Re: [ccp4bb] add ligand with AceDRG

[Oliver Smart]

Hi Stefanie,

If you want to try Grade2 (for a non-confidential ligand) then this is easy to 
do using the Grade Web Server

https://grade.globalphasing.org/

We have altered our default "3-letter code” (aka PDB chemical component ID) to 
“LIG”. 
The reserved PDB two letter codes 01 to 99 are also fine (as are INH and DRG). 
We  understand from users that Grade2 restraint dictionaries work well with 
REFMAC (as to AceDG)
Checking my installation of CCP4 8.0 there are no distributed dictionaries for 
LIG, DRG or 01 to 99.

There was a PDB component LIG that was obsoleted in 2021 
https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/LIG.cif
And there was a restraint dictionary for this distributed with CCP4 7.0.

Perhaps you are picking up things from an old CCP4 installation

Hope this helps,

Oliver 




> On 26 Apr 2024, at 11:21, FREITAG-POHL, STEFANIE 
>  wrote:
> 
> Dear all,
> 
> thank you so much for all your suggestions.
> 
> Unfortunately, nothing helped. Whatever 3-letter code I choose Refmac is 
> complaining that there is a clash with an already existing ligand (even DRG, 
> LIG, numbers) and AceDRG in CCP4i2 insists on 3 letters.
> 
> I am not quite sure how to bypass this issue as I think Refmac is also 
> insisting on 3-letters for ligands (???)
> 
> I have not tried Grade yet.
> 
> Any advise much appreciated.
> 
> Best wishes,
> Stefanie
> 
> 
> 
> Dr. Stefanie Freitag-Pohl (she/her)
> Durham University
> Department of Chemistry
> South Road, Durham
> DH1 3LE
> United Kingdom
> 0191 334 2596
> stefanie.freitag-p...@durham.ac.uk 
> From: CCP4 bulletin board  > on behalf of FREITAG-POHL, STEFANIE 
>  >
> Sent: 25 April 2024 13:01
> To: CCP4BB@JISCMAIL.AC.UK  
> mailto:CCP4BB@JISCMAIL.AC.UK>>
> Subject: [ccp4bb] add ligand with AceDRG
>  
> [EXTERNAL EMAIL]
> Hi all,
> 
> 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.
> Is there any way around this? How do I add a novel ligand?
> 
> Thanks so much for your help.
> 
> Best wishes,
> Stefanie
> 
> 
> 
> Dr. Stefanie Freitag-Pohl (she/her)
> Durham University
> Department of Chemistry
> South Road, Durham
> DH1 3LE
> United Kingdom
> 0191 334 2596
> stefanie.freitag-p...@durham.ac.uk 
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Re: [ccp4bb] eLBOW aromatic restraints

[Oliver Smart]

Dear Henry,

First of all, directly asking for help about eLBOW on the ccp4bb is a little 
bit impolite. It is a bit like asking a 
Nottingham Forest* fan about how Derby City* played on the weekend. Anyway this 
is my suggestion
(as kind of a Leicester City* supporter).

Directly asking any restraint generator to produce good restraints for a 
complicated iridium complex is
Unlikely to produce optimal results. The way I would approach your problem is 
to:

(a) produce restraints for phenanthroline. This is likely to be PDB component 

 PHN https://www.rcsb.org/ligand/PHN "1,10-phenanthroline”

There should be no problems in CCP4 Acedrg or eLBOW doing this and 
producing planar rings
Of course you could use
Global Phasing Grade2 on the Grade Web Server: 
https://grade.globalphasing.org/ 


(b) produce restraints for a cyclopentadienide anion from the SMILES string 
[cH-]11

(c) work out sensible restraint for the iridium to ligand contact distances by 
using CCDC conquest

 https://www.ccdc.cam.ac.uk/solutions/software/conquest/

 to datamine the CSD (Nottingham School of Pharmacy must have a licence for 
this).

I had a quick at this and found for instance CSD entry ODUPUS that looks 
relevant 

https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=ODUPOS

but you should do a search based on the input geometry of your ligand.

(d) manually edit the results of (a) (b) (c) to produce a restraint file for 
the complex.

An alternative to (d) is use the restraints (a) and (b) to refine the complex 
without explicitly
Restraint the iridium to ligand complex distances. This may well be appropriate 
if your diffraction
data goes to high resolution.


Hope this helps,

Oliver

p.s. I you get stuck I would be happy to help contact me off ccp4bb.


* for CCP4bb readers who are not familiar these are 3 English soccer teams 
close to Nottingham that
are traditional rivals.

> On 12 Jun 2023, at 10:56, Henry Padley 
>  wrote:
> 
> Hi all, 
> 
> 
> I'm trying to generate a CIF file of an iridium piano stool complex ligand 
> (Cp*Ir-Phenanthroline).
> 
> Can Phenix eLBOW generate correctly restrained aromatic ring systems which 
> stay flat in refinement? 
> 
> The phenanthroline bonds in the output CIF are listed as "aromatic" in the 
> REEL text table but they are not recognised as such in refinement. I've tried 
> manually editing the CIF via this text table to produce the alternating 
> "double/single bond" structure but it still puckers slightly in refinement. 
> 
> My eLBOW input is a PDB file of the ligand (I have also tried SDF input). I 
> have tried Automatic and eLBOW AM1 QM settings. Might a different Geometry 
> optimisation software selectable within eLBOW  generate the restrained 
> phenanthroline?
> 
> Any advice greatly appreciated. 
> 
> 
> Henry Padley, MSci
> School of Pharmacy 
> University of Nottingham
> 
> This message and any attachment are intended solely for the addressee
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> 
> 
> 
> 
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Re: [ccp4bb] isopeptide bond and shelx topology file

[Oliver Smart]

Hi Amit,

If you are interested in generating restraints for SHELX then Grade2 supports 
this (apply the cosine rule like Jon suggests) and producing ‘dfix’ files
for SHELXL (is this what you mean by a “shelxl” topology file)?

The Grade Web Server:

https://grade.globalphasing.org 

can be used for any non-confidential ligand. Please note that  --shelx is an 
option that you must turn on.

