0
>>   -1.42890.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
>>2.0809   -1.53650. O   0  0  0  0  0  0  0  0  0  0  0  0
>> 10  1  2  0  0  0  0
>>  1  2  1  0  0  0  0
>> 14  2  1  0  0  0  0
>>  8  3  1  0  0  0  0
>>  4  3  2  0  0  0  0
>>  7  4  1  0  0  0  0
>>  1  5  1  0  0  0  0
>>  5  3  1  0  0  0  0
>> 12  5  1  0  0  0  0
>>  6  2  1  0  0  0  0
>>  6  4  1  0  0  0  0
>> 11  6  2  0  0  0  0
>>  9  7  1  0  0  0  0
>> 13  7  1  0  0  0  0
>>  9  8  2  0  0  0  0
>> M  END
>> 
> 
> Harry
> 
> 



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[ccp4bb] ligands found in ChEBI...

[Harry Powell]

Hi folks

Can anyone help with this?

I must have missed something in the documentation, because I don’t understand 
why the .mol and .sdf files downloaded from 

https://www.ebi.ac.uk/chebi

seem to have aromatic C-C bonds that are 0.825 Å long (it’s a few decades now 
since I solved any small molecule structures, but something around 1.395Å rings 
a faint bell).

I need to have ligands that have realistic sizes, and while I’m perfectly at 
ease scaling the models to what I think are sensible sizes, I can’t help but 
think that this isn’t necessary and I’ve missed something somewhere.

Here’s an example of a molecule that I used this morning - 


https://www.ebi.ac.uk/chebi/saveStructure.do?defaultImage=true&chebiId=31332&imageId=0

contents of downloaded file - 
> 
>   Marvin  01140911122D  
> 
>  15 15  0  0  0  0999 V2000
>-0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>-0.71450.41250. N   0  0  0  0  0  0  0  0  0  0  0  0
> 0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
> 0.71450.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
> 0.   -0.82500. N   0  0  0  0  0  0  0  0  0  0  0  0
> 0.0.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
> 1.49920.66740. N   0  0  0  0  0  0  0  0  0  0  0  0
> 1.4992   -0.66750. N   0  0  0  0  0  0  0  0  0  0  0  0
> 1.98410.0. C   0  0  0  0  0  0  0  0  0  0  0  0
>-1.4289   -0.82500. O   0  0  0  0  0  0  0  0  0  0  0  0
> 0.00011.65000. O   0  0  0  0  0  0  0  0  0  0  0  0
> 0.0001   -1.65000. C   0  0  0  0  0  0  0  0  0  0  0  0
> 1.75411.45200. C   0  0  0  0  0  0  0  0  0  0  0  0
>-1.42890.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
> 2.0809   -1.53650. O   0  0  0  0  0  0  0  0  0  0  0  0
>  10  1  2  0  0  0  0
>   1  2  1  0  0  0  0
>  14  2  1  0  0  0  0
>   8  3  1  0  0  0  0
>   4  3  2  0  0  0  0
>   7  4  1  0  0  0  0
>   1  5  1  0  0  0  0
>   5  3  1  0  0  0  0
>  12  5  1  0  0  0  0
>   6  2  1  0  0  0  0
>   6  4  1  0  0  0  0
>  11  6  2  0  0  0  0
>   9  7  1  0  0  0  0
>  13  7  1  0  0  0  0
>   9  8  2  0  0  0  0
> M  END
> 

Harry



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Re: [ccp4bb] occupancy factors for alternate conformations and alternate ligands

[Harry Powell]

Hi MIke

Beyond the obvious that they should sum to no more than unity, if they are 
similar to or not hugely greater than other temperature factors in your 
structure, they are probably okay.

People often apply restraints or constraints to keep the temperature factors 
similar for equivalent atoms in different partially occupied conformations, but 
I’m not sure there is a real justification for this apart from making the 
solution refine more stably. No doubt someone here will correct me!

Harry 

> On 28 Nov 2022, at 19:31, Michael Colaneri  wrote:
> 
> Dear colleagues,
> If I have alternate ligands overlapping in the same electron density or 
> alternate conformations of the protein chain overlapping in the same electron 
> density, how accurate are the occupancy factors?  (Res 2A - temp factors are 
> fine)
> Thanks, Mike Colaneri
> 
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Re: [ccp4bb] ChEBI and SMILES

[Harry Powell]

Hi Gerard

API good, web pages bad for this - I’d need to do this 100s of times a day (in 
spite of AlphaFold, Phyre gets used > 1000 times a day, and I anticipate many 
users wanting this feature).

