Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

[Paul Emsley]

On 06/06/2024 04:00, Devbrat Kumar wrote:



--

Dear Paul,

Thank you for your response. I wanted to compare a Coulomb potential 
map to an electron density map. Before aligning these maps, I need to 
bring them to similar parameters, which requires rescaling one map to 
match the other. After that, I can proceed with density subtraction.


I hope this clarifies my query. Sorry for any confusion.
Thank you again.
Regards
Devbrat


On Wed, Jun 5, 2024, 7:56 PM Paul Emsley  
wrote:



On 05/06/2024 07:00, Devbrat Kumar wrote:



--

Hello Everyone,


Hello Devbrat,


I have a query regarding the resampling of cryoEM density to
match crystal density to obtain a density difference map.
Specifically, I am trying to determine if it is feasible to
resample a cryoEM map with an XRD density map. However, each time
I attempt this, the resampling output provides an arbitrary ASU
resample map, resulting in a significant loss of major density.

I have been using Coot and Chimera for this process but have not
achieved the desired outcome. Please guide me or suggest how to
move forward with this. My goal is to create an accurate final
density difference map.




It is not clear to me exactly what the problem is.

In Coot speak, "resampling" is (merely) changing the grid sampling
so that the map appears (typically) on a finer grid.

I don't think that this is what you want.

You want is, I think, "Transform Map by LSQ Model-fit" and if that
is what you used, then I can't help until I am more clear about
what you think has gone wrong.

Regards,

Paul.


Ah, OK, so you want to *rescale* not resample. The tool (in our world) 
to do that is EMDA (available in CCPEM).


Paul.




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Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

[Paul Emsley]

On 05/06/2024 07:00, Devbrat Kumar wrote:



--

Hello Everyone,


Hello Devbrat,


I have a query regarding the resampling of cryoEM density to match 
crystal density to obtain a density difference map. Specifically, I am 
trying to determine if it is feasible to resample a cryoEM map with an 
XRD density map. However, each time I attempt this, the resampling 
output provides an arbitrary ASU resample map, resulting in a 
significant loss of major density.


I have been using Coot and Chimera for this process but have not 
achieved the desired outcome. Please guide me or suggest how to move 
forward with this. My goal is to create an accurate final density 
difference map.





It is not clear to me exactly what the problem is.

In Coot speak, "resampling" is (merely) changing the grid sampling so 
that the map appears (typically) on a finer grid.


I don't think that this is what you want.

You want is, I think, "Transform Map by LSQ Model-fit" and if that is 
what you used, then I can't help until I am more clear about what you 
think has gone wrong.


Regards,

Paul.




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Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

[Paul Emsley]

On 01/06/2024 14:28, Jon Cooper wrote:

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


PDBe is to RCSB as DVLA is to HMRC (surely?)



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Re: [ccp4bb] CCP4i2 COOT no showing model or map?

[Paul Emsley]

On 31/05/2024 07:44, Marco Bravo wrote:


Has anyone had the issue where they run coot from ccp4i2 on say a refmac5 job 
and when coot opens the model or even the map do not show up? its just empty? 
Does anyone know how to fix this and display the model and map? I like ccp4i2 
so far more than ccp4 and I did not have this issue with ccp4 but of course I 
had to manually load the model and map. I can see that I can export the mtz 
from refmac5 jobs, but I don't know where the pdb file is for the refmac 5 jobs?


What does it say in the log file?

Paul.



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

[Paul Emsley]

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

CAUTION: This email originated from outside of the LMB:
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Do not click links or open attachments unless you recognize the sender 
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If you think this is a phishing email, please forward it to 
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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] 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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Re: [ccp4bb] Request for help in optimizing Coot for AMD 5950x CPU and RX6600XT GPU hardware PC

[Paul Emsley]

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.




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Re: [ccp4bb] coot - how to define a keyboard shortcut for "update NCS ghosts with local match" ?

[Paul Emsley]

On 13/05/2024 11:23, Laurent Maveyraud wrote:

Hello,
I like the function "update NCS ghosts with local match" found in the 
calculate/NCT tools menu. It's really helpful when NCS is not really 
strict. However, I find it clumsy that you have to go in a submenu to 
get it, so I would like to define a keyboard shortcut... this would be 
much faster.


Which function should I use to  do that ?

(add_key_binding "Update ghosts" "a" (unknown function)



(add-key-binding "Update NCS Ghosts" "a" update-ncs-ghosts-by-local-sphere)

P.



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Re: [ccp4bb] COOT 1.1 and DNA mutation

[Paul Emsley]

On 26/04/2024 02:44, Paul Emsley wrote:



On 25/04/2024 16:07, Simon Vecchioni wrote:



Paul,

Many thanks for fixing the [simple mutate] button for DNA in 
v1.1.08--works like a charm!


I would ask about two other DNA features--
1) The [add terminal residue] button seems unresponsive for DNA,


I see what you mean. From the terminal output it seems to want to try 
to add a residue via a peptide bond.


I have made a note of this bug.


and is often quite useful;


OK.

This has been fixed and is in the HEAD of main (I will be busy with 
other things for the next few weeks so there won't be a release soon).


You will probably need some local refinement/regularization to anneal 
the phosphodiester link.



Paul.



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Re: [ccp4bb] add ligand with AceDRG

[Paul Emsley]

On 25/04/2024 13:01, FREITAG-POHL, STEFANIE wrote:



I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement:

I put in a smilesstring and the ligand is written ok, but since I can 
only chose already 'taken' 3-letter-codes the refinement always 
crashes as there is a clash with existing library entries.



I suspect that the issue is not what you think it is.

Look at the refmac log and tell us the refmac command line and the 
failure message.



Paul.




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Re: [ccp4bb] COOT 1.1 and DNA mutation

[Paul Emsley]

On 25/04/2024 16:07, Simon Vecchioni wrote:



--

Paul,

Many thanks for fixing the [simple mutate] button for DNA in 
v1.1.08--works like a charm!


I would ask about two other DNA features--
1) The [add terminal residue] button seems unresponsive for DNA,


I see what you mean. From the terminal output it seems to want to try to 
add a residue via a peptide bond.


I have made a note of this bug.


and is often quite useful;


OK.

2) There was a button chain in v0.8.9 to add base pair restraints, 
Calculate--Modules--Restraints, and then Restraints--DNA-Bform. Is 
this still present but moved? I haven't been able to dig this one out.


That code didn't make the transition. The whole module needs to be 
reworked, I see now.


OK, well I will do that.

My intention was that base pairing restraints should be applied 
automatically now. While RSR (Sphere, say) is active, give an atom in a 
DG a little tug in the opposite direction to the DC - if the DC follows 
then the base pair restraints are being applied (it would seem to me).


Paul



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Re: [ccp4bb] COOT 1.1 and DNA mutation

[Paul Emsley]

On 04/04/2024 02:27, Simon Vecchioni wrote:



Dear CCP4 Wizards,

Hello Simon.


I've upgraded to COOT v1.1.07 from 0.9.6, and am working on DNA model 
refinement.

exciting.


The current setup does not seem to let me sequence mutate (simple 
mutate or mutate residue range), as it's hard coded to an amino acid 
drop down menu. Edit-->Replace residue with three letter code (for DNA 
"DC", "DA", etc.) also does not seem to swap residues.


I see what you mean. The first is an oversight, the second is a bug.

The first of these will be easy to fix, I think the second not so easy 
as it involves the Python gui interface. However, I can give it a bash 
and it should be available on Monday if you are using the HEAD build.




Am I missing a setting or button click/centering/toggle? Is there a 
workaround for this short of reverting to an older version where these 
features were well oiled?


Not until next week - or somewhat longer than that probably if you are 
only using releases.


Paul.



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Re: [ccp4bb] Coot function - closest symmetry atom?

[Paul Emsley]

On 18/03/2024 10:26, Petr Pachl wrote:

--


Does anybody know if there is a function (or procedure) how to get info
about closest symmetry atom? For picking coot is performing something
like "Model atom pick (if failed) -> Symmetry atom pick", then it
returns to console and atom info at the bottom of the screen the found
atom. But can that be obtained in a function? My idea is to have a
shortcut "go to original atom based on symmetry related one".


Your second question is easier to answer than the first one - because it 
has been coded up already (in 2009). It's called "undo-symmetry-view" 
and all you need to do is bind it to a key. In fact, it's already bound 
to a key (Shift-V) if you have installed the key-bindings.


Paul.



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Re: [ccp4bb] EM maps

[Paul Emsley]

On 08/03/2024 10:47, Dean Derbyshire wrote:



Hi, I’m almost certain this has been addressed before so apologies… 
but is there a trick to import EM map files into COOT, it keeps 
crashing when I’ve tried.






My guess is that your computer is running out of memory. A pint into a 
quart port? Sometime EM maps can be multi-gigs. And there was a memory 
leak that I discovered just last week in fact.



It's somewhat disappointing that Coot crashes rather than giving you a 
useful error message. Are you using the latest and greatest in the 0.9.x 
series?



(The patch has not been back-ported to the 0.9.x series. I should do 
that before the release of 0.9.8.94.)



Regards,

Paul.




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Re: [ccp4bb] Coot SSM Superpose Problem

[Paul Emsley]

On 16/02/2024 01:45, zx2...@connect.hku.hk wrote:

Dear all,

Hello Xin,


I encountered an issue while attempting to calculate the RMSD between 
two PDB files (each containing 4 ASUs)


do they really though?


using the SSM Superpose tool in Coot. Unfortunately, the tool was 
unable to superpose all ASUs accurately.



That's because you have mismatched bundles. It seem to me that you need 
some "Symm Shift Reference Chain Here" action.



Paul.




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Re: [ccp4bb] program to complete (or to change) side chains to specific rotamers

[Paul Emsley]

I agree with James and for the record, the function that it seem to me 
that you want is


set_residue_to_rotamer_name(imol, chain_id, res_no, ins_code, alt_conf, 
rotamer_name)


Paul.



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Re: [ccp4bb] low resolution data refinement

[Paul Emsley]

On 21/11/2023 12:02, Yahui Liu wrote:


Dear all,
I got a protein crystal dataset of 4.3 A and would like to some the 
structure with MR.

Now I am suffering with the refinement.



Just for the record, then intention of refinement is not to make you suffer.


Paul.



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Re: [ccp4bb] About model building

[Paul Emsley]

On 04/11/2023 14:04, Sam Tang wrote:


Dear community,

I am solving the structure of a complex between proteins A and B, 
where A is a protein with known homologs and B is a novel protein 
isolated from plant. The diffraction data was at 1.9 Ang collected 
in-house, indexed to P321. Using A as the search model, we have got a 
reasonable solution where, after one round of refinement, the A chain 
fits the map pretty well. What's left was to extend the termini and 
fit a few rotamers.


For protein B (B chain) I have tried the web version of ARP/wARP but 
the outcome was not really good. The model was not successfully built 
as indicated by low model completeness and score. The tricky thing may 
be that we do not have the complete sequence information of this 
protein B in-hand. (The other way round, we more or less wish to rely 
on the high resolution data to confirm its sequence.) What approach 
would you then recommend to build the B chain in this scenario?





There are two steps:


(i) get poly-ALA trace fragments for B

(ii) convert poly-ALA fragments to true sequence


If you want to use Coot:

You can do the former by placing a helix and extending it by "Add 
Terminal Residue" (hot-key "Y") or (as you saw) by running APR/wARP 
ModelCraft or res_tracer (leave the pir filename as blank of course).


You can do the latter by using

   (a) the tool in Cryo-EM module "Auto-assign sequence based on map" 
and then BLASTing that sequence (or set of sequences, one presumes)


    once you have the correct sequence then use "Align and Mutate" or

   (b) export the poly-ALA model and use coot-identify-protein using 
each of the fragments in your poly-ALA and the genome of you organism


 (in FASTA format). That will tell you the sequence of the 
fragment so that you can then "Mutate Sequence."



If you can't see at least tubes for the missing chain, then this 
approach is hopeless.



Paul.



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Re: [ccp4bb] wwPDB NEWS - Coming Soon: PDB Entries with Novel Ligands Distributed Only in PDBx/mmCIF and PDBML File Formats

[Paul Emsley]

On 19/09/2023 09:34, Deborah Harrus wrote:


Dear all,



Dear Deborah,


wwPDB asks users and software developers to review code to remove any 
current limitations on CCD ID lengths, and to enable use of PDBx/mmCIF 
format files. Example files with extended CCD IDs are available via 
GitHub  
to assist code revisions. Information about the PDBx/mmCIF dictionary 
and file format is provided at mmcif.wwpdb.org .




It is not clear to me where it is reasonable to expect the curve to 
cross the axis. Are the data for this plot available at mmcif.wwpdb.org? 
If so, I didn't find them.