Hope this helps,

Oliver

P.S. a general tip for posting any question or softwate bug report anywhere is 
to never say “ALSO NEED”
If you are asking for help ask one question at a time. This makes replying and 
following threads much easier.


> On 29 Apr 2023, at 09:58, Jon Cooper 
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hello Amit, without PRODRG I don't know of another way to make the SHELX 
> dictionary restraints but it can be done by hand with a small-molecule 
> structure to measure the bond lengths and 1-3 atom distances from. You can 
> also use general values for the ideal bond lengths and angles and the cosine 
> rule will give you the 1-3 distances, if things get really desperate. It 
> would be worth looking at pdb2ins. I remember Ian Tickle wrote a program to 
> make distance restraints for Restrain from a ligand pub file and I have a 
> copy somewhere. The restrain dictionary was similar to the shelx one. 
> 
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
> 
> Sent from Proton Mail mobile
> 
> 
> 
>  Original Message 
> On 28 Apr 2023, 08:41, StrBio < biophysics.w...@gmail.com> wrote:
> 
> Hello,
> 
> Can you suggest how to make isopeptide bond in coot and generate .cif file to 
> refine the structure in phenix?
> 
> Also need suggestions to create shelxl topology file for non standard amino 
> acids.
> I used PRODGR before but seems like the sever is down last couple of months. 
> Any alternatives?
> 
> Thank you
> Amit 
> 
> 
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[ccp4bb] Grade Web Server 11th Anniversary and a major upgrade

[Oliver Smart]

Dear all,

The generation of reliable restraints for novel small-molecule ligands in 
macromolecular complexes is of great importance for both ligand placement into 
density maps and subsequent refinement. 

Eleven years ago we announced on the ccp4bb the availability of the Grade Web 
Server (GWS):   

https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;94bd95fa.1203

The GWS is still going strong and can be found at

https://grade.globalphasing.org/

The GWS allowed users to run the Grade ligand restraint generator on any 
non-confidential ligand. The main source of restraint information for Grade is 
the Cambridge Structural Database (CSD) of small-molecule crystal structures, 
queried using the MOGUL program developed by the CCDC. Where small-molecule 
information is lacking, Grade uses computational chemistry procedures to obtain 
the restraint values. As well as CIF restraints (that can be used with Coot, 
Refmac, BUSTER and many other programs), the GWS has the option to produce 
restraints for SHELX refinement. The GWS allows users to produce restraints 
without installing the CSD or other software.

In December the GWS had a major upgrade and now runs Grade2 
https://gphl.gitlab.io/grade2/. The GWS user interface has been simplified. 
Also included is support for a wider range of input and output file formats 
such as SDF. Grade2 has many improvements over Grade, such as better treatment 
of planar groups.

In these first eleven years of service, the GWS has been used to produce 
restraints for over 22,000 ligands. The GWS is used by scientists from across 
the world so far: this year it has been used in 31 different countries. We 
would like to thank users for bug reports, suggestions, discussions, and 
feedback. We are grateful to the CCDC for their continued support of the 
service.

With best wishes,

The Global Phasing developers: Gerard Bricogne, Claus Flensburg, Peter Keller, 
Wlodek Paciorek, Andrew Sharff, Oliver Smart, Clemens Vonrhein, and Thomas 
Womack.


P.S. There is now a wide range of excellent restraint generation programs 
available, as reviewed by Steiner and Tucker, 2017 
(https://doi.org/10.1107/S2059798316017964), including CCP4 ACEDRG and Phenix 
eLBOW.  In most cases, good results can be obtained with all of these but for 
unusual chemistry it is often worth trying another program.


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Re: [ccp4bb] ChEBI and SMILES

[Oliver Smart]

Please see https://gitlab.com/-/snippets/2468156 
 an extension that downloads SDF files

> On 7 Oct 2022, at 10:12, Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi
> 
> Probably a silly question, but I was wondering how to search for a ligand in 
> ChEBI with a SMILES string? It’s not immediately obvious to my Friday-morning 
> mind ...
> 
> Harry
> 
> 
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Re: [ccp4bb] ligands found in ChEBI...

[Oliver Smart]

Hi Harry,

The SDF found at ChEBI is a 2D SDF with the coordinates used for the diagram. I 
do not think that ChEBI has
3D coordinates. Why not use PubChem instead as this does provide 3D sdf files?

For your caffeine example:

https://pubchem.ncbi.nlm.nih.gov/compound/64119 
 

There 

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/2519/record/SDF/?record_type=3d_type=save_basename=Conformer3D_CID_2519
 

 

Provides a  SDF file.

Hope this helps

Oliver

p.s. I you are stuck with ChEBI identifiers it would be possible to 
programatically find the equivalent PubChem CID.




