Re: [ccp4bb] Computational crystallography in 2024

[Paul Emsley]

On 16/05/2024 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?



Python is popular for this sort of thing:

GEMMI: https://gemmi.readthedocs.io/en/latest/

CCTBX: https://cctbx.github.io/

Clipper-Python: https://pypi.org/project/clipper-python/

libcootapi: 
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/docs/api/html/




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[ccp4bb] Computational crystallography in 2024

[Lucas Bleicher]

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] Experimental phasing Selenomethionine data collection etc. tips

[James Holton]

Thank you to all who provided helpful suggestions so far.

A few things I'd recommend for this particular beamline (which I have 
been running for 20+ years)


Do NOT collect one wavelength at a time. This was a good strategy on old 
beamlines with noisy detectors and slow, drifty monochromators. This is 
not the case at any of the ALS beamlines today. With modern 
zero-read-noise detectors there is no penalty to spreading your photons 
over a lot more images, and round-robin changes between at least two 
wavelengths will double your phasing power for the same dose. With 
8.3.1's monochromator, wavelength changes take about 1 second and are 
reproducible to well within the intrinsic width of the Se peak.  So you 
don't need to worry about missing or drifting off the peak or 
inflection. The only thing you need to worry about is over-cooking your 
crystal before you get all the data you need.


No matter what beamline you use the number of photons your crystal will 
give off before it dies is a fixed number. All you get to do is decide 
how to spread them over the images. Doing two wavelengths within this 
photon budget doesn't hurt. You can always scale and merge them 
together. But keeping them separate gives you both kinds of anomalous 
differences, which are 90 deg apart. So, when one zigs the other zags. 
It is like having twice as many sites without the extra damage you would 
get from them. Also, by taking shorter/weaker exposures you maximize 
your chances of winning over radiation damage "in-post" by cutting off 
images that degrade your signal.


And before anybody says it: NO! Collecting fainter images does NOT 
degrade your resolution. I don't know where this idea comes from, but it 
never seems to die. It was true with film and image plates, but with 
pixel arrays and modern CCDs there is no penalty to weak images.  Don't 
believe me? Read the manual for your detector. Modern PADs actually sum 
a bunch of weak images internally before writing them to disk. You can 
do the same "in post" if you want to.


Yes, there are many cases where SAD is good enough, but my advice is 
never to tempt fate.


What I recommend is:
1) collect two wavelengths: remote, and halfway between the peak and 
inflection.

        this will maximize both kinds of anomalous differences
2) calculate your Bijvoet ratio here: 
https://bl831.als.lbl.gov/xtalsize.html
3) convert this into MGy. I.E. if your Bijvoet ratio is 3%, then 3 MGy 
is the max dose to avoid.

4) do a strategy and start at the recommended phi value
5) set delta-phi to be 1/3 of your estimated mosaic spread, or 0.2 deg, 
whichever is lower

    this is all done automatically by the "index" program at 8.3.1
6) set your exposure time to be 0.1 s or more.
    This is because the Pilatus M 6M has a 1 ms read-out and you want 
that to be 1% of the exposure.
7) attenuate the beam so that you will get complete data in less than 
1/2 your Bijvoet ratio in MGy.

    This is handled by the exposure_time program at 8.3.1
8) collect data in inverse beam and round-robin for both wavelengths (45 
deg wedges)

    In BLU-ICE, just enter the wavelengths into the list on the Collect tab
9) keep collecting until you get 360 deg for both wavelengths
10) move the detector up by ~5 mm, this puts the next sphere of spots 
onto new pixels

11) multiply your exposure or de-attenuate by a factor of 4
12) goto 8

When the diffraction image is noticeably damaged, you are done with this 
crystal. If it is bigger than the beam, move to a fresh spot and do this 
again. When the crystal is all burnt up, mount the next one and do this 
again.


If you're lucky, the automatic processing will finish before you mount 
your next crystal and you can try SHELXC/D/E on the 448-core 
shared-memory computer we have for doing such things. I expect it might 
be faster than the cloud.