Please make available the data for the plot.


Thank you,

Paul.




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Re: [ccp4bb] effect of torsion angle definition in cif file

[Paul Emsley]

On 17/08/2023 11:18, Palm, Gottfried wrote:
>
> I copied the EDO.cif from the library and changed the C1-C2 torsion
> angle definition to
> EDO sp3_sp3_4  O1  C1  C2 
> O2 180.000    10.0 1
>
> After loading EDO in coot via "import cif dictionary" with "generate a
> molecule", regularize zone should now push the dihedral to 180°,
> because the periodicity was changed to 1. Instead, it refines to
> 58.86°. After manually setting it to 110° by "edit chi angles" it
> still refines to 58°. After setting it to 130° it refines to 179°. It
> thus behaves like periodicity 3, not periodicity 1. The modified cif
> file was correctly read, in "edit chi angles" it clearly states
> sp3_sp3_4 C1 <--> C2 ref 180.00 per: 1.
> What am I missing?
>
You missed turning on torsion angle refinement? (It's off by default)

Paul.





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Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7]

[Paul Emsley]

On 09/08/2023 10:54, David Lawson (JIC) wrote:

Hi Paul,

Just wondering where we are with this fix.


The blog is generally the place to turn for this sort of thing.

Having said that, I missed the post about 0.9.8.9! But I have added one 
for 0.9.8.91 (that revision fixed the missing peptide omega graph and 
fixes "Replace Residue" (needed for the upcoming Summer School)).


As to if/when that gets added to CCP4, that is up to Charles.


Is it safe to apply the latest CCP4 updates?



Isn't it always?


Paul.




Many thanks

Dave

---

Prof. David M. Lawson
Department of Biochemistry and Metabolism,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk


-Original Message-
From: CCP4 bulletin board  On Behalf Of Paul Emsley
Sent: Tuesday, July 18, 2023 5:11 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is 
broken in 0.9.8.7]

On 18/07/2023 03:55, Mark Saper wrote:

I reported this problem to Paul and to the group at least 2-3 months ago.

Your email didn't arrive.

Just to be clear, Coot's real space refinement is not (was not) broken, the 
problem is that the version of Coot distributed by CCP4 and the version of the 
monomer library distributed by CCP4 were not compatible.


It affects protein as well as [nucleic] acid.  I never heard back from
Paul if a fix was in progress.

Keitaro Yamashita alerted me to the problem in a timely fashion and an update 
to Coot was added and documented in early June.


[To Charles in particular] My commitments will be out of the way at the
end of the week and I hereby commit to making the 0.9.8.9 release early
next week.


Paul.



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Re: [ccp4bb] problems starting pandda.inspect - maybe COOT / CCP4 related

[Paul Emsley]

On 08/08/2023 09:57, Schaefer, Martina wrote:
>
> Hello,
>
>  
>
> I have a problem running pandda.inspect after successful running
> pandda.analyse with the newest ccp4 version of pandda.
>
>  
>
> What do we have:
>
>   * We use Ubuntu as our Linux system
>   * We installed CCP4-8.0.012
>   * When I start pandda.inspect COOT 0.9.8.8.EL opens and the
> following error message appears in the terminal window:
>
>  
>
> INFO:: There are 1 command line scripts to run
>
>    
> /opt/remote/ccp4-8.0.012/bin/../lib/python3.7/site-packages/pandda/inspect/__init__.py
>
> calling run_script() for file
> /opt/remote/ccp4-8.0.012/bin/../lib/python3.7/site-packages/pandda/inspect/__init__.py
>
> debug:: run_script() on
> /opt/remote/ccp4-8.0.012/bin/../lib/python3.7/site-packages/pandda/inspect/__init__.py
>
> Running python script
> /opt/remote/ccp4-8.0.012/bin/../lib/python3.7/site-packages/pandda/inspect/__init__.py
>
> /opt/remote/ccp4-8.0.012/bin/../lib/python3.7/site-packages/pandda/inspect/../resources
>
> No module named matplotlib
>
> Traceback (most recent call last):
>
>   File "", line 1, in 
>
>   File
> "/opt/remote/ccp4-8.0.012/bin/../lib/python3.7/site-packages/pandda/inspect/__init__.py",
> line 1725, in 
>
>     import matplotlib as mpl
>
> *ImportError: No module named matplotlib*
>
> (use-graphics-interface-state)
>
>  
>
> I checked and we do have a matplotlib python module installed (version
> 3.3.4)
>
>  
>
> Has anybody an idea how to tell COOT that the correct matplotlib
> module is present….
>
>  
>

I don't really understand what CCP4 do when packaging Coot.

I can say that I don't like the look of the above though. Coot 0.9.x
uses python 2 (only). Your above error message mentions python3.7 - so
that seems muddled.

It might be that you have a python in the same directory as the coot
executable, so you can (I guess) use that to install matplotllib:

$ which coot

/opt/remote/coot-0.9/bin/coot

so then:

$ /opt/remote/coot-0.9/bin/python -m pip install matplotlib

I suspect that that's not much help.

Paul.





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Re: [ccp4bb] anomalous map in Coot - Linux vs. Win difference?

[Paul Emsley]

On 02/08/2023 13:53, Andrea Smith wrote:

Dear all,

I used refmac in CCP4Cloud and then I opened the generated .pdb and 
.mtz from the CCP4Cloud job both in Linux Coot 0.9.6. and WinCoot 
0.9.6. I can see different anomalous maps in Coot and Wincoot - see 
attached printscreen where on the left there is a green electron 
density between the aspartates while on the right there is none. I 
tried to search if this is a bug but couldn't find info about this.




Did you press "Apply" in both cases?

To check/set the contour level, normally I just scroll the scroll wheel.

Paul.



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[ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7]

[Paul Emsley]

On 18/07/2023 03:55, Mark Saper wrote:

I reported this problem to Paul and to the group at least 2-3 months ago.


Your email didn't arrive.

Just to be clear, Coot's real space refinement is not (was not) broken, 
the problem is that the version of Coot distributed by CCP4 and the 
version of the monomer library distributed by CCP4 were not compatible.


It affects protein as well as [nucleic] acid.  I never heard back from 
Paul if a fix was in progress.


Keitaro Yamashita alerted me to the problem in a timely fashion and an 
update to Coot was added and documented in early June.



[To Charles in particular] My commitments will be out of the way at the 
end of the week and I hereby commit to making the 0.9.8.9 release early 
next week.



Paul.



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] How to change keyboard shortcuts in Coot

[Paul Emsley]

On 15/07/2023 17:27, Gong, Zhen wrote:


Hi Paul,

Thank you very much for the hint. The shift key was messed up in Coot 
somehow. The G and Control + G both did a Reverse JED Flip, and shift 
+ Control + G did go to the specific atoms. I checked the shift and 
Caps lock keys in word, everything seems fine. Maybe this is a bug in 
Coot 0.9.8.8 EL?




I doubt that it's a bug in Coot. A bug in Ventura though... that does 
seem possible.



Paul.



Zhen

*From: *Paul Emsley 
*Date: *Saturday, July 15, 2023 at 11:04
*To: *Gong, Zhen , CCP4BB@JISCMAIL.AC.UK 

*Subject: *Re: [EXTERNAL] Re: [ccp4bb] How to change keyboard 
shortcuts in Coot


On 15/07/2023 13:39, Gong, Zhen wrote:

Hi Paul,

Thank you very much for your reply. I am using Coot 0.9.8.8 EL

OK good.

and Mac Ventura.

Ah.

I did a few more tests and I think the problem is the G. If I
press G, it changes the rotation angle of a bond and Control + G
did the same thing. Do you have any clue what could be the problem?

Well, Shift G does a Reverse JED Flip (as does Ctrl Shift G) - that 
sounds similar to what you are seeing. Perhaps you have the Caps Lock 
key pressed?


Paul.

Zhen

*From: *Paul Emsley 
<mailto:pems...@mrc-lmb.cam.ac.uk>
*Date: *Saturday, July 15, 2023 at 02:40
*To: *Gong, Zhen 
<mailto:zg2...@cumc.columbia.edu>, CCP4BB@JISCMAIL.AC.UK
 <mailto:CCP4BB@JISCMAIL.AC.UK>
*Subject: *[EXTERNAL] Re: [ccp4bb] How to change keyboard
shortcuts in Coot

On 15/07/2023 03:22, Gong, Zhen wrote:

Dear all,

Can anyone kindly tell me how to change the keyboard shortcuts
settings in Coot? My “control + g” did not go to the specified
atoms anymore. I might have changed the shortcut settings by
accident. Thank you very much for your help!

Ctrl-G is a built-in in Coot 0.9.x (which I presume that you are
using) and can't be changed.

For Ctrl-G to work, you need to have focus in the main window and
the active residue (the residue at the centre of the screen) is in
the same molecule as the residue to which you wish to "go to."

Paul.


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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] How to change keyboard shortcuts in Coot

[Paul Emsley]

On 15/07/2023 13:39, Gong, Zhen wrote:


Hi Paul,

Thank you very much for your reply. I am using Coot 0.9.8.8 EL


OK good.


and Mac Ventura.


Ah.


I did a few more tests and I think the problem is the G. If I press G, 
it changes the rotation angle of a bond and Control + G did the same 
thing. Do you have any clue what could be the problem?




Well, Shift G does a Reverse JED Flip (as does Ctrl Shift G) - that 
sounds similar to what you are seeing. Perhaps you have the Caps Lock 
key pressed?



Paul.




Zhen

*From: *Paul Emsley 
*Date: *Saturday, July 15, 2023 at 02:40
*To: *Gong, Zhen , CCP4BB@JISCMAIL.AC.UK 

*Subject: *[EXTERNAL] Re: [ccp4bb] How to change keyboard shortcuts in 
Coot


On 15/07/2023 03:22, Gong, Zhen wrote:

Dear all,

Can anyone kindly tell me how to change the keyboard shortcuts
settings in Coot? My “control + g” did not go to the specified
atoms anymore. I might have changed the shortcut settings by
accident. Thank you very much for your help!

Ctrl-G is a built-in in Coot 0.9.x (which I presume that you are 
using) and can't be changed.


For Ctrl-G to work, you need to have focus in the main window and the 
active residue (the residue at the centre of the screen) is in the 
same molecule as the residue to which you wish to "go to."


Paul.


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Re: [ccp4bb] How to change keyboard shortcuts in Coot

[Paul Emsley]

On 15/07/2023 03:22, Gong, Zhen wrote:


Dear all,

Can anyone kindly tell me how to change the keyboard shortcuts 
settings in Coot? My “control + g” did not go to the specified atoms 
anymore. I might have changed the shortcut settings by accident. Thank 
you very much for your help!


Ctrl-G is a built-in in Coot 0.9.x (which I presume that you are using) 
and can't be changed.


For Ctrl-G to work, you need to have focus in the main window and the 
active residue (the residue at the centre of the screen) is in the same 
molecule as the residue to which you wish to "go to."


Paul.




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Re: [ccp4bb] Ligand superposition!

[Paul Emsley]

On 15/07/2023 03:49, Subramanian, Ramaswamy wrote:
I have over 50 pdb files that I have downloaded from PDB that all have 
the same ligand bound.


I wamt to superpose the ligands (and move the protein coordinates 
using that matrix).  The goal is for me to see how difference in 
ligand environments in different complexes.


Is there an easy way to do it?  I am sure it has been done before and 
I do not want to reinvent the wheel.



A script of some sort - that'll help.

Does the ligand have the same chain-id and residue number in all the PDB 
files?




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Re: [ccp4bb] O-glycans in coot and phenix/refmac

[Paul Emsley]

On 14/07/2023 08:52, Jonas Emsley wrote:


Dear All

We have a crystal structure with O-glycans for the first time attached 
to a Ser and a Thr sidechain


If anyone can recommend the procedure for adding these in coot and 
refining them in phenix /refmac that would be greatly appreciated



Hi Jonas,

I didn't get around to adjusting Coot's carbohydrate to build O-linked 
glycans :-(.


If I wanted to build  one today, I'd have to use cut, paste, superpose, 
copy fragment, merge molecules and change chain-ids. Meh.


Once you have built it however, and used Make Link to add the link to 
the header, the refinement linking should be automatic in Coot (because 
the details of the link are in the CCP4 monomer library).


Regards,

Paul.




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Re: [ccp4bb] Coot query

[Paul Emsley]

On 06/07/2023 08:51, Tom Peat wrote:

Hello All,

I just had a very strange experience- I rebooted my linux machine 
(Ubuntu jammy 7.81.0) and tried to start up Coot and received the 
following error message:



It is my understanding that jammy jellyfish, by default, uses Wayland as 
the display server. It seems to me then that running an X11-based 
application will have to go via XWayland, and who knows what goodies 
that could bring. So my suggestion to you is to try rebooting and using 
an X11-based display manager.