> On 6 Dec 2022, at 11:31, Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi folks
> 
> Can anyone help with this?
> 
> I must have missed something in the documentation, because I don’t understand 
> why the .mol and .sdf files downloaded from 
> 
>   https://www.ebi.ac.uk/chebi
> 
> seem to have aromatic C-C bonds that are 0.825 Å long (it’s a few decades now 
> since I solved any small molecule structures, but something around 1.395Å 
> rings a faint bell).
> 
> I need to have ligands that have realistic sizes, and while I’m perfectly at 
> ease scaling the models to what I think are sensible sizes, I can’t help but 
> think that this isn’t necessary and I’ve missed something somewhere.
> 
> Here’s an example of a molecule that I used this morning - 
> 
>   
> https://www.ebi.ac.uk/chebi/saveStructure.do?defaultImage=true=31332=0
> 
> contents of downloaded file - 
>> 
>>  Marvin  01140911122D  
>> 
>> 15 15  0  0  0  0999 V2000
>>   -0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>   -0.71450.41250. N   0  0  0  0  0  0  0  0  0  0  0  0
>>0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>0.71450.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>0.   -0.82500. N   0  0  0  0  0  0  0  0  0  0  0  0
>>0.0.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
>>1.49920.66740. N   0  0  0  0  0  0  0  0  0  0  0  0
>>1.4992   -0.66750. N   0  0  0  0  0  0  0  0  0  0  0  0
>>1.98410.0. C   0  0  0  0  0  0  0  0  0  0  0  0
>>   -1.4289   -0.82500. O   0  0  0  0  0  0  0  0  0  0  0  0
>>0.00011.65000. O   0  0  0  0  0  0  0  0  0  0  0  0
>>0.0001   -1.65000. C   0  0  0  0  0  0  0  0  0  0  0  0
>>1.75411.45200. C   0  0  0  0  0  0  0  0  0  0  0  0
>>   -1.42890.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
>>2.0809   -1.53650. O   0  0  0  0  0  0  0  0  0  0  0  0
>> 10  1  2  0  0  0  0
>>  1  2  1  0  0  0  0
>> 14  2  1  0  0  0  0
>>  8  3  1  0  0  0  0
>>  4  3  2  0  0  0  0
>>  7  4  1  0  0  0  0
>>  1  5  1  0  0  0  0
>>  5  3  1  0  0  0  0
>> 12  5  1  0  0  0  0
>>  6  2  1  0  0  0  0
>>  6  4  1  0  0  0  0
>> 11  6  2  0  0  0  0
>>  9  7  1  0  0  0  0
>> 13  7  1  0  0  0  0
>>  9  8  2  0  0  0  0
>> M  END
>> 
> 
> Harry
> 
> 
> 
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Re: [ccp4bb] Question about CCP4 monomer dictionaries

[Oliver Smart]

Hi everyone,

Prompted by this discussion I ran a series of CSD conquest searches for 
peroxide in various environments.
CSD conquest makes it easy to perform fairly complex searches (and was used for 
the Engh & Huber amino
acid restraint library for amino acids still extensively used today).

Searching for isolated hydrogen peroxide H2O2 results in 66 CSD entries as hits 
There are 87 oxygen-oxygen distances with a mean value 1.454Å and a standard 
deviation 0.022Å

So the CCP4 monomer library entry for hydrogen peroxide H2O2 PEO.cif with a 
distance of 1.461Å and an esd 0.012Å is good.

Using conquest to search for a singly charge hydrogen peroxide ion HO2- that is 
bound to any metal atom (M-O-O-H) results in
17 CSD hits, There are 27 oxygen-oxygen distances with a mean value 1.473Å and 
a standard deviation 0.060Å

There is no PDB component or CCP4 monomer for a singly charged hydrogen 
peroxide ion.

Using conquest to search for a doubly charged peroxide ion O2- that is bound to 
any metal atom (M-O-O) results in only 3 CSD
CSD hits, The 3 O-O distances are:

| CSD entry | coordinated to.| distance | 
| ETBSCB | Co 
cobalt  |  1.348Å  |
| EWOPEM | Pd 
palladium ion.  |  1.293Å  |
| NUNJOX | Co 
cobalt ion. |  1.301Å  |

So the oxygen-oxygen distance for doubly charged peroxide ions that coordinate 
metals is shorter than isolate hydrogen peroxide
Or the more normal singly charged peroxide ion with one hydrogen atom. 

Your observed distance of 1.15Å would seem to be consistent with a doubly 
charged peroxide coordinated to a metal ion,
Particularly after Boaz’s comment.

There is a PDB component and CCP4 monomer library entry for a  doubly charged 
peroxide ion O2- PER
* The current CCP4 8.0 monomer library uses a O-O distance  1.150 ± 0.020Å 
* Global Phasing Grade2 uses a O-O distance 1.316 ± 0.030Å based on the UFF 
force field. 

Looking a PDB entries with PER modelled it is normally not next to a metal atom.
I think it is unlikely that these would be doubly negatively charged so using 
PER would likely lead to unrealistic short O-O distances.
Most hydrogen peroxide ions are likely to be hydrogenperoxide(1-) 
https://pubchem.ncbi.nlm.nih.gov/compound/18500 
 
Perhaps there could be a new PDB component for this species? Otherwise it would 
be a much better idea to model
the molecules as PEO 

Hope this helps,

Oliver

p.s. I think that it is a great idea for restraint dictionary to include 
information as to the source of a parameter so Global Phasing Grade2
 
https://www.globalphasing.com/buster/manual/grade2/manual/introduction.html 
  

includes information as to the source of restraints for instance for PER:

#
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1   
_chem_comp_bond.atom_id_2   
_chem_comp_bond.type
_chem_comp_bond.aromatic
_chem_comp_bond.value_dist_nucleus  
_chem_comp_bond.value_dist_nucleus_esd  
_chem_comp_bond.value_dist  
_chem_comp_bond.value_dist_esd  
_chem_comp_bond.source_value_dist_nucleus   
_chem_comp_bond.source_value_dist_nucleus_esd   
_chem_comp_bond.source_value_dist   
_chem_comp_bond.source_value_dist_esd   
PEO O1  O2 single n 1.444 0.069 1.444 0.069 Mogul_mean_118_hits Mogul_sd 
Mogul_mean_118_hits Mogul_sd
PEO O1 HO1 single n 0.972 0.020 0.850 0.020 MMFF94s_equilibrium default_to_H
  ecloud   ecloud
PEO O2 HO2 single n 0.972 0.020 0.850 0.020 MMFF94s_equilibrium default_to_H
  ecloud   ecloud
#

So you can see that the O1-O2 distance is based on Mogul results. This makes 
tracking down information easier.