Using things like SMILES, InChi etc is all to make users’ lives easier - I have 
to see what’s best. 

Many thanks for this - your colleagues at EBI have already been very helpful 
(but chose to reply off-list) - I’ll prepare a digest RSN…

Harry

> On 7 Oct 2022, at 15:15, Gerard Kleywegt  wrote:
> 
> Hi Harry,
> 
> On the ChEBI website, if I type a simple SMILES string into the search box 
> (c1c1) it takes me to the corresponding entity page. I don't know if they 
> have an API that supports this but I'm sure the friendly folks of the ChEBI 
> helpdesk (https://www.ebi.ac.uk/chebi/emailChebiForward.do) can tell you.
> 
> Another resource that may be of use in this context is UniChem 
> (https://www.ebi.ac.uk/unichem/). You provide an InChI (not SMILES 
> unfortunately) and it will then return a list of the identifiers of the 
> compound in bunch of resources (incl. ChEMBL, ChEBI, PDB, PubChem, Zinc, 
> etc.) - if they exist in that resource of course. (It offers an API so is 
> good for programmatic access - https://www.ebi.ac.uk/unichem/api/docs )
> 
> You can also provide a compound ID from any of those resources to find out 
> what it is called in the other resources (if it exists there), e.g. 
> https://www.ebi.ac.uk/unichem/compoundsources?type=sourceID&compound=BNZ&sourceID=3
>  searches for the compound we know as BNZ in the PDB.
> 
> Hope this helps,
> 
> --Gerard
> 
> 
> 
> 
> On Fri, 7 Oct 2022, Harry Powell wrote:
> 
>> Hi Jeet
>> 
>> This is very useful - many thanks.
>> 
>> I was hoping there might be some kind of API for searching the ChEBI 
>> database online, but there we go…
>> 
>> It looks like downloading the ChEBI database is the first step here, since 
>> many entries appear to have SMILES information.
>> 
>> But (important to note) ChEBI ≠ ChEMBL, although there is an overlap (a 
>> considerable ione…).
>> 
>> Harry
>> 
>>> On 7 Oct 2022, at 10:29, jeet balraj  wrote:
>>> 
>>> Hi Harry
>>> To search the ligand of interest in the ChEMBL database, you can follow 
>>> these simple steps:
>>> 1. download the ChEMBL database and extract all its SMILES.
>>> 2. calculate the MorganFingerprint of each of the SMILES in the database.
>>> 3. calculate the MorganFingerprint of your ligand.
>>> 4. use the FPSim2 package from ChEMBL for the Tanimoto similarity search.
>>> you can use RDKit to calculate the morgan fingerprints of each SMILES 
>>> string.
>>> Note: you have to first convert each SMILES in the database to canonical 
>>> form.
>>> I hope this helps.
>>> Thanks
>>> Jitendra Kuldeep
>>> Postdoc researcher
>>> Machine learning and precision oncology group
>>> Cancer research center of marseille, INSERM
>>> France 13009
>>> 
>>> 
>>> On Fri, Oct 7, 2022 at 11:13 AM Harry Powell 
>>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>>> Hi
>>> 
>>> Probably a silly question, but I was wondering how to search for a ligand 
>>> in ChEBI with a SMILES string? It’s not immediately obvious to my 
>>> Friday-morning mind ...
>>> 
>>> Harry
>>> 
>>> 
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Re: [ccp4bb] ChEBI and SMILES

[Harry Powell]

Hi Jeet

This is very useful - many thanks. 

I was hoping there might be some kind of API for searching the ChEBI database 
online, but there we go…

It looks like downloading the ChEBI database is the first step here, since many 
entries appear to have SMILES information.

But (important to note) ChEBI ≠ ChEMBL, although there is an overlap (a 
considerable ione…). 