I will note here that a person such as yourself Tom could compile the 
gtk4 branch of Coot, which can now run on Wayland directly.



Paul.




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Re: [ccp4bb] Need suggestion

[Paul Emsley]

On 27/06/2023 15:01, Afshan Begum wrote:


Dear expert,

I am currently working on building my cryo-EM data using COOT. 
However, I have encountered an issue when trying to add monomers such 
as Glycerol or BCT using their letter code from the "Get monomer" 
option in COOT. Whenever I attempt to merge them into my coordinate, 
COOT crashes.


I would greatly appreciate any suggestions or advice on how to 
overcome this issue. I am currently using version 0.9.8.5 of COOT on a 
Mac operating system. I am unsure if this is a bug or if there is a 
specific workaround for this situation.




This bug rings a bell. Which means that I may have already fixed it. The 
version of Coot from CCP4 on my Mac is 0.9.8.7. Maybe that will work for 
you?


(All crashes are bugs)

Regards,

Paul.




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Re: [ccp4bb] Script to refine water molecules - help

[Paul Emsley]

The Coot API is quite useful for this sort of thing


imol = 0 # replace as needed
residues = residues_matching_criteria(imol, lambda chain_id, res_no, 
ins_code, serial: residue_name(imol, chain_id, res_no, ins_code) == "HOH")

refine_residues(0, residues)


Regards,

Paul.


On 26/06/2023 22:14, De La Torre Marquez, Pedro Luis wrote:


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Do not click links or open attachments unless you recognize the sender 
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*.-owner-ccp...@jiscmail.ac.uk-.*

Dear Eleanor,

My apologies. Just to be more specific, I am just trying to run a Real 
Space Refinement for the water molecules of my crystal structure with 
COOT.


Thanks for all the help.

Pedro.



*From:* Eleanor Dodson 
*Sent:* Monday, June 26, 2023 4:54 PM
*To:* De La Torre Marquez, Pedro Luis 


*Cc:* CCP4BB@jiscmail.ac.uk 
*Subject:* Re: [ccp4bb] Script to refine water molecules - help

External Email - Use Caution

Wel - one way to do that is to use LABI FPART1=FS_from non-waters 
PHIP1=PHIC_from non-waters.
You would need to split your model file into two - one containing the 
atoms you want to fix, and the other the bits you want to refine.
Run 0 cycles of REFMAC to get an output with Fobs SIGFobs and FC PHIC 
from the atoms you want to fix (0 cycles to prevent the protein moving 
towards water positions)

Then refine the waters assigning LABI FP=..SIGFP=.. FPART1  and PHIP1

But I am not sure that is a very good idea? - there will be no 
restraint terms between the atoms contributing to FPART and the waters

Good luck Eleanor


On Mon, 26 Jun 2023 at 21:44, De La Torre Marquez, Pedro Luis 
 wrote:


Thanks Eleanor.

Yes, only refine waters.

Best regards,

Pedro

*From:* Eleanor Dodson 
*Sent:* Monday, June 26, 2023 4:42 PM
*To:* De La Torre Marquez, Pedro Luis

*Cc:* CCP4BB@jiscmail.ac.uk 
*Subject:* Re: [ccp4bb] Script to refine water molecules - help

External Email - Use Caution

Do you mean only refine waters? In a general refinement run the
waters will be refined along with protin/ligands etc..
Eleanor

On Mon, 26 Jun 2023 at 20:54, De La Torre Marquez, Pedro Luis
 wrote:

Dear all,

I hope everything is going well.
Back in 2019, I was using a script to refine all water
molecules automatically during the refinement of an X-ray
crystal structure. I no longer remember such script. Any
suggestion?

I will really appreciate it.

Pedro.

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Re: [ccp4bb] Apple glasses

[Paul Emsley]

On 06/06/2023 08:19, Goldman, Adrian wrote:

I’m hoping for a coot implementation that allows immersive stereo…



Well, (a) you're in luck - Coot is Free Software and can develop it 
however you like. I am happy to collaborate and handle the technical 
details of integration and distribution. If you don't want to do this 
yourself then you can hire someone to do it for you - I imagine that it 
would cost less then $100,000 - and (b) over the last couple of years I 
have, with help from the moorhen team, separated out the Coot "Engine" 
from the part of the program that handles the mouse, keyboard and 
display, so the combination of that library and Apple's developer kit 
looks like some juicy low hanging fruit! Go for it!



Paul.



Sent from my iPhone


Of course it was.



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Re: [ccp4bb] Issue with CSO in Coot & Refmac

[Paul Emsley]

On 27/05/2023 03:46, Nicholas Clark wrote:

Paul,

Yes, it appears that the upper level group is "NON-POLYMER". However, 
there is an alias at the bottom that does state polymer.



Hi Nick,


In Coot: Edit -> Restraints... -> CSO -> OK -> Change "Non-POLYMER" to 
"peptide" and press enter in the entry, then "Apply"


Now you can refine your CSO in Coot.

Paul.




Best,

Nick Clark


On Fri, May 26, 2023 at 10:37 PM Paul Emsley 
 wrote:



On 27/05/2023 03:23, Nicholas Clark wrote:

Hey Paul,

I found the dictionary entry for CSO, it appears to be in the
"peptide" group (under CCP4-8.0->lib->data->monomers->c->CSO.cif):

"loop_
_chem_comp_alias.comp_id
_chem_comp_alias.group
_chem_comp_alias.atom_id
_chem_comp_alias.atom_id_standard
CSO *peptide* HN2 H2"

 I've attached the file I have for your reference, as I may not
be looking in the correct place. Also, if I'm looking in the
wrong file location, please let me know.



Due to other priorities, Coot is not up to speed with the
developments of my colleagues:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10167671/

<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC10167671%2F=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7C1c2231bcf96a46de05d008db5e5b425c%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638207518308847137%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=YnWTARiMSbo8MRMK8ScjTOuVlwN4MQ6GXFag6iRdnxI%3D=0>
(Section 2)

What is the value of _chem_comp.group ? That is (for the moment)
what Coot cares about.


Paul.




--
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



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Re: [ccp4bb] Issue with CSO in Coot & Refmac

[Paul Emsley]

On 27/05/2023 03:23, Nicholas Clark wrote:

Hey Paul,

I found the dictionary entry for CSO, it appears to be in the 
"peptide" group (under CCP4-8.0->lib->data->monomers->c->CSO.cif):


"loop_
_chem_comp_alias.comp_id
_chem_comp_alias.group
_chem_comp_alias.atom_id
_chem_comp_alias.atom_id_standard
CSO *peptide* HN2 H2"

 I've attached the file I have for your reference, as I may not be 
looking in the correct place. Also, if I'm looking in the wrong file 
location, please let me know.




Due to other priorities, Coot is not up to speed with the developments 
of my colleagues:


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10167671/ (Section 2)

What is the value of _chem_comp.group ? That is (for the moment) what 
Coot cares about.



Paul.




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Re: [ccp4bb] Issue with CSO in Coot & Refmac

[Paul Emsley]

On 27/05/2023 00:43, Nicholas Clark wrote:
I have a cysteine residue that is oxidized and needs to be modeled as 
CSO. In the past, when "replace residue" was used to substitute for 
CSO, the CSO would "behave" during real-space refinement and 
essentially take the place of the Cys. However, when Cys is replaced 
by CSO now the CSO is behaving as an "external ligand" and does not 
maintain covalent bonds to the residue before or after (repulsion 
between CSO & preceding and subsequent residue). The only way I can 
get it to maintain covalent bonds in Coot is to add CSO as a monomer 
and place it before merging into the chain and renumbering the residue 
(afterwards, real space refinement behaves the same as direct 
replacement of CYS->CSO). Similarly, during refinement with Refmac, 
only one of the CSO conformations will maintain its position, the 
alternate conformation breaks the linkage to the preceding residue.


*TLDR: CSO replacement of CYS not working in Coot or Refmac, acting as 
external ligand*.




As you may know the monomer library has been undergoing substantial 
reworking over the last several months. Is the group of the CSO in your 
dictionary "peptide"?


Paul.




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Re: [ccp4bb] how to get mol files from PDB and restraint CIF?

[Paul Emsley]

On 19/05/2023 10:28, Frank von Delft wrote:
Hello - as in the subject line, does anybody know of, or have, code 
that will parse (1) a PDB (or mmCIF?) file with a ligand, and (2) the 
restraints CIF file used in refinement, and generate a .mol (or .sdf) 
file?



Isn't this a bit of strange request? .sdf files are for coordinates, it 
is not clear to me how they would encode restraint information (other 
than simply minimizing the ligand of course (and if you are using the 
monomer library it is likely that Refmac has done this for you)).


Here's how you convert a residue/ligand to an sdf using coot:


import coot
imol = coot.get_monomer("AMP")
coot.residue_to_sdf_file(imol, "A", 1, "", "AMP.sdf")

Paul.



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Re: [ccp4bb] isopeptide bond and shelx topology file

[Paul Emsley]

On 28/04/2023 08:41, StrBio wrote:


CAUTION: This email originated from outside of the LMB.
Do not click links or open attachments unless you recognize the sender 
and know the content is safe.

*.-owner-ccp...@jiscmail.ac.uk-.*

Hello,


Can you suggest how to make isopeptide bond in coot and generate .cif 
file to refine the structure in phenix?



Well, for the Coot part I would use Acedrg in Link mode:

https://www.youtube.com/watch?v=p4oTJ0bjD3M (first part)

https://journals.iucr.org/d/issues/2021/06/00/ir5021/index.html

I image that there would be some interest in how useful you find that 
link description when refining using phenix.




Also need suggestions to create shelxl topology file for non standard 
amino acids.


If you build your Coot, coot-make-shelx-restraints converts cif 
dictionaries to shelx input.


Paul.




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[ccp4bb] Coot Delete Item on MacOS Ventura

[Paul Emsley]

Last week I was using 13.2 and could reproduce the snap iconification on 
delete item.


This morning I updated to 13.3 and the iconification problem is no more 
- so the update fixed it. Apple didn't mention XQuartz or Coot in the 
release notes (fwiw).



Paul.



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Re: [ccp4bb] Structural alignment and classification

[Paul Emsley]

On 06/03/2023 07:35, Armando Albert wrote:

I want to align several structures we obtained from a fragment screening 
campaign and cluster them according to RMSD.


To what end, may I ask?

I would use LSQKAB, parse the log files for the RMSD and create an input 
file for R.


(One cannot just do this in Coot, because, for LSQ fitting, Coot only 
returns the transformation matrix, not any fitting statistics - in 
retrospect this is obviously an oversight.)



Paul.



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Re: [ccp4bb] Coot on MacOS Ventura

[Paul Emsley]

Hello Elsa,

On 30/12/2022 17:13, Elsa Garcin wrote:

Is it possible to run coot on MacOS Ventura and xquartz version 2.8.4?
I believe so, but people have reported minimizing window when they try 
to do so.

I tried installing coot with homebrew (instructions from Scottlab webpage),


This is a quite different beast.


  but was not successful.
I have been trying to work out what has gone wrong and how to fix it. 
Still trying.

Has anyone figured out how to install it so it runs properly? If so, could you 
please share how you did it?


Mac OSX is not my most frequently-used platoform. I will keep bashing 
away at it.


The situation is under discussion in issue 33 on the github page.

Paul.



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Re: [ccp4bb] Copying NCS chain to heteroligomer

[Paul Emsley]

On 17/11/2022 19:03, Alessandro S. Nascimento wrote:

Dear all,

We are refining a 24-mer complex composed of 12 copies of protein A 
and 12 copies of protein B. Since the resolution is not very high 
(~3.0 Ang), we will probably want to copy the modifications made in 
Coot for one chain to the other chains of the same protein (but not 
for the other protein).


Unfortunately, we did not find a way to do that in Coot. Is there any 
option for this?



Calculate -> NCS  Tools -> Copy NCS Chain.

If protein B has high sequence similarity to protein A then you'd need 
to do a "Copy Fragment" of the "B" chains beforehand and then "Replace 
Fragment" after the NCS copy.


Paul.



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Re: [ccp4bb] Problem in generating restraint file for 5.2kDa ligand

[Paul Emsley]

On 09/11/2022 13:59, Deepak Deepak wrote:

Dear CCP4 users,

I am working towards solving a protein-ligand complex structure. The 
ligand is 5.2 kDa (495 atoms) and made of 3 distinctive repetitive 
monomers. [...]

I will happily provide more information if I am missing something here.



You're missing practically everything.

From a software developers point view "It doesn't work" is worse than 
no bug report at all.