> On 29 Nov 2022, at 07:01, stephen.c...@rc-harwell.ac.uk 
> <8f3604def7f0-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Dear Boaz,
> 
> You're quite right, in my haste to reply last night I only related part of 
> the discussion relating to peroxide.  In a bid to identify the diatomic 
> ligand, which appears on oxygen exposure,  I quoted the peroxide bond length 
> as being too long, then went on to say it is much more like dioxygen in 
> oxyhaemoglobin/myoglobin and referenced structures from yourself and Simon 
> Phillips.
> 
> Best wishes,
> Steve
> 
> 
> Dr Stephen Carr
> Research Complex at Harwell (RCaH)
> Rutherford Appleton Laboratory
> Harwell Oxford
> Didcot
> Oxon OX11 0FA
> United Kingdom
> Email stephen.c...@rc-harwell.ac.uk 
> tel 01235 567717
> From: Boaz Shaanan mailto:bshaa...@bgu.ac.il>>

Re: [ccp4bb] ChEBI and SMILES

[Oliver Smart]

On 7 Oct 2022, at 10:12, Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:HiProbably a silly question, but I was wondering how to search for a ligand in ChEBI with a SMILES string? It’s not immediately obvious to my Friday-morning mind ...HarryTo unsubscribe from the CCP4BB list, click the following link:https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/Dear Harry,Although ChEBI has an API this uses SOAP and I am not familiar with ithttps://www.ebi.ac.uk/chebi/webServices.doBut PubChem has a great API system and pubchempy https://github.com/mcs07/PubChemPy provides an easy way to interact with it.Pubchem entries appear to have the CHEBI identifier as one of there synonyms. The attached python script access this information.For instance:$ ./lookup_smiles_in_pubchem.py   "c1c1O"                                                       PubChem_CID:996 ChEBI_ID:15882 (phenol)$./lookup_smiles_in_pubchem.py   "Cn1cnc2n(C)c(=O)n(C)c(=O)c12"PubChem_CID:2519 ChEBI_ID:27732 (caffeine)$./lookup_smiles_in_pubchem.py   "1=NN(C2=C1N=C(NC2=O)C3=C(C=CC(=C3)S(=O)(=O)N4CCN(CC4)C)OCC)C"PubChem_CID:135398744 ChEBI_ID:9139 (sildenafil)Hope this is usefulOliver

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#!/usr/bin/env python
"""
little script to lookup a SMILES string at PubChem
and print out the CHEBI and ChEMBL identifiers
"""
import pubchempy as pcp
import argparse

# get smiles from command line
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('smiles', metavar='SMILES',
help='SMILES string to lookup')
args = parser.parse_args()
smiles = args.smiles

compound = pcp.get_compounds(smiles, 'smiles')[0]
if compound:
cid = compound.cid
synonyms = compound.synonyms
chebi_ids = [s for s in synonyms if s.startswith('CHEBI:')]
if chebi_ids:
chebi_id = chebi_ids[0].replace('CHEBI:', '')
else:
chebi_id = None
print(f'PubChem_CID:{cid} ChEBI_ID:{chebi_id} ({synonyms[0]})')
else:
print('smiles string not found')



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

[Oliver Smart]

Dear Rafal,

Apologies my email client rather scrambled the text from my previous message, 
so I will send again here

Please find attached (in the previous message!) a restraint CIF file and a 
corresponding PDB file for your FESAN ligand.

Details:

Your ligand FESAN is a difficult test case for all restraint generation and 
refinement programs. It combines two carborane groups with a charged iron atom. 
Carborane groups have unusual chemistry that does not conform to normal valence 
models (they have carbon atoms bonded to six other atoms). Combining these 
groups with an iron atom that is bonded to 12 other atoms makes things even 
more complicated. Starting from a SMILES string is not wise for such a molecule.

Fortunately, such chemistry can be handled by the Grade2 restraint generator, 
that is supplied with BUSTER:

https://gphl.gitlab.io/grade2_docs/ <https://gphl.gitlab.io/grade2_docs/>
Starting from the PDB file you supplied I converted to MOL2 format using CSD 
Mercury. Grade2 can read the MOL2 file and produce restraints (despite RDKit 
not being able to handle carboranes). All bond restraints are based on Mogul 
searches of CSD small molecule structures.

I manually edited the restraint CIF because there were too many bond angles to 
be useful. In the carborane cluster, each non-hydrogen atom is bonded to 5 
others to form an icosahedral shell, so that the bond length restraints alone 
are sufficient to fully define the geometry since all angles are implied. 
Additional bond angle restraints both within the cluster and for the 
12-coordinated FE atom are unnecessary and likely to be counter-productive.

It appears from CSD entries that FESAN is a cation carrying an overall charge 
of +1. But I did not correct this.

Please note that the atom names are slightly different from your PDB file as 
the FE atom has an uppercase atom name.

Unfortunately, the current CCP4 distribution of Coot 0.8.9.2-pre EL (revision 
count 7766) cannot cope this molecule as 'Send in the bond angels! Ahem I mean 
"Regularize Zone (Click two atoms)' produces a lock-up using all the CPU that 
has to be terminated by a kill. But you should be able to do a manual fit in 
Coot. BUSTER has no difficulty refining a structure with such restraints, as 
shown in this test using PDB entry 3I8W with FESAN replacing the CB5 ligand:

(Picture attached to previous message)
I hope that the restraint dictionary works for you.

All the best,

Oliver Smart, Andrew Sharff for BUSTER Developers.


> On 7 Jun 2022, at 08:35, Rafal Dolot  wrote:
> 
> Dear all,
> 
> Thank you very much for all your messages. Unfortunately, I'm still on the 
> same place, as yesterday...
> 
> First of all, I prepared a pdb/cif file of the ligand based on CCDC entry 
> 1176355 containing FESAN molecule. Also, I prepared SMILES file based on 
> SMILES of CB5 ligand (COSAN) available on PDB, where I simply switched Co 
> into Fe atom.
> 
> -> When I tried use acedrg with SMILES, I received an error info:
> 
> Input file: FSM.smi
> Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.cif
> Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.pdb
> workMode :  12
> Can not generate a molecule from the input SMILES string!
> Check your SMILES or report the bug
> Can not get the element symbols of atoms. Check input file format
> Error : The job stops because of errors
> 
> -> When I tried use acedrg with *pdb/*cif files I received no output files:
> 
> Input file: fsm.cif
> Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.cif
> Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.pdb
> workMode :  11
> Number of atoms in the cif file  0
> 
> -> When I tried use acedrg with *.mol file I received no output files:
> 
> Input file: fsm.mol
> Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.cif
> Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.pdb
> workMode :  13
> The system contains atoms of the following elements
> C B   Fe  H
> The input ligands/molecules contains metal or other heavier atoms
> Acedrg currently deals with ligands/molecules with following elements only
> C, N, O, S, P, B, F, Cl, Br, I, H
> The job finishes succesfully
> 
> 
> -> When I tried use prodrg, the program has been crashed:
> 
> The program run with command: cprodrg XYZIN 
> "C:/data_cryst/hsa_fesan_04/fsm.pdb" LIBOUT 
> "C:/data_cryst/hsa_fesan_04/fsm_prodrg1.cif" XYZOUT 
> "C:/data_cryst/hsa_fesan_04/fsm_prodrg1.pdb" MOLOUT 
> "C:/data_cryst/hsa_fesan_04/fsm_prodrg1.mol"
> has failed with error message
> forrtl: severe (157): Program Exception - access violation
> Image  PCRoutineLineSource
> 