Harry

> On 7 Oct 2022, at 10:29, jeet balraj  wrote:
> 
> Hi Harry
> To search the ligand of interest in the ChEMBL database, you can follow these 
> simple steps:
> 1. download the ChEMBL database and extract all its SMILES.
> 2. calculate the MorganFingerprint of each of the SMILES in the database.
> 3. calculate the MorganFingerprint of your ligand.
> 4. use the FPSim2 package from ChEMBL for the Tanimoto similarity search. 
> you can use RDKit to calculate the morgan fingerprints of each SMILES string.
> Note: you have to first convert each SMILES in the database to canonical form.
> I hope this helps.
> Thanks
> Jitendra Kuldeep
> Postdoc researcher
> Machine learning and precision oncology group
> Cancer research center of marseille, INSERM 
> France 13009
> 
> 
> On Fri, Oct 7, 2022 at 11:13 AM Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hi
> 
> Probably a silly question, but I was wondering how to search for a ligand in 
> ChEBI with a SMILES string? It’s not immediately obvious to my Friday-morning 
> mind ...
> 
> Harry
> 
> 
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[ccp4bb] ChEBI and SMILES

[Harry Powell]

Hi

Probably a silly question, but I was wondering how to search for a ligand in 
ChEBI with a SMILES string? It’s not immediately obvious to my Friday-morning 
mind ...

Harry


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Re: [ccp4bb] Lower b-factors with increasing T

[Harry Powell]

Hi Graeme

good to know that I haven’t forgotten everything.

Rgarding the data collection - I don’t think the OP mentioned how many crystals 
were used in the data collection (unless, of course, I’ve been reading even 
less carefully than normal…).

Harry

> On 8 Sep 2022, at 10:29, Winter, Graeme (DLSLtd,RAL,LSCI) 
> <6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi Harry,
> 
> You’re not wrong - “conventional wisdom” these days is pointing to CC of 
> about 0.3 but I suspect that the difference is pretty modest in general
> 
> However, in the case, the difference could have an impact as the higher 
> resolution reflections may have something to say about the overall B factors
> 
> I also wondered about the order of the data collection in this case, since 
> there will probably be a certain amount of radiation damage across this 
> number of data sets at non-cryo temperatures
> 
> Best wishes Graeme
> 
>> On 8 Sep 2022, at 10:21, Harry Powell 
>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> hi folks
>> 
>> I’ve been away from data processing for a while, but am I alone in thinking 
>> that scaling to ~0.6 CC 1/2 cutoff might be ignoring a lot of useful data? I 
>> seem to remember that AutoProc and xia2.multiplex use a default of >= 0.3.
>> 
>> Harry
>> 
>>> On 7 Sep 2022, at 19:46, Matt McLeod  wrote:
>>> 
>>> Hi everyone,
>>> 
>>> I have a series of datasets at 253K (~2.0A), 273K (2.0A), 293K (2.0A), 313K 
>>> (2.2A) and I am curious as to the details in determining B-factors.
>>> 
>>> I have treated these datasets more-or-less identically for comparison's 
>>> sake.  I used DIALS to index, integrate, and scale the data.  I scaled the 
>>> data to a ~0.6 CC1/2 cutoff.  
>>> 
>>> After fully refining the datasets, there is an odd trend with respect to 
>>> temperature (from what has been previously published) and I assume that 
>>> this is because of "behind-the-scenes" computation rather than a 
>>> biophysical observation.  The B-factors slightly decrease from 252-293K, 
>>> and then significantly drop at 313K.  The maps look pretty well identical 
>>> across the datasets.
>>> 
>>> 253K - 53.8 A^2
>>> 273K - 48.4 A^2
>>> 293K - 45.5 A^2
>>> 313K - 18.6 A^2
>>> 
>>> I compared the wilson intensity plots from DIALS scaling for 273K and 313K 
>>> and they are very comparable.
>>> 
>>> I am looking for suggestions as to where to look at how these b-factors are 
>>> selected or how to validate that these B-factor are or are not accurate.  
>>> Also, any relevant literature would be welcomed.  From what I have read, 
>>> there is a general trend that as T increase, the atoms have more thermal 
>>> energy which raises the b-factors and this trend is universal when 
>>> comparing datasets from different temperatures.
>>> 
>>> Thank you and happy to supply more information if that is helpful,
>>> Matt
>>> 
>>> 
>>> 
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Re: [ccp4bb] Lower b-factors with increasing T

[Harry Powell]

hi folks

I’ve been away from data processing for a while, but am I alone in thinking 
that scaling to ~0.6 CC 1/2 cutoff might be ignoring a lot of useful data? I 
seem to remember that AutoProc and xia2.multiplex use a default of >= 0.3.