I wrote this for Coot in particular, but much also applies to CCP4 
software (where for "terminal" read "log")


https://pemsley.github.io/coot/blog/2020/09/21/how-to-make-a-bug-report.html


Paul.




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Re: [ccp4bb] mutate Methionine to Norleucine in Coot.

[Paul Emsley]

On 20/10/2022 02:06, Jiang Xu wrote:

Hi Garib,
   I deleted the Met residue and imported the nle.cif file



Import the dictionary for NLE, make sure that the group is L-peptide, 
then centre on your Met and Calculate -> Modelling -> Replace Residue -> NLE



Paul.



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Re: [ccp4bb] Coot installation issue

[Paul Emsley]

Coot is not (yet) an official part of brewsci, so the goocanvas update 
bonked coot.


This morning I uninstalled my coot and rebuilt it with YoshitakaMo's 
coot.rb. The second time it worked (i.e. build and installed just fine).


You can see from the patch

https://github.com/brewsci/homebrew-bio/commit/9f57646721018f584dffe700fccbfcb44105304e

that there are a couple of environment variables in the wrapper script. 
They didn't work for me, so I set them on the terminal (and that worked).


They were discovered (if that's the right verb - "ferreted out" or 
"unearthed" maybe?) by Charles Ballard's diligent reading of the 
Inkscape mailing list. For me they increased the fps by 70-100% - which 
makes GTK3 Coot almost usable (on an Intel MacBook Pro, maybe on an M1 
it is *actually* usable).



Paul.


On 30/09/2022 16:17, William G. Scott wrote:

homebrew heavy-handedly wiped out coocanvas v. 2 when upgrading.

I made a temp fix with a sym link as follows:

ln -s /usr/local/Cellar/goocanvas/3.0.0/lib/libgoocanvas-3.0.9.dylib 
/usr/local/lib/libgoocanvas-2.0.9.dylib

your path prefix will be different, but you get the idea.




On Sep 30, 2022, at 7:38 AM, tim smith  wrote:

Hi All,

I am having an issue with installing coot. Here is the outcome when I type coot 
in command line. I am using M1 mac pro. Thank you.

Best regards
Tim


CSI363227 ~ % coot
dyld[11265]: Library not loaded: 
'/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib'
   Referenced from: '/opt/homebrew/Cellar/coot/HEAD-4c7971f/libexec/coot-bin'
   Reason: tried: '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib' 
(no such file), 
'/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no such 
file), '/opt/homebrew/Cellar/goocanvas/3.0.0/lib/libgoocanvas-2.0.9.dylib' (no 
such file), 
'/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no such 
file)
/opt/homebrew/bin/coot: line 211: 11265 Abort trap: 6   $coot_bin "$@"
Coot crashed.



CSI363227 ~ % coot --version
dyld[11238]: Library not loaded: 
'/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib'
   Referenced from: '/opt/homebrew/Cellar/coot/HEAD-4c7971f/libexec/coot-bin'
   Reason: tried: '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib' 
(no such file), 
'/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no such 
file), '/opt/homebrew/Cellar/goocanvas/3.0.0/lib/libgoocanvas-2.0.9.dylib' (no 
such file), 
'/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no such 
file)
/opt/homebrew/bin/coot: line 211: 11238 Abort trap: 6   $coot_bin "$@"
Coot crashed.

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Re: [ccp4bb] Help with isomer ligand from PDB database

[Paul Emsley]

On 17/09/2022 15:48, Marion Schuller wrote:
>
>  
>
> Dear CCP4bb community,
>
>  
>
> I am writing regarding a problem with the refinement of an isomer
> ligand. I try to refine a structure which has the ligand “Carba-NAD”
> (as beta isomer) bound. This ligand is already in the pdb database as
> “CNA”. Although the ligand is in its beta-Carba-NAD form in the
> database, it is loaded into WinCoot as alpha isomer. When generating
> the restraints of Carba-NAD (via the grade server, calling it also
> “CNA”), I can load and refine the correct beta isomer ligand as long
> as I provide the grade-generated .cif file otherwise it would refine
> it back to the alpha isomer. Yet, in the preliminary preparation of
> the wwPDB X-ray validation report for structure deposition, the
> message flags up that the ligand “could not be matched to an existing
> wwPDB Chemical Component Dictionary definition”. With an older ccp4
> version in the background, I noticed that WinCoot would however load
> the beta isomer and I am now wondering if this problem lies in the
> .cif file of the new ccp4 library. Is there a possibility to
> check/correct the CNA file in the current ccp4 library or would there
> be a different way for solving this problem? I would be very grateful
> for support and help!
>
>  
>
Dear Marion,

As a rule, if a molecule has a different anomericity it has a different
ligand-id (three-letter-code) in the CCD. It seems to me that you need a
new entry in the CCD. It is a good thing that the wwPDB X-ray validation
flags this up as a ligand that matched with and existing entry.

So take the entry for CNA:

https://files.rcsb.org/ligands/view/CNA.cif

change the stereo_config from S to an R for C2D (I am guessing that that
is the anomeric carbon atom) in the atom table. Then feed that to
Acedrg. (I'd chop off the _pdbx_chem_comp_descriptor block so that that
Acedrg doesn't get distracted by the out of date SMILES).

Using that dictionary your refinement should be smooth sailing.

Upon deposition, the wwPDB will then reward you with one of the last
ever three letter codes - hooray!


Paul





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Re: [ccp4bb] Problem downloading models maps in from PDBe in Coot

[Paul Emsley]

Hopefully 0.9.8.4 should fix that.

Paul.

On 16/09/2022 13:54, Jan Dohnalek wrote:

This has been quite variable in (several?) last versions of Coot.
I have some three latest versions available and when one does not work 
I start another one. Sad but true.


Jan


On Thu, Sep 15, 2022 at 11:39 AM Robbie Joosten 
 wrote:


Not sure if this is a PDBe bug or a Coot bug (or a combination
thereof)...

I'm using the latest WinCoot in CCP4 8.0. When I try to 'Fetch PDB
using Accession Code', I do not get any models so I guess the
target URL is wrong.
When I use Fetch PDB & Map using EDS, I sometimes get a map (1cbs,
3fvl), sometimes I don't (1ctn, 1lee and many more). All of these
maps used to be available and PDB-REDO versions of all these
entries exist. Does anyone know what is going on?

Cheers,
Robbie



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--
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Vestec near Prague
Czech Republic

Tel. +420 325 873 758



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[ccp4bb] PDBx-format utilities

[Paul Emsley]

A spectre is haunting structural biology - it is the spectre of the PDBx 
format.


We at CCP4 are interested in providing tools that are equivalents of 
those that one might have trivially made with utilities such as grep or sed.


For example:

    delete the hydrogen atoms

    extract the hydrogen atoms

    extract the SD of MET

    find the atoms with B-factors greater than 100.0


So, what useful tool have you made can that works because it based on 
the PDB format - that (of course) doesn't work with PDBx?



Thanks,

Paul.



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Re: [ccp4bb] Missing restrains for standard amino acid

[Paul Emsley]

On 07/08/2022 07:00, Cryo EM wrote:

Hi everyone,

I am using Coot 0.9.8.3 EL (ccp4) on my iMac M1 with MacOS Monterey. 
The phenix version I am using is 1.20.1-4487.


At the end of validation run or real space refinement for my cryo-EM 
map, I want to fix the problems in the model interactively by the 
"open in coot" button displayed in phenix. As soon as I click on the 
problems list in phenix, coot takes me to that atom but I am not able 
to do any local real space refinement in coot since it complains about 
the missing restrains for even standard amino acids and nucleotides 
(screenshot attached).


Please note that coot alone (when not connected to phenix) works for 
me flawlessly. I guess it has something to do with the missing monomer 
library path in coot when connected to phenix but I am unable to fix 
this. Can someone please redirect me to the solution?



Sounds like the monomer library installation is borked.

What does it say in the terminal?

Paul.



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Re: [ccp4bb] Coot RNA bases Mutate

[Paul Emsley]

On 06/08/2022 09:08, Cryo EM wrote:

Hi everyone,

I am trying to mutate modified RNA nucleotide to standard nucleotide 
by coot using "Simple Mutate" button. But it is not working despite 
selecting the correct residue from the standard base list that pop up 
on clicking "simple mutate button". Does anyone and an idea what 
could be the problem? Or is this wrong way to do that?


I am using coot 0.9.8.3 EL (Ccp4) on my Mac.



What does it say in the terminal? - that should give you a clue. My 
guess is that coot can't auto-superpose onto a non-standard nucleotide.


Try "Replace Residue" instead.

Paul



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[ccp4bb] PDB to AlphaFold via Uniprot

[Paul Emsley]

I wonder if others are curious about (or know how to solve) the 
following problem:


I am looking at a PDB file that I've downloaded from a wwPDB site and I 
would like to see the AlphaFold model(s) overlaid. What the best (or 
easiest) way of doing that? (let's imagine that I can do a bit of 
scripting in python (including urllib) and can use the functions in Coot 
for the superposition).


Thanks,

Paul.



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Re: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

[Paul Emsley]

On 27/07/2022 01:44, Dale C wrote:

Hi all,

I recently updated my ccp4 package to Program suite v8.0.002 and i have now run 
into a few issues with other programs. The issues are highlighted below...

- When i click 'Open in Coot' on any output through Phenix (so far only tested 
phenix.refine and phenix.phaser), i no longer see anything open. Nor do i see the 
"Connected to Phenix" button in the toolbar on Coot.
There is probably useful information written to the terminal. AFAIR, you 
are not the first person to experience this, I forget what the problem 
and solution was but I think that it was trivial.


- Coot also seems to have an issue with not loading the amino acid restraints 
so when i click real-space refine, i get the error 'unable to find restraints 
for residue x,y,z'.

When you start Coot, what does it say as it tries to load the 
dictionaries for the standard residues?


Paul.



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Re: [ccp4bb] Modified nucleotides

[Paul Emsley]

On 18/07/2022 07:59, Cryo EM wrote:

Hi all,

I am working on a pdb of RNA where I intend to change the modified 
nucleotides to their parent unmodified original residues. For example, 
PSU to U, 1MG to G and so on.
I was wondering if there is a better way to do that by either manually 
editing the pdb or changing them manually in coot one by one (in Edit: 
Replace residues)?



Sounds hideous. That's what the API is for.


(define imol (read-pdb "rna.pdb"))

(let ((mutation-list (list ;; chain-id res-no new/standard-type
  (list "A" 1 "A")
  (list "A" 2 "C")
  (list "A" 3 "G" ;; mutate to U seems broken

  (for-each (lambda (m)

  (let ((chain-id (list-ref m 0))
    (res-no   (list-ref m 1))
    (new-type (list-ref m 2)))

    (mutate-by-overlap imol chain-id res-no new-type)))
    mutation-list))

You could do something similar in Python.


Despite changing the residues by latter way, there is an error while 
running servalcat refinement. (attached).




Because of a naive implementation of is-nucleotide? Coot fails to detect 
that the modified nucleotide is a nucleotide and so doesn't delete OP3 
for you.


From coot-utils.scm:

    (if (is-nucleotide? imol chain-id-in resno)
    (if (residue-exists? imol chain-id-in (- resno 1) "")
    (delete-atom imol-ligand "A" 1 "" " OP3" "")))

You know the residues that need to be replaced, so just loop over them 
and call delete-atom for the "OP3".



Paul.



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Re: [ccp4bb] Help with One dimensional electron density calculation

[Paul Emsley]

On 13/07/2022 19:18, Ravikumar wrote:


I would like to calculate One-dimension electron density profiles of 
the different number of ions bound to an ion channel. Are there any 
programs in CCP4/ Phenix which can do the same job as the MAPMAN 
(UPPSALA electron density server) program to extract the electron 
density values to plot electron density values versus pore axis? I 
have attached an example figure.





Here's how to do it in Coot (see attached).


Paul.





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from __future__ import print_function
import math

imol = read_pdb('pdb6qkc.ent')
imol_map = read_ccp4_map('emd_4572.map', 0)
n_steps = 250

start_point = [154, 154, 133]
end_point   = [154, 154, 180]



imol_map_smooth = sharpen_blur_map_with_resampling(imol_map, 0.0, 2.3)
delta = [x - y for x, y in zip(end_point, start_point)]
delta_step = [ x/float(n_steps) for x in delta]
delta_step_size = math.sqrt(sum([x*x for x in delta_step]))

print(delta)
print(delta_step)
print(delta_step_size)

with open('line-of-density.table', 'w') as f:
for i_step in range(n_steps + 1):
p = [x + i_step * y for x, y in zip(start_point, delta_step)]
r = density_at_point(imol_map_smooth, p[0], p[1], p[2])
d = delta_step_size * i_step
f.write('{} {} {} {} {}\n'.format(p[0], p[1], p[2], d, r))

Re: [ccp4bb] Phenix.refine sequence check equivalent in CCP4?