Re: [ccp4bb] on space group P 3 2 1

[Oliver Smart]

Dear Lee,

I would recommend that you visit: 
https://www.ebi.ac.uk/pdbe/entry/pdb/1g4a/analysis there you can download the 
assembly indicated by the REMARK 350 Octadecamer that describes the "AUTHOR 
DETERMINED BIOLOGICAL UNIT". The download will be in mmcif format that many 
programs can support. If you need the coordinates in PDB format then there are 
a number of ways to convert. I would recommend using CCP4 coot to load and save.

Hope this helps,

Oliver



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Re: [ccp4bb] Cation-channel pore representation for solvent accessible area

[Oliver Smart]

Ashok,

If you are still persisting with the original HOLE rather than the coot HOLE 
clone or Caver:
The HOLE input card you need is 'endrad'  as described at 
http://www.holeprogram.org/doc/#_example_application 
an alternative is to edit the .sph output file.

Please contact me directly if you want any further assistance on HOLE.

Best regards,

Oliver

Oliver Smart, Anglia Ruskin University 
oliver.smart AT anglia.ac.uk



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Re: [ccp4bb] Blob Game

[Oliver Smart]

on 23/2/15 6:57 PM, jens Preben Morth j.p.mo...@ncmm.uio.no wrote:

 a horrible water molecule would fit in there :-)

 On 23/02/15 19:42, Keller, Jacob wrote:
 A little more info:

 -Resolution is 1.75 Ang at edge of detector, but I/sig was still ~3;
 pushing integration to corners gives 1.66 Ang, but completeness is
horrible.
 The home setup was at the limit (without 2 theta.)

 -Data are horribly twinned with fractions of 58/42%, spacegroup is P3212.
 Besides that, though, the data are really excellent.

 -Peak is 6.40 rmsd in Refmac-generated difference map.

 -Distance from blob-peak to Arg-N is 3.43 Ang, but the peak is obviously
 not spherical.

 JPK

Jacob,

Jens may be correct. Is it possible it is a water molecule mixed with an
alternate conformation for the
Arg side chain? Notice a little blob of positive density next to the
nitrogen atom. Could the guanidino group be partly flipped? (Just a
suggestion to consider it probably is not).

If you cannot find a convincing model it is a good idea to  add a UNK/UNX
atom to indicate ambiguity.

Good luck

Oliver

[ccp4bb] future of MolProbity?

[Oliver Smart]

If you find MolProbity a useful tool then please look at the statement
at the top of

 http://molprobity.biochem.duke.edu/

The statement reads:

URGENT: For the survival of MolProbity, we need your supporting
comments or letters.
The MolProbity renewal NIH grant scored well but not well enough,
and reviewers specifically
asked for more user feedback. Please send us your stories about
how you use MolProbity,
why you value it, and how it has helped your research. We are
resubmitting the grant -- to
maintain the   resource, update features, and develop new ways to
help people do much
better at low resolution.

Send to david.richard...@duke.edu, before February 20 -- either a
formal letter of support,
or just useful, quotable comments in email. 

I find MolProbity very useful and am just drafting such an email.

Hope it is OK to send this to the ccp4bb. Many people use MolProbity
from their own sites, or
using 3rd party software tools (such as buster-report or the wwPDB
validation server) so they
would not have seen the message.

Oliver

--
Dr Oliver Smart
Director SmartSci Limited
http://www.smartsci.uk/
 Consultant Global Phasing Ltd
http://www.globalphasing.com/

Re: [ccp4bb] molprobity clashscore, symmetry-related molecules?

[Oliver Smart]

on 23/10/14 11:52 AM, Tim tim.schu...@rub.de wrote:

 Hi everybody,
 Molprobity does not take into account contacts/clashes from
 symmetry-related molecules, or does it?
 Thanks in advance,
 Tim


Tim,

I am not sure. In my experience MolProbity reduce does not take crystal
contacts
into account (but reduce does a great job otherwise). But this might have
been improved.

Oliver
-
Dr Oliver Smart

Director SmartSci Limited  http://www.smartsci.uk/
 Consultant Global Phasing Ltd http://www.globalphasing.com/

Re: [ccp4bb] Refinement of Iron-sulphur clusters

[Oliver Smart]

on 13/10/14 6:33 PM, Pedro Matias mat...@itqb.unl.pt wrote:

 In relation to this topic, I'd like to mention that SF4 has replaced FS4
 as the Fe4S4 monomer in the CCP4 monomer library.

 However, the dictionary values for bond lengths and angles are not
 correct, and this is especially noticeable when the dictionary is used
 in a high-resolution refinement (e.g., 1.05 A). In particular, the
 Fe-S-Fe angles are all set to 90 degrees, when in fact some are smaller
 and others are larger.

 This introduces a bias in the final rms angle deviation values. Fe4S4 is
 a distorted cubane, not a perfect cube.


Pedro,

Yes you are 100% correct

The dictionaries I sent have values that are obtained from an analysis of
small
molecule crystal structures in the CSD (by hand with conquest). For
instance
the Fe-Scluster-Fe angle has a mean of  73.4 degree with a standard
deviation
of 0.7 degrees. The restraints are compatible with Engh and Huber restraints
you
will be using for your protein and for that matter the Parkinson et al
restraints used
for any nucleic acid (because they come from a similar data mining
procedure).
So if Stephen used this dictionary he would not  introduce a bias in the
final rms
angle deviation value because the restraint values would be sensible.