Harry

> On 7 Sep 2022, at 19:46, Matt McLeod  wrote:
> 
> Hi everyone,
> 
> I have a series of datasets at 253K (~2.0A), 273K (2.0A), 293K (2.0A), 313K 
> (2.2A) and I am curious as to the details in determining B-factors.
> 
> I have treated these datasets more-or-less identically for comparison's sake. 
>  I used DIALS to index, integrate, and scale the data.  I scaled the data to 
> a ~0.6 CC1/2 cutoff.  
> 
> After fully refining the datasets, there is an odd trend with respect to 
> temperature (from what has been previously published) and I assume that this 
> is because of "behind-the-scenes" computation rather than a biophysical 
> observation.  The B-factors slightly decrease from 252-293K, and then 
> significantly drop at 313K.  The maps look pretty well identical across the 
> datasets.
> 
> 253K - 53.8 A^2
> 273K - 48.4 A^2
> 293K - 45.5 A^2
> 313K - 18.6 A^2
> 
> I compared the wilson intensity plots from DIALS scaling for 273K and 313K 
> and they are very comparable.
> 
> I am looking for suggestions as to where to look at how these b-factors are 
> selected or how to validate that these B-factor are or are not accurate.  
> Also, any relevant literature would be welcomed.  From what I have read, 
> there is a general trend that as T increase, the atoms have more thermal 
> energy which raises the b-factors and this trend is universal when comparing 
> datasets from different temperatures.
> 
> Thank you and happy to supply more information if that is helpful,
> 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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Re: [ccp4bb] ISO model with large groups of atoms in alternative conformations

[Harry Powell]

Crambin (quick search for “Martha Teeter” and “Crambin” should yield 
dividends)? There are some very high resolution structures of that with 
multiple conformations.

Harry

> On 23 Aug 2022, at 23:02, Pavel Afonine  wrote:
> 
> Dear community,
>  
> I’m looking for an example of a crystal structure where a large group of 
> atoms (as large as a whole chain or even a domain) have more than one 
> distinct conformation that would require modeling of such chain/domain as 
> more than one individual copy, with each copy having partial occupancy. I’m 
> not sure if that even exists but if someone can share an example that'd be 
> very much appreciated!
>  
> Thanks!
> Pavel
> 
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Re: [ccp4bb] scitbx issue....

[Harry Powell]

Hi Billy

Many thanks for this - unfortunately, there are other dependencies that appear 
not to be included in

> conda create -n new_environment -c conda-forge cctbx-base python=3.9

e.g. 

> [MacPro:~] harry% conda activate phenix_env
> (phenix_env) [MacPro:~] harry% python
> Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 17:00:52) 
> [Clang 13.0.1 ] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import scitbx
> Traceback (most recent call last):
>   File "", line 1, in 
>   File 
> "/Volumes/Users/harry/.local/lib/python3.9/site-packages/scitbx/__init__.py", 
> line 1, in 
> from .manage_yaml import Yaml
>   File 
> "/Volumes/Users/harry/.local/lib/python3.9/site-packages/scitbx/manage_yaml.py",
>  line 1, in 
> import yaml
> ModuleNotFoundError: No module named 'yaml'
> >>> 

(WHAT? No YAML?).

I’ll continue this discussion off-BB…

Regarding the PAE matrix reader, I wrote my own since I need to read them for 
other applications. But it’s good to know that (once I get 
process_predicted_model working) you guys are on the case.