Sorry if any of this sounds gruff, I don't mean to shout down on anyone, 
but I want the message to be clear. This is something Gerard B and I 
have struggled to communicate for decades:
Collecting one wavelength at a time is not MAD, but rather M-SAD. 
Multiple, non-isomorphous SAD data sets.


-James Holton
MAD Scientist

On 5/13/2024 10:23 PM, dbellini wrote:

Hi Marco,

A few suggestions that I like to follow for MAD experiments:

Before everything, check you have at least about 1 SeMet per 100 residues
Then before crystallisation check by MassSpec that SeMet is properly 
incorporated in your protein
After crystallisation collect first on the peak with (very) high 
redundancy and as little/gentle dose as possible
Collecting the other wavelengths should give you better starting 
phases/maps, which might be very helpful at your resolution of 2.8 
(especially if it is a very anisotropic 2.8...)


Automated pipelines are so good nowadays, if you collect good data 
they should solve it without problems (as long as your crystal is not 
suffering from other pathologies like twinning or pseudosymmtries).


Good luck!

Re: [ccp4bb] Request for help in optimizing Coot for AMD 5950x CPU and RX6600XT GPU hardware PC

[Bernhard Lohkamp]

On 15/05/2024 19:03, Paul Emsley wrote:


On 13/05/2024 17:38, Otsile Mojanaga wrote:


*From:*Otsile Mojanaga
*Sent:* Monday, May 13, 2024 3:29 PM
*To:* Paul Emsley 
*Subject:* RE: [ccp4bb] Request for help in optimizing Coot for AMD 
5950x CPU and RX6600XT GPU hardware PC


Dear Paul/All

Thank you for the response. I am on Windows 11 and I tried looking 
around Coot to see where I could input the commands you have suggested 
but I cannot find anything . I also cannot seem to type the commands 
into the ‘Command prompt’ that opens alongside Coot. I also tried 
inputting the commands in the ‘Coot Python scripting’ within Coot but 
this did not work. Please advise on when you can input these commands.







On 13/05/2024 13:03, Otsile Mojanaga wrote:

Dear All

I have been using coot as part of my normal workflow but since
last week I have been having issues with Coot after I built my own
PC which contains the following Hardware:

CPU - AMD Ryzen 9 5950X 16-Core Processor - 16 Cores, 32 Threads

RAM - 64 GB

GPU - AMD Radeon RX 6600 XT - Primary/Discrete

GPU VRAM - 8176 MB - GDDR6 2000 MHz

Despite the improvement in hardware, Coot is now having issues
refining molecules when using the ‘real space refine’ tool and
other related tools. When trying to refine, the program becomes
stuttering and slow such that it becomes unfeasible to use the
program in a reasonable amount of time. My current work around is
to run Coot through CCP4 cloud but this greatly slows down my
workflow. >From what I can see Coot is not be optimised for the
AMD CPU.

You don't mention the operating system.

Maybe you have too many threads for Coot? Try setting the 
COOT_N_THREADS to various values (starting, say, with 2) and see what 
happens.


But maybe it's a graphics (driver) issue and not a CPU/threads issue. 
glxgears is the classic test for that.


Paul.



What I mean here is that COOT_N_THREADS is an environment variable. It 
needs to be set in the environment from which Coot is launched - before 
Coot is launched, just to be clear.


 From a quick googling, I see that environment variables are a thing 
under windows, but it is not clear to me how they could actually be used 
in the context of Coot.


Paul.



You can add the environment variable in the coot startup script, i.e. 
edit wincoot.bat and insert the following line (*) before coot-bin.exe 
is called:


set COOT_N_THREADS=2

Having said this, for me this doesnt make any difference but more 
importantly I dont think this is the issue. Your issue is almost 
certainly the graphics card drivers. Please make sure you install the 
appropriate drivers directly from the AMD rather than relying on the 
ones provided by Windows. I am confident this will resolve your issue. 
That is unless some old issue with AMD cards shows up again then you may 
have to manually control threading in the Control panel of the graphics 
card.