If you to check the restraint values are sensible then you check them
against atomic
resolution structures for instance
http://www.rcsb.org/pdb/explore/explore.do?structureId=1B0Y
at 0.93 Å resolution structure determined by George Sheldrick. This has SF4
with
Fe-Scluster-Fe angles around 73.3 degrees.

I would strongly advise anyone against using a restraint dictionary for
Fe4S4 that uses
90 degree as the ideal angle because you are restraining towards values that

make no sense. If the dictionary contains chiral volume terms then I would
ask the
question why? But this is just my personal take.

If CCP4 would like to redistribute/work the dictionaries sent then we would
be happy
(please email off-list).

Dr Oliver Smart
Director SmartSci Limited http://www.smartsci.uk/
 Consultant Global Phasing Ltd http://www.globalphasing.com/

Re: [ccp4bb] Refinement of Iron-sulphur clusters

[Oliver Smart]

Stephen,

Robbie advice is 100% correct. Be careful about the naming of the sulphur
atoms (is S1 opposite S4 or next to it). I recall that the distributed CCP4
dictionaries have different atom naming than the PDB chemical components
dictionary.  If this is the problem is that the naming is different this
should result
in large restraint violations that should be appear in the REFMAC output
(others can tell you where).

In general diffraction from Fe S clusters is so strong that the atom
positions
are pretty much determined from the electron density. But in case it helps
I did some work data mining restraints for Fe2S2 and Fe4S4 from CSD
structures (this has to be done manually). Please find attached the
resulting FES.cif and SF4.cif restraint dictionaries (distributed with
BUSTER).

Good luck,

Oliver
---
Dr Oliver Smart
Director SmartSci Limited http://www.smartsci.uk/
 Consultant Global Phasing Ltd http://www.globalphasing.com/

on 10/10/14 5:33 PM, Robbie Joosten robbie_joos...@hotmail.com wrote:

 Dear Stephen,

 The dictionary is very specific about atom names. If you have them swapped
 (as many PDB entries do). The angle and chiral volume restraints will
wreck
 your cluster. You also need to make sure to provide LINK records to attach
 the cluster to the surrounding cysteines.

 HTH,
 Robbie

 Sent from my Windows Phone
 
 Van: Stephen Carr
 Verzonden: 10-10-2014 18:07
 Aan: CCP4BB@JISCMAIL.AC.UK
 Onderwerp: [ccp4bb] Refinement of Iron-sulphur clusters

 Dear CCP4 BBers,

 I am currently refining a model of a protein containing three iron sulphur
 clusters using Refmac (v5.8.0078) and am getting some unusual results.
One
 of the clusters (3fe 4s) seems to behave resonably and the refined
electron
 density looks very nice.  The atoms in the others clusters (4Fe4S and
 4Fe3S), however, migrate towards the centre of the cluster producing Fo-Fc
 difference maps with strong negative density at the centre surrounded by
 blobs of positive density where the atoms should be.

 I have checkedthe refmac dictionaries and there are entries for each of
the
 clusters, so I shouldn't have to explicitly include a cif file for the
 clusters as an input right?  In fact, when I did try to include a
dictionary
 file for one of the clusters refmac gave a warning message in the log
about
 duplicate monomers dictionaries and it made no difference to the
 refinement/maps anyway.

 On checking the refmac log file there is no specific mention that there
are
 hetero-groups in the pdb file and no explicit mention that it is using any
 dictionaries during the refinement.  How can I tell if refmac is
 reading/using the dictionaries?  Also bonds within the clusters are
flagged
 up as outliers and deviating by more than 10 sigma from ideal suggesting
 that they are not getting read?

 I realise that something chemically odd could be going on at the centres,
 but if I omit them from the model and calculate maps very strong density
 comes back around where the atoms sat before refinement, so I am pretty
 confident that they are in the right place to start with.

 Any help with this problem would be greatly appreciated, I'm sure there is
 something obvious that I am missing but can't see what that is at the
 moment.  It is particularly confusing since one cluster apparently behaves
 while the others do not.  I could, of course, try phenix or buster, but I
 would like to get to the bottom of the problem with refmac if possible.

 Thanks very much in advance,

 Steve

 Dr Stephen Carr
 Research Complex at Harwell (RCaH)
 Rutherford Appleton Laboratory
 Harwell Oxford
 Didcot
 Oxon OX11 0FA
 United Kingdom
 Email stephen.c...@rc-harwell.ac.uk
 tel 01235 567717
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FES.cif
Description: CIF chemical test


SF4.cif
Description: CIF chemical test

Re: [ccp4bb] how to measure the angle between two aromatic ring plane in PYMOL?

[Oliver Smart]

On Thu, 25 Sep 2014, Wang, Bing wrote:


Hi everyone,

I want to tell an angel between two aromatic planes which comes from two 
different molecules and cross each other.

First, I tried the easier ways. I presume these two aromatic rings are in the 
perfect planes, that is why I tried
plane_wizard.py and draw_plane_cgo.py which work very well. However after I got 
two plates by plane_wizard or draw_plane, I
don't know how to measure the angle between these two plates. I also don't know 
whether I could get the angle I wanted from
these two ways. I tried vector_angly.py which cann't loaded into pymol 
properly. If it could, how can i do to get the angel from
these two plates I drew. Solutions? Since I am in the beginner state, please 
show me details which i could follow step by step.

Second, If these two aromatic rings are not in the perfect planes, how can i 
find the best fit planes? And then find the angle
between the best fit planes? I tried svdplos.py and makeCGOplates.py which are 
downloaded on line. unfortunately both of these
can't be loaded into pymol properly. Solutions?

Thanks!