[Paul Emsley]

On 11/07/2022 12:36, Colin Levy wrote:

Hi All,

Is there an equivalent functionality to Phenix.refine Sequence check 
in CCP4?  A quick alignment tool of model sequence from pdb to the 
provided sequence?




It seems to me there are a number of ways that one can check a model 
(and map) against a sequence. One ways is by Coot. If you have your 
desired/expected sequence as a pir file:



Validate -> Alignment vs PIR...


Paul.




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Re: [ccp4bb] Coot sporadically crashes

[Paul Emsley]

On 09/07/2022 12:36, Goldman, Adrian wrote:
On a related theme, Paul, I often find that the undo button doesn’t 
work, but I can’t figure out why it sometimes does and sometimes 
doesn’t.  Is this something to do with how I open .pdb files - that 
somehow Coot can’t find the backup files, even though they exist? 
 What should I do to rectify this problem?



There should be some diagnostic message in the console/terminal.

Are you using Windows?

Paul.



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Re: [ccp4bb] Coot sporadically crashes

[Paul Emsley]

 Is there an option to save the session automatically every 10-15 
minutes or so?







And now to actually answer your question:

yes: Edit -> Settings ->Enable Quick-Save Check-pointing... (the default 
is 30 seconds)






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Re: [ccp4bb] Coot sporadically crashes

[Paul Emsley]

On 08/07/2022 16:30, Oganesyan, Vaheh wrote:


Hi All,

Sorry for posting on CCP4BB.



This is an appropriate venue for such a message.


Coot installed together with latest CCP4 on Win10 crashes time to time 
with no messages/warnings. Is there an option to save the session 
automatically every 10-15 minutes or so?



Coot backs up your model at every edit. Look in the coot-backup 
directory to find the latest update (actually it saves the model before 
the last edit - that's how undo & redo work in Coot).


Additionally there is the "Quick-save-as" function - bound to Ctrl-S - 
it saves the session file and all edited models with versioning (hence 
the "as" part, merely "Quick-save" would imply overwriting your file - 
and I didn't want Coot to do that).



Paul




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Re: [ccp4bb] Missing double bonds in the ligand

[Paul Emsley]

The ligand is acetamido-thiadiazole-2-sulfonamide and has code AZM - do 
your PDB atom names match the CCD?




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Re: [ccp4bb] Easy/Silly question

[Paul Emsley]

On 01/07/2022 04:50, Joel Tyndall wrote:


Hi folks,

I frustratingly cant find “maltose” as a ligand in the pdb or ccp4 
database. Does any one have the code for the ligand? Surely its been 
used before.




In Coot:

File -> Search Monomer Library -> "maltose" -> Search

-> MAL




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Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

[Paul Emsley]

Although it may not be apparent, there has been a lot of work going on 
in Acedrg development regarding Boron.


One cannot say the same for Coot though and I can reproduce the 
behaviour reported by Rafa Dolot. If/when I can fix it, it will be 
available in 0.9.8.4.


Paul.


On 06/06/2022 13:24, Boaz Shaanan wrote:

Hi,
In case you don't have a cif file for the ligand, I would load the 
SMILES expression into acedrg (or use any other input option) to 
create a cif file which you can then read into Coot.

Cheers,
Boaz
On Jun 6, 2022 15:06, Rafal Dolot  wrote:
Dear CCP4 Users,

I am working with data containing a possible complex of protein with
FESAN (iron bis(1,2-dicarbollide)). Unfortunately, to my knowledge, this
ligand is not available in PDB. The closest molecule is COSAN (cobalt
bis(1,2-dicarbollide)), which is labelled as CB5 and is available in two
PDB entries. I can load this molecule into Coot, but attempts at ligand
search or refinement of the manually matched molecule result in freezing
of the Coot window. FESAN is not present in CCDC as a single molecule,
but only in some complexes. Could you give me some advice on how to
prepare a new ligand like this one, for incorporation into the protein
and further refinement?




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Re: [ccp4bb] coot 0.9.8.1 and phenix mtz files

[Paul Emsley]

On 27/05/2022 19:22, Jan Abendroth wrote:

Hi all,
not sure if this appropriate for this BB, since right at the interface 
between CCP4, Coot and Phenix.


I wonder if someone else also experiences these issues after upgrading 
to CCP4 8.0 (or 8.001) and with that to Coot 0.9.8.1. This happens 
both on OSX and windows.


  * coot /mydata/.pdb /mydata/.mtz


coot --pdb mydata.pdb --auto mydata.mtz

I removed the globbed data files for style reasons (Bernhard didn't 
think that was a good idea).



  * will only open up the PDB but ont the mtz file. The latter can be
opened via the Load menu.


Yes.


  * The Coot window launched from the phenix gui does not displany the
pdb or the map.


That doesn't sound good. I don't know what's going on there - I'd need 
to see the console log.



Paul.




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Re: [ccp4bb] How to prevent acetate ion clash into ZN in refmac5 and COOT?

[Paul Emsley]

On 11/04/2022 15:55, Martin Moche wrote:


Dear colleagues,

We are refining a structure where an acetate ion (ACT) binds a zinc 
ion, Zn+2 (ZN), using an excellent quality 1.38Å dataset, [...]


When doing COOT sphere refinement, the acetate ion moves on top of the 
ZN? like the ZN was not there? [...] Why is the acetate ion not aware 
of the ZN in COOT?




That is not the intended behaviour. Seems like a bug. How can I 
reproduce it?


0.9.8.1 is the latest version of Coot in the 0.9.x series.

Paul




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Re: [ccp4bb] Add secondary structure definition into an alphafold PDB

[Paul Emsley]

On 07/04/2022 09:24, Munoz.Ines wrote:

Dear all,

Is there any program or server that automatically assign the secondary 
structure elements into a pdb generated by alpha fold?




If you are using Coot, you can use

Calculate -> Scripting -> Python

add_header_secondary_structure_info(imol)



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Re: [ccp4bb] Coot and Pandda questions

[Paul Emsley]

On 06/04/2022 07:05, Laurent wrote:

Good morning (French time…)

Two unrelated questions…
Using Coot, I would like to define some key binding… How can I find 
the command that is actually issued from an option in the 
« calculate » menu ? I would like to define a key binding for the 
function « NCS Tools -> Update NCS ghost using local match ».



This is what the coot source code says:

--

def update_ncs_ghosts_by_local_sphere():
    """Update NCS ghosts based on local environment (residues within 6A of
    (and including) the active residue).

    Typically one would bind this function to a key."""

--


add_key_binding("NCS Matrix Update", "U", lambda: 
update_ncs_ghosts_by_local_sphere())


You will need to use the ncs module in the new version.


Paul.



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Re: [ccp4bb] Coot 1

[Paul Emsley]

That, for the record, is more or less what Ralf said 18 years ago.

On 01/04/2022 23:38, Pavel Afonine wrote:

It's April 1st today, isn't it? -;)


On Fri, Apr 1, 2022 at 3:15 AM Paul Emsley  
wrote:


Coot 1

18 years after the release of Coot 0 it's time that I actually
released
Coot 1.





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[ccp4bb] Coot 1

[Paul Emsley]

Coot 1

18 years after the release of Coot 0 it's time that I actually released 
Coot 1.


Coot 1 is a major change beyond Coot 0. It has required a lot of writing 
and rewriting [1]
and has been the preponderance of my work since 2017. I have had to 
learn how to program
graphics from scratch using the new style. Much of the GUI internals has 
been

rewritten [2].

My experience with 0.9 was that I sat on it, bug-fixing for a long time, 
releasing it
too late. I don't want to repeat that mistake. So here we are, there's a 
lot of good new

stuff in Coot 1, but it's not as slick as it might be (or will become).

  o Update graphics to use OpenGL 3.3
  o Update Python to use version 3.9
  o Update GTK+ to use version 3

While many of the features that were available in 0.9.x have been 
reworked or
re-implemented, there are some gaps. Dropped features include 
Cross-hairs, Stereo, Pisa
interface, built-in key-bindings, NCS Ghosts, Edit Phi/Psi, 
anti-aliasing, Kleywegt
plots, the clipping dialog, Chemical Feature Clustering, 
Dynamically-Transformed/NCS

Maps, LSQ plane distances, dynamic distances, CABLAM-markup, the test suite,
user-defined colour schemes, anisotropic atoms, CURLEW, Scheme GUI 
scripting,

Skeletonization and Baton-Building.

"So, is there anything that _does_ work?" - you might ask...

The GUI has been updated, I have tried to cut down on the number of 
dialogs, the Real
Space Refinement in particular has seen quite a lot of work. The GUI now 
uses dark mode
if the theme is installed [3]. Several menu items have been relocated. 
More menus are now

alphabetically ordered [4].

The graphics is, by default, now based on triangles instead of lines 
which affords a
more pleasing representation (density maps can be represented using both 
modes) and one
can have a more expeditious if not pleasant experience with a fast 
graphics card and a
big screen. The various graphics effects and filters can be tailored to 
some extent by
changing the configuration using the GUI or by editing/replacing the 
shaders.

Full-screen mode is now an option [5].

Overall, the GUI has only had light testing. At the moment, it's 
probably best to
avoid closing dialogs using the window manager. The "OK" button now 
appears after the

"Cancel" button in dialogs.

Python scripting now has uses a history from previous sessions and the 
functions need
to be used with namespaces/modules (e.g. "coot", or "coot_utils"). Coot 
(or coot) is

now a module that can be imported into python.

This build compiles with the RDKit and optionally MoleculestoTriangles 
from Martin Noble.


The map and the model can now be exported to glTF files (for use in 
Blender and other

3D modelling software).

The build script for Coot 1, called build-it-3-3 can be found in the 
"Build from Scratch"
menu on the web page (you will need to have already installed cmake and 
Gtk+). The catch
though is that (at least in my hands) Python and friends are 
frustratingly difficult to

install, so it's possible/likely that the build script won't work. Likewise,
the script doesn't work for Mac OS either. But it is currently the best 
method to get
binaries so I will support it if you try it [6]. (Homebrew might be 
another method.)


Bernhard Lohkamp has been working on the WinCoot version - I will defer 
WinCoot

questions to him.

Mac Coot is now native (no X11/XQuartz needed). I would be interested to 
see how a

natively-compiled [7] version works on an M1 Max processor [8,9].

Judging from previous experience, a few rapid iterations of bug-fix 
releases will be
needed. After this, the version numbers will become sane - it's my plan 
to release a new

major version every year or so.

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-1.tar.gz

Normally I don't cross-post releases, but this one I thought I should.


[1] new as in OpenGL 3.3 or later - using shaders - I don't mean Vulkan 
(that's for the

    future)
[2] the patch from the 0.9.x version is 285k lines
[3] I recommend it
[4] rather than chronologically
[5] double-tap Esc key (the first time) to revert to standard display
[6] I have be working with CCP4 collaborators to use their system to 
build Coot binaries.
    Hopefully the binaries will be available stand-alone, as well as 
integrated into

    the CCP4 Suite via that method
[7] so that's a different meaning of "native"
[8] the little testing I have done on a recent intel MacBook Pro shows 
unimpressive

    performance (Iris graphics, retina display)
[9] Thanks to my Mac-using colleagues for their feedback.



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Re: [ccp4bb] Maps on mobile phones.

[Paul Emsley]

On 27/03/2022 00:17, Jon Cooper wrote:
Hello, I have been trying to put together a thing for viewing small 
blocks of CCP4 electron density maps with a mobile web browser. If 
anyone is interested, the current state of it is here:


http://ic50.org/jbctest14.html



Have you seen/heard about uglymol? The name is an insult but the project 
is interesting.


https://github.com/uglymol/uglymol




Sorry, the link is not https yet, but nothing gets uploaded to the 
server! It seems to work OK on Android and iPhone and the maps (note: 
only maps; it doesn't do MTZ's, sorry) look similar when viewed in 
Coot (taken as the gold standard ;-),


For the record, I've never much liked the contouring of Coot - too many 
close lines and tiny triangles. I've wanted to change it for a long 
time, but it's never been the most important thing to fix.



but I have a few questions about the contouring algorithm that I have 
used. It is "surfacenets.js" from here:


https://github.com/mikolalysenko/isosurface

and a paper describing it is here:

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

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


uglymol makes the transformation that you need - so does CootVR for that 
matter


https://github.com/hamishtodd1/hamishtodd1.github.io/tree/master/cvr

Here's Chris Hassall playing with it:

https://www.youtube.com/watch?v=-wfopgdN8o4

Just to be clear, this is running inside Firefox.