HTH,

B


(*) there is another way in Windows to restrict the number of threads 
used (in the example to 2). To do so, insert the following BEFORE 
coot-bin.exe in the wincoot.bat file (i.e. in the same line):


start /affinity 2





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

[Frances C. Bernstein]

The old BNL PDB format documents are available at

https://www.wwpdb.org/documentation/file-format

I looked at the Feb 1992 document to be certain that my memory was 
correct [I am 6 days shy of 82 and am reassured that my recollection 
was,in fact, correct] for information about the representation of 
hydrogen naming as we had to violate the rule of two characters 
right-adjusted for the chemical symbol and two following location 
characters left-adjusted as we would have needed three location 
characters for hydrogens.  I then looked at 2MB5 which was deposited in 
1989 and has hydrogens.  At BNL we would have put, e.g., 1HD1, 2HD1, 
3HD1 for leucine hydrogens and the current version of the entry has 
HD11, HD12, HD13.  And the redone representation of HEM is totally 
confusing to me,


Given the revisions made by the RCSB PDB it makes sense to use the 
element type and not the atom name.


  Frances Bernstein

On 2024-05-15 11:34, Harry Powell wrote:

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

[Phil Jeffrey]

It says in aforementioned docs:

"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.

"
and no, hopefully they don't mean that, since their example shows plenty 
of 2-letter and 3-letter atom names starting at column 14 in the Example 
section below which directly contradicts that statement.


They mean one-letter and two-letter element names, where possible, but 
as previously discussed there are many atom names that don't fit that 
model.  Plus, since they define element names elsewhere they perhaps 
don't want to conflate this data.


PDB's own format definition is both incorrect and confusing.

Sadly I couldn't find PDB format v2 definitions, to see if the 
description changed.


Phil

(Column names starting at 1, I'm having a brief moment of Fortran nostalgia)

On 5/15/24 2:16 PM, Paul Emsley wrote:


On 15/05/2024 18:45, Filipe Maia wrote:

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--

It is, I think you would agree, unconventional to put a CA label for a
main-chain carbon at positions 13 and 14 (I have never seen such a
thing). But is it wrong ("Incorrect" - as Harry labels it)? In this
case, putting "CHA" in positions 13-15 is unconventional (again, I
have
never seen such a thing) - but is it wrong? The official PDB
documentation, according to my reading at least, is not clear.


As Harry pointed out the documentation at 
https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM says in the "Details" that it's incorrect.




Maybe I am being dense, sorry, but could you be more clear about what 
you mean here?


Paul.




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

[Ian Tickle]

'CA' for carbon-alpha is a 2-letter atom name so applying the rule exactly
as stated it should start in column 13; it states that only 1-letter atom
names (C, N, O) go in column 14.  This must be a case of poorly-written
documentation; it must mean 'element symbol' not 'atom name' in those cases
where the 'atom name' begins with the 'element symbol', though as Robbie
points out there's no rule that the atom name must begin with the element
symbol.

COLUMNSDATA TYPEFIELD   DEFINITION

13 - 16Atom  name Atom name.

77 - 78LString(2)element  Element symbol, right-justified.


   - 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.

I.


On Wed, May 15, 2024 at 11:56 AM Harry Powell <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> 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:
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> >>>
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> >
> > 
> >
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> > 

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

[Paul Emsley]

On 15/05/2024 18:45, Filipe Maia wrote:

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--

It is, I think you would agree, unconventional to put a CA label for a
main-chain carbon at positions 13 and 14 (I have never seen such a
thing). But is it wrong ("Incorrect" - as Harry labels it)? In this
case, putting "CHA" in positions 13-15 is unconventional (again, I
have
never seen such a thing) - but is it wrong? The official PDB
documentation, according to my reading at least, is not clear.