Bing Wang




Wang,

I am sure the other replies will sort your problem in PyMOL itself. But I 
thought it might be useful for you to consider checking any calculation of 
the angle works properly by using the well-established CCP4 tool GEOMCALC:


http://www.ccp4.ac.uk/html/geomcalc.html

I (and others) use the tool to calculate butterfly bend angles in flavin 
rings (this involves finding the angle between two mean-plane rings). If 
you want any help on running it then contact me off list and I would be 
happy to help.


Good luck,

Oliver

PS. I really like the phrase tell an angel. Paul Emsley's coot refers to
geometry only optimization as send in the bond angels.

| Dr Oliver Smart |
| Global Phasing Ltd., Cambridge UK   |
| http://www.globalphasing.com/people/osmart/ |

[ccp4bb] HOLE program availability

[Oliver Smart]

On Thu, 7 Aug 2014, Oliver Clarke wrote:


Dear all,

Apologies for the non-CCP4 related post, but does anyone know where the 
HOLE program for mapping the conduction pathways of ion channels may be 
obtained from these days? Preferably in a form that may be run on Mac or 
Linux systems.


It no longer appears to be available from the Sansom laboratory website 
where it was previously hosted, and I have been unable to identify an 
alternate location from which to download it.


Alternatively, suggestions of similar software would also be welcome. I 
have tried MOLE, CAVER, 3V, Molaxis and HOLLOW, all of which have their 
advantages, but for some cases I still like the output of HOLE.


Many thanks,

Oliver.


Oliver,

Apologies for the disappearance of the HOLE program. I am now working to 
resurrect it (building for linux and OSX). There is a bit of work to do - 
it should be ready by 1st September.


Regards,

Oliver Smart

[ccp4bb] Grade other ligand tools was Re: ccp4 ligand tools..

[Oliver Smart]

...

On 13/06/14 00:19, Ethan A Merritt wrote:


Earlier this year for the first time I got back a validation report 
from the PDB for a deposited structure that included wwPDB validation 
of a ligand. This is great stuff. I approve. I am happy.


Unfortunately the validation check reported problems with my ligand.
This is bad. I am unhappy.

...

On Fri, 13 Jun 2014, Paul Emsley wrote:

In the mean-time you can use the Coot's Mogul plug-in to update the restraint 
information from cprodrg.  Or of course, Just Use Grade (as you imply :-).



Ethan,

As you and Paul mentioned the use of Grade, I thought it might be
useful to point out that as well as being included with
BUSTER (so free for Academics) the Grade Web Server:

 http://grade.globalphasing.org/

This allows you to produce Grade dictionaries (for non-confidential 
ligands) without having to install BUSTER or CSDS (for the Mogul program). 
Grade generates geometrical restraints for novel small molecules. It does 
so by querying the Cambridge Structural Database (CSD) as a main source of 
restraint information (using Mogul), and then invoking quantum chemical 
procedures to obtain whatever information the CSD is unable to supply.
Grade CIF restraint dictionaries can be used in Coot and REFMAC. In 
addition Grade and the Grade Web Server can produce SHELX restraint files.


Mogul provides additional very useful validation measures for dihedrals 
and rings that go beyond the bond and angle results included in the wwPDB 
Structure Validation Report. These can be obtained using Mogul itself or 
using CSDS Mercury but I tend to get a bit lost using these. So we have 
added Mogul analysis to our buster-report tool and use colored 2D diagrams 
to quickly show the information. For details see


http://www.globalphasing.com/buster/wiki/index.cgi?BusterReport

For an example where Mogul validation metrics help to diagnose a
ligand that has been mis-fit see:

http://grade.globalphasing.org/tut/erice_workshop/1pmq_tutorial/

For difficult ligands BUSTER provides the facility to use a weighted
Quantum Chemical or Force Field Energy in place of convential
restraint terms. A recent advance is support for the MMFF94 force field 
using a helper program from OpenEye. This is particularly attractive
as it is the force field used by many computational chemists. For details 
see


http://www.globalphasing.com/buster/wiki/index.cgi?AutobusterLigandQM

If you have concerns about Grade or other dictionaries then using MMFF94
instead provides a really good 2nd opinion.

Hope that ccp4bb will forgive this bit of promotion but Grade can be used 
with CCP4 (and SHELX).


Regards,

Oliver

| Dr Oliver Smart |
| Global Phasing Ltd., Cambridge UK   |
| http://www.globalphasing.com/people/osmart/ |

[ccp4bb] Vitamin B12 (cobalamin) geometry issues

[Oliver Smart]

If you are working on a protein that binds vitamin B12 (cobalamin) then 
you may be interested that there appears to be an issue with geometry of 
the B12 dictionary currently distributed by ccp4. The problem is that atom 
C19 in the corrin ring is defined as being SP2, planar with no hydrogen 
atom attached. Small molecule structures of B12 clearly show this atom is 
tetrahedral (as do high resolution protein complexes). A survey of 53 PDB 
structures containing B12 reveals that 19 have C19 atoms that are not 
sufficiently chiral. All are recent - structures prior to 2008 are all OK. 
The problem also effects the PDB chemical components definition of B12.


Please see

https://www.globalphasing.com/buster/wiki/index.cgi?B12Dictionary

This page provides a dictionary for B12 with the problem fixed.

Hope this proves useful.

Regards,

Oliver


| Dr Oliver Smart |
| Global Phasing Ltd., Cambridge UK   |
| http://www.globalphasing.com/people/osmart/ |

Re: [ccp4bb] mtz2cif capable of handling map coefficients

[Oliver Smart]

On Thu, 5 Apr 2012, Ethan Merritt wrote:


On Thursday, April 05, 2012 09:30:25 am Phil Jeffrey wrote:

Fc doesn't contain the weighting scheme used in the creation of the map
coefficients, so Fc would require some sort of program to be run to
recreate those for both 2Fo-Fc and Fo-Fc maps.


The viewers I am familiar with do this for themselves on the fly.
No need to involve additional programs. In fact, generating and storing
map coefficients is not part of my work flow, since none of the programs
I normally use need them to be pre-calculated.