Best wishes

Harry

> On 2 Aug 2022, at 06:52, Billy Poon  wrote:
> 
> Hi Harry,
> 
> Can you try creating a new environment with cctbx-base?
> 
> conda create -n new_environment -c conda-forge cctbx-base python=3.9
> 
> Then activate the environment to test
> 
> [bkpoon@eeyore:~] conda activate new_environment
> (new_environment) [bkpoon@eeyore:~] python
> Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 17:00:33) 
> [Clang 13.0.1 ] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import scitbx
> >>> import scitbx.array_family
> >>> 
> 
> It looks like you are installing cctbx-base into the Anaconda version of 
> python which is from the defaults channel. Mixing packages from different 
> channels does not always work, even though newer packages in the defaults 
> channel tend to be compatible with packages from conda-forge.
> 
> Also, if you do not need all the packages that come with the standard 
> Anaconda installation, I would recommend the miniconda or miniforge 
> installers for getting the conda tool.
> 
> As for the PAE format, some updates have just been committed 
> (https://github.com/cctbx/cctbx_project/pull/775). The latest nightly builds 
> for the cctbx-base conda package will have those. To get them, prepend the 
> "cctbx-nightly" channel to your conda command.
> 
> conda create -n new_environment -c cctbx-nightly -c conda-forge cctbx-base 
> python=3.9
> 
> You should see that the version for cctbx-base is 2022.8a2. I just made an 
> update for conda-forge that does not have those changes, but I can make a 
> point release if it is helpful.
> 
> If the PAE code or your installation still does not work, please create an 
> issue on GitHub and we can sort it out.
> 
> --
> Billy K. Poon
> Research Scientist, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Road, M/S 33R0345
> Berkeley, CA 94720
> Fax: (510) 486-5909
> Web: https://phenix-online.org
> 
> 
> On Mon, Aug 1, 2022 at 7:06 AM Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hi folks
> 
> No doubt someone will tell me that I should be posting this on the Phenix BB, 
> but since everyone on there reads ccp4BB as well (:-)), I’m likely to reach 
> the right audience anyway!
> 
> Two Qs - 
> 
> (1) most important - scitbx.array_family seems to have disappeared (see stuff 
> below Q2).
> 
> (2) Does process_predicted_model.py (when I get it working) read the 
> new-style PAE matrices that Sameer told us about last week?
> 
> Since “upgrading” my conda env so that I am using Python 3.9, I’m getting an 
> error with “process_predicted_model”, which is used for splitting up 
> AlphaFold models into (cough, cough) “domains”, based on the PAE matrix. It 
> ran before I did the move from Python 3.7.something…
> 
> I had to remove and reinstall conda to upgrade because I managed to screw up 
> the environment (and didn’t notice that the Python I was using wasnot 
> actually the conda one…). So this is on a freshly installed conda...
> 
> The error I get when trying to run process_predicted_model.py is - 
> 
> > [MacPro:~/icl/test] harry% python3 process_predicted_model.py 
> > pae/AF-Q8W3K0-F1-predicted_aligned_error_v2.json
> > Traceback (most recent call last):
> >   File "/Volumes/Users/harry/icl/test/process_predicted_m

[ccp4bb] scitbx issue....

[Harry Powell]

Hi folks

No doubt someone will tell me that I should be posting this on the Phenix BB, 
but since everyone on there reads ccp4BB as well (:-)), I’m likely to reach the 
right audience anyway!

Two Qs - 

(1) most important - scitbx.array_family seems to have disappeared (see stuff 
below Q2).

(2) Does process_predicted_model.py (when I get it working) read the new-style 
PAE matrices that Sameer told us about last week?

Since “upgrading” my conda env so that I am using Python 3.9, I’m getting an 
error with “process_predicted_model”, which is used for splitting up AlphaFold 
models into (cough, cough) “domains”, based on the PAE matrix. It ran before I 
did the move from Python 3.7.something…

I had to remove and reinstall conda to upgrade because I managed to screw up 
the environment (and didn’t notice that the Python I was using wasnot actually 
the conda one…). So this is on a freshly installed conda...

The error I get when trying to run process_predicted_model.py is - 

> [MacPro:~/icl/test] harry% python3 process_predicted_model.py 
> pae/AF-Q8W3K0-F1-predicted_aligned_error_v2.json
> Traceback (most recent call last):
>   File "/Volumes/Users/harry/icl/test/process_predicted_model.py", line 14, 
> in 
> from scitbx.array_family import flex
> ModuleNotFoundError: No module named ‘scitbx.array_family'

I’ve tried things like - 

conda install -c conda-forge cctbx-base

which installs a load of useful stuff, but not, apparently, scitbx.array_family 
- 

> Python 3.9.12 (main, Jun  1 2022, 06:36:29) 
> [Clang 12.0.0 ] :: Anaconda, Inc. on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import scitbx
> >>> import scitbx.array_family
> Traceback (most recent call last):
>   File "", line 1, in 
> ModuleNotFoundError: No module named ‘scitbx.array_family'

What do I need to do to get this working? Go back to Python 3.7?

Harry


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