As Harry pointed out the documentation at 
https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM 
says in the "Details" that it's incorrect.




Maybe I am being dense, sorry, but could you be more clear about what 
you mean here?


Paul.




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

[Filipe Maia]

It is, I think you would agree, unconventional to put a CA label for a
main-chain carbon at positions 13 and 14 (I have never seen such a
thing). But is it wrong ("Incorrect" - as Harry labels it)? In this
case, putting "CHA" in positions 13-15 is unconventional (again, I have
never seen such a thing) - but is it wrong? The official PDB
documentation, according to my reading at least, is not clear.

As Harry pointed out the documentation at 
https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
 says in the "Details" that it's incorrect.

Cheers,
Filipe








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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] Request for help in optimizing Coot for AMD 5950x CPU and RX6600XT GPU hardware PC

[Paul Emsley]

On 13/05/2024 17:38, Otsile Mojanaga wrote:


*From:*Otsile Mojanaga
*Sent:* Monday, May 13, 2024 3:29 PM
*To:* Paul Emsley 
*Subject:* RE: [ccp4bb] Request for help in optimizing Coot for AMD 
5950x CPU and RX6600XT GPU hardware PC


Dear Paul/All

Thank you for the response. I am on Windows 11 and I tried looking 
around Coot to see where I could input the commands you have suggested 
but I cannot find anything . I also cannot seem to type the commands 
into the ‘Command prompt’ that opens alongside Coot. I also tried 
inputting the commands in the ‘Coot Python scripting’ within Coot but 
this did not work. Please advise on when you can input these commands.







On 13/05/2024 13:03, Otsile Mojanaga wrote:

Dear All

I have been using coot as part of my normal workflow but since
last week I have been having issues with Coot after I built my own
PC which contains the following Hardware:

CPU - AMD Ryzen 9 5950X 16-Core Processor - 16 Cores, 32 Threads

RAM - 64 GB

GPU - AMD Radeon RX 6600 XT - Primary/Discrete

GPU VRAM - 8176 MB - GDDR6 2000 MHz

Despite the improvement in hardware, Coot is now having issues
refining molecules when using the ‘real space refine’ tool and
other related tools. When trying to refine, the program becomes
stuttering and slow such that it becomes unfeasible to use the
program in a reasonable amount of time. My current work around is
to run Coot through CCP4 cloud but this greatly slows down my
workflow. >From what I can see Coot is not be optimised for the
AMD CPU.

You don't mention the operating system.

Maybe you have too many threads for Coot? Try setting the 
COOT_N_THREADS to various values (starting, say, with 2) and see what 
happens.


But maybe it's a graphics (driver) issue and not a CPU/threads issue. 
glxgears is the classic test for that.


Paul.



What I mean here is that COOT_N_THREADS is an environment variable. It 
needs to be set in the environment from which Coot is launched - before 
Coot is launched, just to be clear.


From a quick googling, I see that environment variables are a thing 
under windows, but it is not clear to me how they could actually be used 
in the context of Coot.


Paul.




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

[Paul Emsley]

On 15/05/2024 11:28, Harry Powell wrote:

Hi folks
[...]

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.

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 have a different slant on this - "is there anything that I need to do 
to fix the parsing of the above file?" - or to put it another way, 
"Who's wrong? Moorhen or this file?"


It is, I think you would agree, unconventional to put a CA label for a 
main-chain carbon at positions 13 and 14 (I have never seen such a 
thing). But is it wrong ("Incorrect" - as Harry labels it)? In this 
case, putting "CHA" in positions 13-15 is unconventional (again, I have 
never seen such a thing) - but is it wrong? The official PDB 
documentation, according to my reading at least, is not clear.


Regards,

Paul.



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[ccp4bb] Attn: UK Based research groups - UK CryoEM community Meeting - 19th July @Royal Society

[Walsh, Martin (DLSLtd,RAL,LSCI)]

Dear all,



On behalf of the UK cellular structural biology community, with support from 
Diamond and Instruct-ERI (UK centre), we would like to alert all UK based 
groups using or intending to use CryoEM as part of their research, the 
opportunity to attend a one-day community meeting together with relevant 
funders at the Royal Society, London on the 19th July 2024.