(It looks like he discovered a contouring bug when he zooms out)




Another thing is that the results of the contouring are sent out in 
groups of 3 points which are the vertices of triangles forming the 
surface. Hence, I orthogonalize them and get three.js to draw them as 
just that - triangles. My worry is that, since the triangles all have 
edges in common, nearly all of the contour lines (except the ones at 
the edges of the map box) get drawn twice, or at least are sent to 
three.js twicefor drawing, which doesn't seem terribly efficient?!


Coot used to remove double drawing. The large speed up in contouring in 
the 0.9 series is a result of removing that test and just drawing the 
lines twice.



Is there a nicer way of doing this? I think it might be better to have 
FRODO-style contouring just on the 2D sections of the map, rather than 
having lots of diagonal lines?


I think so too, especially as a larger Shannon sampling factor is now 
not much of an issue.



Anyway, my 5 YO phone takes about 3 seconds to step from one  residue 
to the next, so it seems not too bad, although not ideal!



FWIW, Kevin Cowtan recently advertised a position to "develop next 
generation web based molecular graphics software" - sounds related.





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



I just use a script that runs mapmask - using a GUI seems like an overhead.


Paul.





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Re: [ccp4bb] Cysteine-S-Iodine interaction

[Paul Emsley]

On 17/03/2022 17:37, Mohd Syed Ahangar wrote:



I have been doing some protein crystal soaking with some covalently 
binding fragments and in one structure I have got an extra density on 
Cysteine but that density doesn't match with the expected fragment. 
The fragment was in the form of iodide salt. when I fit the Iodine in 
the density, it fitted fairly well than any other possible chemical 
entity. From the density map it looks like something is covalently 
bound to Cysteine.
Now my question is, can a sulphur atom of Cysteine have such an 
interaction with Iodine.



No, they are both electronegative, C-S-I is not a thing.


The distance between S and Iodine is 2.76A in this case as shown in 
the attached figure.

I would be grateful if someone can shed some light on this.



Your map (this figure) is a textbook example of a covalently linked atom 
incorrectly refined with a non-bonded contact.



Paul.



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Re: [ccp4bb] Adding hydrogens to a specific residue using Coot

[Paul Emsley]

On 13/03/2022 14:05, Tomas Malinauskas wrote:

Dear All,

Is it possible to add hydrogens to a specific residue using Coot?
Something like Calculate -> Scripting -> Python -> coot_reduce(0) but
targeting one residue only.



sprout_hydrogens(0, "L", 101, "")  # or some such: molecule-number 
chain-id res-no ins-code




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Re: [ccp4bb] Coot on Mac OSX Monterey

[Paul Emsley]

On 11/02/2022 21:53, Laurence Pearl wrote:
Does anyone know where I can download a pre-built Coot that will work 
on OS X Monterey  (12.2) on an iMac with an Intel i7 ?


The packages I can find all fail at the File finder which comes up 
blank. X11 latest is installed.


Not an answer to your question but a question about the bug: Classic or 
Modern? Try the other one just to check.


Paul.



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Re: [ccp4bb] Make Ligand error

[Paul Emsley]

On 25/01/2022 04:10, YUVARAJ I wrote:

Respected Prof. Paul
I added this ligand at three places, That why log file showed three 
molecules,
I got multiple densities of the same ligand.  For testing, I  added it 
at only one place and refined it.

It doesn't help, I am getting the same output.
Kindly let me know How I could fix this ligand.
Thank you

Regards
Yuvara

On Tue, Jan 25, 2022 at 12:03 AM Paul Emsley 
mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:



On 24/01/2022 11:11, YUVARAJ I wrote:

Respected Prof. Paul,
Thank you for your kind reply, After refinement using refmac
gives output,
When I visualize in coot, the size of the molecule is small.
but when I do real space refinement with coot, It attains the
original size.
I have attached the output and refmac log file with this mail.
kindly let me know how I could fix this.
Many thanks in advance.

On Mon, Jan 24, 2022 at 12:39 PM Paul Emsley
mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:


On 23/01/2022 09:56, YUVARAJ I wrote:

Respected Prof. Paul,
Thank you so much for your reply, I have followed your
instructions, while during refmac run,
It showed the error of "Error: New ligand has been
encountered. Stopping now"
when I gave the cif file as input in Additional geometry
dictionary option in Refmac ,
It is giving the output (screenshot1) attached. Kindly give
me instructions or any link containing the steps, which I
need to follow.
As mentioned by Prof. Gerard, I have both tetrahedral
((HgI4)2-) and trihedral (HgI3)-) electron densities.
Can you please send another cif file for (HgI3-) as well and
set of instructions, It will be very much helpful.
Thank you in advance.
Regards
Yuvaraj


On Sun, Jan 23, 2022 at 5:07 AM Paul Emsley
mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:


On 22/01/2022 22:10, Georg Mlynek wrote:


Dear Paul,

can you please tell me what the Acedrg Tables reference
(I assume a table of curated stereochemistry values)
and where I can find that table?

Where does coot save these cif files? (Not in
CCP4-7\7.1\Lib\data\monomers\ as I always thought,
before I tried now.)


Many thanks, br Georg.


Am 22.01.2022 um 22:51 schrieb Paul Emsley:



    On 22/01/2022 21:47, Paul Emsley wrote:



On 22/01/2022 17:34, YUVARAJ I wrote:



I have solved a protein structure using anomalous
signal using mercury(II)potassium Iodide(K2HgI4).

I wanted to submit the structure of the protein with
mercury(II) potassium iodide to PDB.

I am facing problems while making the ligand (HGI4)
. HGI4 is not available in the pdb.

Make Ligand in CCP4 is showing error

[...]

I have attached the screenshots for reference.




If it really is tetrahedral you could try the
attached (TIM is already taken so you'll have to
rename it  - or wwPDB will do it for you).

I desalted it of course. I also updated (hand-edited)
the bond distances using the Acedrg Tables reference.

If successful, send us a picture of the
post-refinement maps.



Sorry, I forgot to add:

Use File -> Import CIF dictionary

Tick the "Generate a Molecule" before clicking "Open"




The Acedrg tables are in $CCP4/share/acedrg/tables -
they are tables, not cif files.

The particular file I used today was allMetalBonds.table.

Acedrg is not part of Coot, but it is part of CCP4.

Paul.





Hi Yuvaraj I,


Your log file does not contain a record of the command
invocation arguments unfortunately. But it does seem to me
that you did not specify LIBIN.


Paul.







Hi Yuvaraj I,

The log file says:


 CGMAT cycle number =  1

      VDW
outliers  

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will
be monitored

A    179 TIM I1  . - A    180 TIM I4  . mod.= 0.001 id.= 1.120
dev= -1.12 sig.= 0.20 sym.=  5 -1  1  0 ncs   1 type = 10
A    179 TIM I1  . - A    181 TIM I1  . mod.= 0.001 id.= 1.120
dev= -1.12 sig.= 0.20 sym.=  1 -1  0  0 ncs   1 type = 10
A    179 TIM HG1 . - A    180 TIM HG1 . mod.= 0.000 id.= 2.200
dev= -2.20 sig.= 0.20 sym.=  5 -1  1  0 ncs   1 type = 10
A    179 TIM HG1 . - A    181 TIM HG1 . mod.= 0.000 id.= 2.200
dev= -2.20 sig.= 0.20 sym.=  1 -1  0  0 ncs   1 type = 10
A    179 TIM I2  . - A    180 TIM I3  . mod.= 0.000 i

Re: [ccp4bb] Make Ligand error

[Paul Emsley]

On 24/01/2022 11:11, YUVARAJ I wrote:

Respected Prof. Paul,
Thank you for your kind reply, After refinement using refmac gives 
output,

When I visualize in coot, the size of the molecule is small.
but when I do real space refinement with coot, It attains the original 
size.
I have attached the output and refmac log file with this mail. kindly 
let me know how I could fix this.

Many thanks in advance.

On Mon, Jan 24, 2022 at 12:39 PM Paul Emsley 
mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:



On 23/01/2022 09:56, YUVARAJ I wrote:

Respected Prof. Paul,
Thank you so much for your reply, I have followed your
instructions, while during refmac run,
It showed the error of "Error: New ligand has been encountered.
Stopping now"
when I gave the cif file as input in Additional geometry
dictionary option in Refmac ,
It is giving the output (screenshot1) attached. Kindly give me
instructions or any link containing the steps, which I need to
follow.
As mentioned by Prof. Gerard, I have both tetrahedral ((HgI4)2-)
and trihedral (HgI3)-) electron densities.
Can you please send another cif file for (HgI3-) as well and set
of instructions, It will be very much helpful.
Thank you in advance.
Regards
Yuvaraj


On Sun, Jan 23, 2022 at 5:07 AM Paul Emsley
mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:


On 22/01/2022 22:10, Georg Mlynek wrote:


Dear Paul,

can you please tell me what the Acedrg Tables reference (I
assume a table of curated stereochemistry values) and where
I can find that table?

Where does coot save these cif files? (Not in
CCP4-7\7.1\Lib\data\monomers\ as I always thought, before I
tried now.)


Many thanks, br Georg.


Am 22.01.2022 um 22:51 schrieb Paul Emsley:



    On 22/01/2022 21:47, Paul Emsley wrote:



On 22/01/2022 17:34, YUVARAJ I wrote:



I have solved a protein structure using anomalous signal
using mercury(II)potassium Iodide(K2HgI4).

I wanted to submit the structure of the protein with
mercury(II) potassium iodide to PDB.

I am facing problems while making the ligand (HGI4) .
HGI4 is not available in the pdb.

Make Ligand in CCP4 is showing error

[...]

I have attached the screenshots for reference.




If it really is tetrahedral you could try the attached
(TIM is already taken so you'll have to rename it  - or
wwPDB will do it for you).

I desalted it of course. I also updated (hand-edited) the
bond distances using the Acedrg Tables reference.

If successful, send us a picture of the post-refinement maps.



Sorry, I forgot to add:

Use File -> Import CIF dictionary

Tick the "Generate a Molecule" before clicking "Open"




The Acedrg tables are in $CCP4/share/acedrg/tables - they are
tables, not cif files.

The particular file I used today was allMetalBonds.table.

Acedrg is not part of Coot, but it is part of CCP4.

Paul.





Hi Yuvaraj I,


Your log file does not contain a record of the command invocation
arguments unfortunately. But it does seem to me that you did not
specify LIBIN.


Paul.







Hi Yuvaraj I,

The log file says:


 CGMAT cycle number =  1

      VDW 
outliers  


VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be 
monitored


A    179 TIM I1  . - A    180 TIM I4  . mod.= 0.001 id.= 1.120 dev= 
-1.12 sig.= 0.20 sym.=  5 -1  1  0 ncs   1 type = 10
A    179 TIM I1  . - A    181 TIM I1  . mod.= 0.001 id.= 1.120 dev= 
-1.12 sig.= 0.20 sym.=  1 -1  0  0 ncs   1 type = 10
A    179 TIM HG1 . - A    180 TIM HG1 . mod.= 0.000 id.= 2.200 dev= 
-2.20 sig.= 0.20 sym.=  5 -1  1  0 ncs   1 type = 10
A    179 TIM HG1 . - A    181 TIM HG1 . mod.= 0.000 id.= 2.200 dev= 
-2.20 sig.= 0.20 sym.=  1 -1  0  0 ncs   1 type = 10
A    179 TIM I2  . - A    180 TIM I3  . mod.= 0.000 id.= 1.120 dev= 
-1.12 sig.= 0.20 sym.=  5 -1  1  0 ncs   1 type = 10
A    179 TIM I2  . - A    181 TIM I2  . mod.= 0.001 id.= 1.120 dev= 
-1.12 sig.= 0.20 sym.=  1 -1  0  0 ncs   1 type = 10
A    179 TIM I3  . - A    180 TIM I2  . mod.= 0.001 id.= 1.120 dev= 
-1.12 sig.= 0.20 sym.=  5 -1  1  0 ncs   1 type = 10
A    179 TIM I3  . - A    181 TIM I3  . mod.= 0.001 id.= 1.120 dev= 
-1.12 sig.= 0.20 sym.=  1 -1  0  0 ncs   1 type = 10
A    179 TIM I4  . - A    180 TIM I1  . mod.= 0.000 id.= 1.120 dev= 
-1.12 sig.= 0.20 sym.=  5 -1  1  0 ncs   1 type = 10
A    179 TIM I4  . - A    181 TIM I4  . mod.= 0.000 id.= 1.120 dev= 
-1.12 sig.= 0.20 sym.=  1 -1  0  0 ncs   1 type = 10
A    180 TIM I1  . - A    181 TIM I4  . mod.= 0.000 id.= 1.120 dev= 
-1.12 sig.= 0.20 sym.=  5 -1  1  0 ncs   1 type = 10
A    180 TIM HG

Re: [ccp4bb] Make Ligand error

[Paul Emsley]

On 23/01/2022 09:56, YUVARAJ I wrote:

Respected Prof. Paul,
Thank you so much for your reply, I have followed your instructions, 
while during refmac run,
It showed the error of "Error: New ligand has been encountered. 
Stopping now"
when I gave the cif file as input in Additional geometry dictionary 
option in Refmac ,
It is giving the output (screenshot1) attached. Kindly give me 
instructions or any link containing the steps, which I need to follow.
As mentioned by Prof. Gerard, I have both tetrahedral ((HgI4)2-) and 
trihedral (HgI3)-) electron densities.
Can you please send another cif file for (HgI3-) as well and set of 
instructions, It will be very much helpful.