The CryoEM community meeting will provide a forum to highlight the science 
opportunities in the field. We aim to put together a white paper that forms the 
basis for the development of a 10-year strategic roadmap for CryoEM for the UK 
and address funding needs.



Places to attend are limited. Our aim is to make the meeting as inclusive as 
possible so we ask you register your interest in attending the meeting before 
close of day 7th June 2024 here:



UK CryoEM Community meeting, 19th July at the Royal Society London



https://www.diamond.ac.uk/Home/Events/2024/UK-CryoEM-Community-Meeting--.html



There is also the opportunity to register your interest in contributing to the 
meeting organisation through the registration process above.



Thanks



Dave Stuart and Martin Walsh


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

[Robbie Joosten]

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,RobbieOn 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] AW: [ccp4bb] a dinosaur asks ... PDB format query

[Marcin Wojdyr]

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

Or from command-line:
gemmi convert --anisou=no --remove-h in.pdb out.pdb

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

this would be:
gemmi convert --select='CA[C]' --anisou=no --minimal in.pdb out.pdb

(--minimal drops REMARKs and other metadata)



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

[Martin Malý]

Dear Jon,

If I understand your question right, I would use Gemmi for this purpose:
https://gemmi.readthedocs.io/en/latest/mol.html
https://gemmi.readthedocs.io/en/latest/analysis.html

It's not in GUI, it involves scripting in Python. It's a very powerful 
tool and capable of working with both PDB and mmCIF formats and with 
both proteins and nucleic acids.

Cheers,
Martin

On 15/05/2024 13:11, Hughes, Jonathan wrote:

hello CCP4 people,
rather off-topic: is there a purpose-written windows editor for PDF files? with 
interleaved anisotropy lines, missing column delimiters etc., simply extracting 
the B-factors for Ca atoms is hard work using a standard character editor. 
would anyone think of working with DNA without proper tools?
best
jon

--
Prof. Dr. Jon Hughes
Department of Physics
Free University of Berlin
&
Institute for Plant Physiology
Justus Liebig University
Giessen
Germany




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

[Andy Purkiss]

For those wanting a text editor solution, there is the purpose built pdb-mode 
plugin for (x)emacs which works under most operating systems.

The download location has moved around a bit, but a current version is 
available from
https://github.com/mmagnus/emacs-pdb-mode/

with more details at
https://bondxray.org/software/pdb-mode/

Hope this helps,

Andy Purkiss


From: CCP4 bulletin board  on behalf of Hughes, Jonathan 

Sent: 15 May 2024 13:11
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] AW: [ccp4bb] a dinosaur asks ... PDB format query


External Sender: Use caution.


hello CCP4 people,
rather off-topic: is there a purpose-written windows editor for PDF files? with 
interleaved anisotropy lines, missing column delimiters etc., simply extracting 
the B-factors for Ca atoms is hard work using a standard character editor. 
would anyone think of working with DNA without proper tools?
best
jon

--
Prof. Dr. Jon Hughes
Department of Physics
Free University of Berlin
&
Institute for Plant Physiology
Justus Liebig University
Giessen
Germany




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

[Jon Cooper]

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

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

Sent from Proton Mail mobile

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

> It sounds as though you need the power of the script. You can (from memory) 
> run pdbcur to drop the aniso lines and hydrogen atoms, which helps.
>
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>
> Sent from Proton Mail mobile
>
>  Original Message 
> On 15 May 2024, 13:11, Hughes, Jonathan wrote:
>
>> hello CCP4 people, rather off-topic: is there a purpose-written windows 
>> editor for PDF files? with interleaved anisotropy lines, missing column 
>> delimiters etc., simply extracting the B-factors for Ca atoms is hard work 
>> using a standard character editor. would anyone think of working with DNA 
>> without proper tools? best jon -- Prof. Dr. Jon Hughes Department of Physics 
>> Free University of Berlin & Institute for Plant Physiology Justus Liebig 
>> University Giessen Germany 
>>  To 
>> unsubscribe from the CCP4BB list, click the following link: 
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This 
>> message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
>> hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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>>
>> ---
>>
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Re: [ccp4bb] AW: [ccp4bb] a dinosaur asks ... PDB format query