Thank you in advance.
Regards
Yuvaraj


On Sun, Jan 23, 2022 at 5:07 AM Paul Emsley <mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:



On 22/01/2022 22:10, Georg Mlynek wrote:


Dear Paul,

can you please tell me what the Acedrg Tables reference (I assume
a table of curated stereochemistry values) and where I can find
that table?

Where does coot save these cif files? (Not in
CCP4-7\7.1\Lib\data\monomers\ as I always thought, before I tried
now.)


Many thanks, br Georg.


Am 22.01.2022 um 22:51 schrieb Paul Emsley:



On 22/01/2022 21:47, Paul Emsley wrote:



On 22/01/2022 17:34, YUVARAJ I wrote:



I have solved a protein structure using anomalous signal using
mercury(II)potassium Iodide(K2HgI4).

I wanted to submit the structure of the protein with
mercury(II) potassium iodide to PDB.

I am facing problems while making the ligand (HGI4) . HGI4 is
not available in the pdb.

Make Ligand in CCP4 is showing error

[...]

I have attached the screenshots for reference.




If it really is tetrahedral you could try the attached (TIM is
already taken so you'll have to rename it  - or wwPDB will do
it for you).

I desalted it of course. I also updated (hand-edited) the bond
distances using the Acedrg Tables reference.

If successful, send us a picture of the post-refinement maps.



Sorry, I forgot to add:

Use File -> Import CIF dictionary

Tick the "Generate a Molecule" before clicking "Open"




The Acedrg tables are in $CCP4/share/acedrg/tables - they are
tables, not cif files.

The particular file I used today was allMetalBonds.table.

Acedrg is not part of Coot, but it is part of CCP4.

Paul.





Hi Yuvaraj I,


Your log file does not contain a record of the command invocation 
arguments unfortunately. But it does seem to me that you did not specify 
LIBIN.



Paul.







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Re: [ccp4bb] Make Ligand error

[Paul Emsley]

On 22/01/2022 22:10, Georg Mlynek wrote:


Dear Paul,

can you please tell me what the Acedrg Tables reference (I assume a 
table of curated stereochemistry values) and where I can find that table?


Where does coot save these cif files? (Not in 
CCP4-7\7.1\Lib\data\monomers\ as I always thought, before I tried now.)



Many thanks, br Georg.


Am 22.01.2022 um 22:51 schrieb Paul Emsley:



On 22/01/2022 21:47, Paul Emsley wrote:



On 22/01/2022 17:34, YUVARAJ I wrote:



I have solved a protein structure using anomalous signal using 
mercury(II)potassium Iodide(K2HgI4).


I wanted to submit the structure of the protein with mercury(II) 
potassium iodide to PDB.


I am facing problems while making the ligand (HGI4) . HGI4 is not 
available in the pdb.


Make Ligand in CCP4 is showing error

[...]

I have attached the screenshots for reference.




If it really is tetrahedral you could try the attached (TIM is 
already taken so you'll have to rename it  - or wwPDB will do it for 
you).


I desalted it of course. I also updated (hand-edited) the bond 
distances using the Acedrg Tables reference.


If successful, send us a picture of the post-refinement maps.



Sorry, I forgot to add:

Use File -> Import CIF dictionary

Tick the "Generate a Molecule" before clicking "Open"




The Acedrg tables are in $CCP4/share/acedrg/tables - they are tables, 
not cif files.


The particular file I used today was allMetalBonds.table.

Acedrg is not part of Coot, but it is part of CCP4.

Paul.






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Re: [ccp4bb] Make Ligand error

[Paul Emsley]

On 22/01/2022 21:47, Paul Emsley wrote:



On 22/01/2022 17:34, YUVARAJ I wrote:



I have solved a protein structure using anomalous signal using 
mercury(II)potassium Iodide(K2HgI4).


I wanted to submit the structure of the protein with mercury(II) 
potassium iodide to PDB.


I am facing problems while making the ligand (HGI4) . HGI4 is not 
available in the pdb.


Make Ligand in CCP4 is showing error

[...]

I have attached the screenshots for reference.




If it really is tetrahedral you could try the attached (TIM is already 
taken so you'll have to rename it  - or wwPDB will do it for you).


I desalted it of course. I also updated (hand-edited) the bond 
distances using the Acedrg Tables reference.


If successful, send us a picture of the post-refinement maps.



Sorry, I forgot to add:

Use File -> Import CIF dictionary

Tick the "Generate a Molecule" before clicking "Open"





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Re: [ccp4bb] Make Ligand error

[Paul Emsley]

On 22/01/2022 17:34, YUVARAJ I wrote:



I have solved a protein structure using anomalous signal using 
mercury(II)potassium Iodide(K2HgI4).


I wanted to submit the structure of the protein with mercury(II) 
potassium iodide to PDB.


I am facing problems while making the ligand (HGI4) . HGI4 is not 
available in the pdb.


Make Ligand in CCP4 is showing error

[...]

I have attached the screenshots for reference.




If it really is tetrahedral you could try the attached (TIM is already 
taken so you'll have to rename it  - or wwPDB will do it for you).


I desalted it of course. I also updated (hand-edited) the bond distances 
using the Acedrg Tables reference.


If successful, send us a picture of the post-refinement maps.

Paul.





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TIM-pyrogen.cif
Description: CIF chemical test

Re: [ccp4bb] AW: [ccp4bb] COOT RSR

[Paul Emsley]

What's the difference between a dummy water and a real one?

Paul


On 22/11/2021 14:34, Schreuder, Herman /DE wrote:


Dear Paul,

I agree with Oliver and Norbert, in the early phases of refinement, 
when a lot of rebuilding has to be done, the coot RSR is not very 
helpful and in general I leave it to buster do refine the rebuilt 
regions. Knowing now that (dummy) waters may be the culprit, I will 
remove them. However, it would be much more convenient if the 
repulsions with water molecules would not be taken into account.


Thank you,

Herman

*Von:* CCP4 bulletin board  *Im Auftrag von 
*Norbert Straeter

*Gesendet:* Sonntag, 21. November 2021 12:24
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* Re: [ccp4bb] COOT RSR

Dear Paul,

I agree to Oliver. In situations where you want to fit a "dummy water" 
to a difference density peak (to determine distances to the 
environment) or try the fit of solvent molecules to yet unexplained 
density, it would be nice to first obtain an optimal fit and next 
think about the environment and possible bumps and partial occupancy. 
I had this problem already several times, that I could not get a good 
fit because of the model repulsions. Even if two partially occupied 
waters are at closed distance the repulsions appear to be active in 
RSR. It is not about the old method being better.


Best wishes,

Norbert



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Re: [ccp4bb] COOT RSR

[Paul Emsley]

On 20/11/2021 11:31, Weiergräber, Oliver H. wrote:

Dear Paul,

>From my experience, I agree that an option to inactivate the anti-bumping 
restraints in RSR would be very useful.
To be honest, my impression is that it tends to be a hindrance rather than 
helping, at least in cases where extensive rebuilding is required.

Best regards
Oliver



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Paul Emsley 
[pems...@mrc-lmb.cam.ac.uk]
Sent: 20 November 2021 11:37
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] COOT RSR

On 20/11/2021 09:42, Matthew Snee wrote:

I had a bit of trouble getting used to the new COOT real space refine... it 
took me an embarrassingly long time to work out that there is nothing wrong 
with the fitting/restraints..

You are not alone in finding Coot's RSR unintuitive (at least initially).

it just doesn't seem to allow clashes with parts of the model that aren't in 
the selected RSR zone even when the fit would be perfect.

That's right.

To help out, I have added dynamic interaction analysis: use CURLEW to download the 
Refinement Tools and then use Refine -> Contact Dots On. Now when you use RSR 
you can see what's bumping into what (I usually have this feature turned on).

Is there a quick way to toggle this feature on/off?
No.
It seems like a nice addition, but it can cause problems where one incorrect 
part of a partially built model prevents me building another, or for cases 
where two different residues/ligands occupy the same space at partial occupancy.


The solution is to move the wrong parts of the model out of the way first - or 
include them in the set of refining residues.

Paul.


Hello Oliver,

I am willing to change the real space refinement if I see a reason to do 
so.  If you can show me an example where the old method is easier then 
I'd be interested to watch it.


Paul.



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Re: [ccp4bb] COOT RSR

[Paul Emsley]

On 20/11/2021 09:42, Matthew Snee wrote:


I had a bit of trouble getting used to the new COOT real space 
refine... it took me an embarrassingly long time to work out that 
there is nothing wrong with the fitting/restraints..


You are not alone in finding Coot's RSR unintuitive (at least initially).

it just doesn't seem to allow clashes with parts of the model that 
aren't in the selected RSR zone even when the fit would be perfect.


That's right.

To help out, I have added dynamic interaction analysis: use CURLEW to 
download the Refinement Tools and then use Refine -> Contact Dots On. 
Now when you use RSR you can see what's bumping into what (I usually 
have this feature turned on).




Is there a quick way to toggle this feature on/off?

No.
It seems like a nice addition, but it can cause problems where one 
incorrect part of a partially built model prevents me building 
another, or for cases where two different residues/ligands occupy the 
same space at partial occupancy.


The solution is to move the wrong parts of the model out of the way 
first - or include them in the set of refining residues.


Paul.




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Re: [ccp4bb] update 7.1.016, very poor pyrogen restraints

[Paul Emsley]

On 08/11/2021 08:55, Guenter Fritz wrote:

Dear all,

with ccp4 update 7.1.016 pyrogen was updated from pyrogen-0.0-pre revision 10365 to pyrogen-0.0-pre revision 
10625. I saw that the --MMFF (usage of Merck forcefield) option is now missing.


Yes, it's the default now (i.e. without mogul).

I get restraints from the latest version of pyrogen, which do not work in refmac. I added a screenshot of an 
refmac output  opened in coot below. Restraints were generated from smiles. I had also some trouble with 
some aromates in the previous version but not crumpled molecules like now.


My guess from your figure is that Refmac somehow failed to read the cif output of pyrogen and tried its best 
to make some bond restraints. Coot however *can* read the ouptput of pyrogen, which is why you get a nice 
chemical diagram. It might be worth your while to peruse the output of refmac and/or try to parse the output

from pyrogen in a mmCIF validator.

I am a bit hamstrung with helping you at the moment because my main computer has died and the backup laptop 
doesn't have an up to date CCP4 distribution.


In the meantime you might like to try Acedrg:

$ acedrg -i lig.smi

It's a bit slower but will give you more accurate bond lengths and angles (and an mmCIF file that Refmac can 
read).


Paul.



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Re: [ccp4bb] Add hydrogens

[Paul Emsley]

On 29/09/2021 12:03, Sam Tang wrote:



This may appear to be a silly question -- I am trying to add hydrogens 
to the structure in PDB 1CDW. My initial thought is to run a single 
run of refinement with a refinement program.[...] So... is there an 
easy way to do what I want in this case?




Calculate -> Modelling -> Add Hydrogen Atoms

(using Coot)

Paul



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Re: [ccp4bb] COOT running on Macbook Pro M1 chip

[Paul Emsley]

On 16/09/2021 08:40, WENHE ZHONG wrote:

Dear CCP4 community,

The COOT is not running smoothly on my M1 chip Macbook. For example, 
when both model and the electron density map are displayed, the moving 
from one residue to the next (pressing SPACE bar) is lagging/slow 
(>2s). This only happened to my old computer, but I am surprised to 
find it happens in the newest macbook.



Give us some numbers. Try the spin test

https://pemsley.github.io/coot/blog/2018/06/06/coot-spin-test.html

Paul.