[Jon Cooper]

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

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

Sent from Proton Mail mobile

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

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

[Hughes, Jonathan]

hello CCP4 people,
rather off-topic: is there a purpose-written windows editor for PDF files? with 
interleaved anisotropy lines, missing column delimiters etc., simply extracting 
the B-factors for Ca atoms is hard work using a standard character editor. 
would anyone think of working with DNA without proper tools? 
best
jon

--
Prof. Dr. Jon Hughes
Department of Physics
Free University of Berlin
&
Institute for Plant Physiology
Justus Liebig University
Giessen
Germany




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

[Paul Bond]

It would also be good to check the monomer library (expanded with any
user-supplied dictionaries). Cases where an element in columns 77-78 exists
and it does not agree with the component definition should probably be
flagged up.

Cheers,
Paul

On Wed, 15 May 2024 at 12:39, 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
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
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Re: [ccp4bb] a dinosaur asks ... PDB format query

[Marcin Wojdyr]

>
> >  • 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

[Robbie Joosten]

Hi Harry,Deducing the element from the atom name has always been unreliable so since PDB version 3 you have to get it from columns 77-78. There is no implied element in the atom name anymore.HTH,RobbieOn 15 May 2024 12:28, Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk> 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







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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=1
>>> 
>>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
>>> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
>>> https://www.jiscmail.ac.uk/policyandsecurity/
> 
> 
> 
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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=1
>> 
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
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Re: [ccp4bb] a dinosaur asks ... PDB format query

[Ezra Peisach]

If you take a look at 
https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM


you will see the following:

77 - 78    LString(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



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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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[ccp4bb] CCPBioSim Industry Talks - 29 May and 19 June

[Sarah Fegan - STFC UKRI]

Hi all,
I want to remind you about our next industry talk by Brannon Batson a hardware 
design engineer at D. E. Shaw Research. The talk "Using specialized hardware 
pipelines to massively accelerate molecular dynamics simulations in Anton 3" is 
online Wednesday 29 May 2024, 15:00 UK time. Free registration at 
https://www.ccpbiosim.ac.uk/deshaw2024.
Abstract: At D. E. Shaw Research, we have designed and built multiple 
generations of highly successful special-purpose supercomputers for molecular 
dynamics simulations.  The newest generation, Anton 3, achieves simulation 
speeds at least 100-fold faster than any other currently available 
supercomputer on a wide range of biomolecular systems.  Anton machines are an 
essential foundational technology for our scientific and drug discovery 
efforts.  This talk will describe how we co-design hardware, software, and 
algorithms to accelerate both research and drug discovery, focusing on how 
specialized hardware pipelines contribute to the enormous speedups that Anton 
machines achieve.

The June talk is Wednesday 19 June 2024, 14:00 UK time. This online talk 
"MDAnalysis and Alchemical Simulations" will be given by Richard Gowers, the 
project director at the Open Free Energy project. Free registration at 
https://www.ccpbiosim.ac.uk/mda-talk2024.
Abstract: MDAnalysis is a popular Python package for the analysis of molecular 
dynamics simulation data.  After introducing the package in broad strokes, this 
talk will give insight into how this package has been used and extended to 
process data coming from so-called "alchemical simulations"; where molecules 
are perturbed through non-physical states to provide estimates of properties 
such as binding affinities.  Topics included will be biopolymer recognition, 
handling of multistate simulation data and analysing hybrid topology alchemical 
models.

Best wishes,
Sarah



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