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Re: [ccp4bb] Specifying achiral residue as D-amino acid

[Paul Emsley]

On Sun, 2021-08-01 at 00:54 +, Prasun Kumar wrote:
> Hi All:
> 
> I am trying to solve a structure that has got D-amino acids. The sequence has 
> also got few achiral residues but is
> mentioned as a part of L-peptide in the monomer library. For example GLY or 
> AIB. Since my sequence has all D-amino
> acids, I was thinking of some method by which these achiral residues can be 
> treated as a part of D-peptide without
> changing the three-letter code. 
> I have tried copying the cif file from the Coot monomer library and use it as 
> a restrain file after modifying the L-
> peptide to D-peptide. It has not worked. 
> 
> 

Have a look at one (or more) of the Gramicidin structures.

Paul.



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Re: [ccp4bb] sphere refine radius in coot 0.9.5.1

[Paul Emsley]

On Fri, 2021-07-09 at 13:49 -0400, Ashok Nayak wrote:
> 
> Is it possible to increase the radius of real space refinement

Yes. Use sphere_refine with an argument, e.g. sphere_refine(8.5)

You can add your own button to do this using Right Mouse on the Tool bar and 
selecting "Add a User-defined button"

>  while manually adjusting models in Coot with the sphere refine option?

Let me advise you not to use "manual" when describing your work using Coot.

The is an optimizer behind almost every editing tool which means that Coot is 
deciding where there atoms go, not you.
If you want to distinguish between work in Coot and building done by (say) 
buccaneer, then call it "interactive."

Paul.



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Re: [ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine

[Paul Emsley]

On 22/06/2021 06:47, Jiang Xu wrote:
    I have a problem building and refining an xtal structure. My protein has a N-glycosylation site and I 
want to add N-acetylglucosamine and manose to my protein structure. I used Coot's carbohydrate module and 
let Coot automatically build the sugar chain to the electron density. It worked pretty well, but I noticed 
that the bond between the amine group of asparagine and the C1 of N-acetylglucosamine is depicted as a 
dashed line, rather than a solid line in Coot.


Coot draws solid lines for bonds between neighbouring monomers in a polymer.
The bond between NAG and ASN is not such a bond - it is a link.
Links are drawn as dashed lines in Coot.

After refinement of the structure using Phenix.refine, I 
found the bond just disappeared, and the amine group still has two hydrogen atoms, which should contain one 
hydrogen atom.


If there is no link for a ASN, then there should be two hydrogen atoms add to 
the ND2.

I find it fascinating that these programs work so well together that it didn't 
even occur to you to examine
the conduit through which structral information is passed.

Paul.



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Re: [ccp4bb] Non-standard amino acids in Coot

[Paul Emsley]

On Mon, 2021-06-14 at 10:42 -0400, Cheng Zhang wrote:
> I had this issue before and tried several ways to fix it. The best way that 
> works for me is to edit the PDB and cif
> files of this unnatural amino acid for Coot or Phenix.

I am already furrowing my brow...

>  The goal is to allow COOT and Phenix to recognize it as an 'amino acid', not 
> a random HETATM,

Yes, the former would be better than the latter...

>  so they can add peptide bonds and apply appropriate geometry restrictions in 
> the real-space refinement automatically.

That's right.

>  But I will be interested to learn better ways if there are any. 

Let's see...

> Here is how I do it: 1. Make a PDB file with Phenix's elbow based on the 
> chemical structure of this amino acid.

i) that's not what I would do, but then again one would not reasonably be 
expecting Nigel to use pyrogen or acedrg.

ii) This would be a good point to add step 0: "Check that the amino acid is not 
already in the monomer library" 
If so, we can use skip much of what follows. You can use the text search 
tool in Coot or the ligand search tool
at the PDBe:

   https://www.ebi.ac.uk/pdbe-srv/pdbechem/

>  I usually use MDL or SDL files.

If we're starting from scratch, that is reasonable.

>  2. Change the names of atoms in the PDB file. You have to name the main 
> chain atoms of amino acids specifically so
> COOT can read them as 'amino acids'. Open a PDB file of any protein and you 
> will see those specific names (C, O, N, C,
> CA, CB). 3. Use this PDB file to make a cif file.

That all seems a bit Heath Robinson, pyrogen will do that for you.

>  In the cif file, you have to define this amino acid as an 'L-peptide' or 
> 'D-peptide' in the ligand type line.

This is important.

>  I attached a cif file of L-cysteine. Pay attention to the ligand definition 
> ('L-peptide') and the names of atoms.

Yes - the name of the group, that is.

>  4. Open the PDB and cif files in Coot. Merge this amino acid into your 
> structure and change its numbering.

Coot will deal with the numbering for you (hopefully sensibly).

>  Now you should be able to do real space refinement on it as if it is a 
> natural amino acid.

Yay!

> Also, there are already many unnatural amino acids in COOT or Phenix 
> database. You just have to find the right 3-
> letter code.

That's right.

Paul.



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Re: [ccp4bb] Topology diagrams software

[Paul Emsley]

On 10/06/2021 12:14, Gambelli, Lavinia wrote:


I'm looking for a software to make topology diagrams of proteins. Ideally, I'd like to submit a pdb file and 
obtain the topology model. Do you know what alternatives are out there? So far I'm only aware of PDBsum that 
can do this, but I was wondering if there is something else available.




TopDraw?



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Re: [ccp4bb] Coot shortcut key for Mutate

[Paul Emsley]

On Wed, 2021-06-09 at 20:44 +0100, Paul Emsley wrote:
> On Thu, 2021-06-10 at 00:20 +0530, Firdous Tarique wrote:
> > Hello everyone
> > 
> > Can anybody tell me the Coot shortcut key for mutate or mutate and refine. 
> > Is there any way to turn it on or to
> > assign
> > a particular key if it is disabled ? 
> > 
> 
> "Keyboard mutate" Curlew. 

I mean "Keyboard mutate" is available in Curlew. 



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Re: [ccp4bb] Coot shortcut key for Mutate

[Paul Emsley]

On Thu, 2021-06-10 at 00:20 +0530, Firdous Tarique wrote:
> Hello everyone
> 
> Can anybody tell me the Coot shortcut key for mutate or mutate and refine. Is 
> there any way to turn it on or to assign
> a particular key if it is disabled ? 
> 

"Keyboard mutate" Curlew. You will have to remember your single-letter codes. 
It comprehends lowercase to save you a
keystroke. "C" to active it.

"H" will do a bonded-neighbs refine with auto-accept.

Paul.



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Re: [ccp4bb] Problem with peakmax

[Paul Emsley]

On Tue, 2021-06-08 at 19:34 +0200, Mohamed Ibrahim wrote:
> 
> I am trying to get the peak values from omit maps. The peakmax from the GUI 
> works fine. However, I tried to run
> peakmax from the terminal, and it stuck when returning P1. Same map file 
> works fine, when I use the GUI. Any ideas,
> how to solve this problem?
> 
> command used 
> peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"
> 

Ctrl-D



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Re: [ccp4bb] H-bond modelling

[Paul Emsley]

On Mon, 2021-06-07 at 01:35 +0530, vivek sharma wrote:
> 
> How does one validate if 2 atoms (non-hydrogen) which are close enough, 
> actually participate in H-bonding?
> I have a recent data that i am currently working on, the NH2 of ARG is at 
> 2.61A from ligand's oxygen atom (refer to
> attached image), since there is no electron density for hydrogens, how can i 
> be sure if i am modelling ligand
> correctly? 
> 

This doesn't answer your question, but the difference map suggests radiation 
damage to the very site for which you
require optimal clarity. Less dose, more crystals?

Paul.



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Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

[Paul Emsley]

On Tue, 2021-05-25 at 20:04 +, Frank Von Delft wrote:
> Yes I thought so too, but discovered I am too stupid to decode the highly 
> parsimonious manual on the ccp4 pages. 
> 

The first thing that I'd try (using Coot) is Calculate -> PISA -> Assemblies...



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Re: [ccp4bb] Omit maps in phenix and ccp4

[Paul Emsley]

On 07/04/2021 07:46, Hari shankar wrote:



I have a ligand-protein complex and I wish to calculate different kinds of omit maps (say, composite omit 
maps, simulated annealing maps, other unbiased fo-fc maps ). I wish to omit the ligand and 3.5 angstrom 3D 
space around it. I have tried phenix for this purpose but get this error message consistently.


"Fatal problems interpreting model file: no of atoms with unknown nonbonded energy type symbols: 15 Please 
edit the model file to resolve the problems and/of supply a CIF file with matching restraint definitions, 
along with apply_cif_modification and apply_cif_link parameter definitions if necessary."


This error occurs despite supplying the CIF file for the ligand. I have tried to remake the CIF/PDB files 
from SMILES strings, by drawing the molecule in both ccp4 (acedrug) as well as phenix (elBOW and Readyset 
go). Nothing seems to work.


1. Is there something I have missed out that can solve this issue?
2. Is there a program in CCP4i that can be used to generate the required omit 
maps?
3. In general, how do I omit 3.5 ang of the space around the ligand during this 
map calculations?



Let's imagine that you'd like to use refmac.

1: By drawing the ligand [1] or by other means, create a mmCIF restraints file
2: Using Coot or other means, fit the ligand (it doesn't need to be exact) and 
add the ligand to the protein
3: Refine a couple of cycles with refmac (to test that it comprehends the 
ligand)
4: If fine, calculate SFs with refmac (0 cycles) excluding the ligand and other 
residues that you desire
   using keywords: refinement exclude all from A 1001 to A 1 10001 # for example

https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html

Paul

[1] Lidia is part of Coot for the record



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Re: [ccp4bb] coot & other graphics programs draw too many bonds

[Paul Emsley]

On Thu, 2021-04-01 at 15:02 +0200, Fred Vellieux wrote:
> Hello there,
> 
> After running autodock vina on certain small molecules, the graphics 
> software I am using (e.g. Pymol, Coot) draws far too many bonds on the 
> docked small molecule. See enclosed screen capture.
> 
> Is there any way to prevent this from happening? This isn't very 
> satisfactory of you wish to produce figures for a presentation or for 
> publication.
> 

Is this a fish of the month? It looks like you are drawing a mol file
(with bond lengths equal to 1). Is that right? You need to convert it
to a 3D molecule using Acedrg or some such.

Paul.



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Re: [ccp4bb] Why do large blobs show up in the pores of my crystal when I do refinement?

[Paul Emsley]

On Wed, 2021-03-31 at 19:48 -0400, Jessica Besaw wrote:
> 
> I once again am asking for your advice. ☺ I am trying to solve the
> structure of an RBD:Fab complex. 
> 
> After molecular replacement, the density fits the model very well.
> Looking at the overall crystal structure (by applying symmetry mates
> in pymol), I see large pores in the crystal with only little bits of
> density as shown in the figure below.
> 
> After doing refinement in phenix.refine, I now get these HUGE blobs
> of density. But, they don't really interact with any part of the
> structure, mostly just "floating" in the center, as shown in the
> figure below. I have attached my current refinement strategy in case
> I am choosing a poor strategy.
> 
> Question:
> (1) Are these blobs likely to be a protein?  
> (2) If it is not a protein, is there an honest / scientifically-
> approved way to deal with these density blobs. I think they are
> keeping my R values very high.
> 
> Potentially useful information: 
> Rwork/Rfree = 27.1  /  30.1
> Spacegroup: P 32 2 1
> Highest Resolution: 3.35 Angstrom
> Completeness: 99% (99%)
> CC1/2: 0.99 (0.35)
> 

I imagine that the bulk solvent model/structure factor
calculation/scaling is different between the first image and the
second. Try blurring the first set of SFs by 90 A^2 or so and see if
the blobs turn up to some extent. It does *seem* as if there is some
connection to your model at about the 5 o'clock position of the left
circle.

This being CCP4BB, it is not inappropriate to suggest that you try
another refinement program, one which has a different bulk solvent
model (or a number of them from which to choose, even) to see if your
blobs are recapitulated.

So my answers to your questions are currently
(1) I don't know, it's a close call
(2) put atoms in them

Paul.

I always like "what's my blob?" questions.





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Re: [ccp4bb] phaser-MR warning

[Paul Emsley]

On 31/03/2021 04:37, rohit kumar wrote:
I tried to remove H atoms in pdbcur in ccp4 but still there are lots of HD and HH atoms present in the pdb. 
Could anyone please suggest how to fix this problem.


PDBCUR would want to use the element column in order to identify that the atom 
is a Hydrogen atom.
And that's what's missing. One wonders why.

You can do a grep:

$ egrep -v ' HD| HH..| HH. ' input.pdb > selected.pdb

Paul.



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Re: [ccp4bb] phenix refinement for bent DNA

[Paul Emsley]

On 30/03/2021 02:52, Srivastava, Dhiraj wrote:
I am sorry about phenix related question. But since the question was 
refinement related I thought it will be ok to ask on ccp4bb.


For the record, it's not wrong, it just that questions about Phenix are more likely to get accurate and 
timely responses on the phenixbb.


Paul.



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