Ethan,

If you load a mtz file from refmac or BUSTER then this file contains Map 
Coefficients. Different programs and protocols produce different maps. So 
I second Phil's comment that including map coefficients in deposition is a 
really good thing. It will enable people to see exactly the maps as seen 
by the depositor (and to do so in a few years time). Hence we have 
included map coefficients in 3 recent depositions 3syu, 3urp, 3v56 (using 
a prototype mtz2cif tool that is not quite ready for release yet).


We have also worked out how to patch ccp4 cif2mtz so that it can do the 
reverse process see


https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;325e1870.1112


Regards,

Oliver

[ccp4bb] Announcement of a working group for PDBx/mmCIF format adoption

[Oliver Smart]

Announcement of a working group for the adoption of the PDBx/mmCIF format 
for deposition and as an exchange format between programs for 
macromolecular crystallography.


Following a meeting at PDBe Hinxton on 26/27 September 2011 organized by 
the wwPDB it was decided to form a working group for the adoption of the
PDBx/mmCIF format for deposition and as an exchange format between 
programs for macromolecular crystallography.


The old-style PDB format causes an increasingly large number of problems 
particularly for large structures, for structures with complex chemistry, 
and structures determined by methods other than X-ray crystallography. 
Rather than designing an entirely new PDB format it was decided to 
actively switch to the PDBx/mmCIF format, particularly for deposition. The 
facilitation of capturing more information in deposition and archiving 
should be part of this process. Our aim is to enable the direct use of 
PDBx/mmCIF format files in the major macromolecular crystallographic 
software tools.


The working group holds a teleconference about every six weeks. Current 
participants are:


Paul Adams, LBL (Phenix)
Pavel Afonine, LBL (Phenix)
Helen Berman, RCSB
Paul Emsley, Oxford University (Coot)
Rasmus Fogh, Cambridge University (CCPN)
Richard Gildea, LBL (Phenix)
Ralf Grosse-Kunstleve, LBL (Phenix)
Gerard Kleywegt, PDBe
Eugene Krissinel, STFC (CCP4)
Garib Murshudov, LMB-MRC (REFMAC)
Tom Oldfield, PDBe
Sameer Velankar, PDBe
John Westbrook, RCSB
Thomas Womack, Global Phasing (BUSTER)

Oliver Smart, Global Phasing (BUSTER) - Working Group Chair

Please contact me for any further details.

Regards,
Oliver
| Dr Oliver Smart |
| Global Phasing Ltd., Cambridge UK   |
| http://www.globalphasing.com/people/osmart/ |

Re: [ccp4bb] Announcing a Web Server for the Grade ligand restraints generator.

[Oliver Smart]

On Tue, 20 Mar 2012, George Sheldrick wrote:


Dear Gerard,

That will be an extremely useful facility. Is a 'regrading' of the monomer 
library planned, at least for common cofactors and crystallization additives?


Best wishes, George



George,

Gerard asked me to reply. Yes providing pre-calculated grade results for 
all existing PDB chemical components is something we need to do.


The Grade Web Server is work in progress: there are a number of 
limitations that need to be tackled:


http://www.globalphasing.com/buster/wiki/index.cgi?GradeWebServer#restrictions

But we hope that people find grade restraint dictionary useful.

Many thanks

Oliver

| Dr Oliver Smart |
| Global Phasing Ltd., Cambridge UK   |
| http://www.globalphasing.com/people/osmart/ |

Re: [ccp4bb] unusual bond lengths in PRODRG cif file (Grade Web Server)

[Oliver Smart]

On Tue, 10 Jan 2012, Stephen Graham wrote:


On 10 January 2012 09:50, John Liebeschuetz j...@ccdc.cam.ac.uk wrote:
...available to anyone who has access to the Cambridge Structural
Database System

How many academic labs will bother / can afford to buy a CCSD license
just to check the geometry of small molecule ligands, especially when
they need to do so them only once every blue moon?

The ability for the PDB to check a ligand against the CCSD upon
deposition would be great.  The ability to generate the restraint
definition for free via the web before deposition is better: that's
why people use PRODRG!

Stephen



Stephen,

We had anticipated your request and got permission from the CCDC to 
provide a public Web server that would include the use of MOGUL in its 
invocation of Grade. The Grade Web Server has been publicly launched 
today, so for ligand restraint definitions that are (partly) based 
on CSD small molecule structures try using:


http://grade.globalphasing.org

Regards,

Oliver


| Dr Oliver Smart |
| Global Phasing Ltd., Cambridge UK   |
| http://www.globalphasing.com/people/osmart/ |

Re: [ccp4bb] unusual bond lengths in PRODRG cif file

[Oliver Smart]

On Mon, 9 Jan 2012, Soisson, Stephen M wrote:

I will second Ian's recommendation for GRADE from the Global Phasing 
group.  GRADE overcomes nearly all of the shortcomings we have 
encountered with other approaches for ligand dictionary generation.




Steve,

Thanks to you and to Ian Tickle for the positive comments about grade. We 
have just launched the Grade Web Server so it should be now be much easier 
for academic and occasional users to generate ligand restraints with it.


http://grade.globalphasing.org

Regards,

Oliver


| Dr Oliver Smart |
| Global Phasing Ltd., Cambridge UK   |
| http://www.globalphasing.com/people/osmart/ |

Re: [ccp4bb] unusual bond lengths in PRODRG cif file (Another possibility - direct use of QM)

[Oliver Smart]

On Mon, 9 Jan 2012, krish wrote:



You can use Phenix.elbow or phenix.reel to load the coordinates of the 
small moleucle and optimize with AM1 (semi-empirical), then you should 
get reasonable geometirc parameters suc as bond length, bond angles and 
etc.  



Hope this helps !
 
Cheers,
Krishna
 
Krishna Chinthalapudi, PhD
Hannover Medical School


Shveta and Krishna,

Just to point out that an alternative to using QM methods as a source of 
ligand restraints for refinement is to directly use the methods to 
represent the ligand chemistry during refinement. BUSTER provides the 
facility to do this see:


http://www.globalphasing.com/buster/wiki/index.cgi?AutobusterLigandQMIntroduction

It is pretty easy to do, particularly for semi-empirical QM methods (such 
as AM1 or the superior RM1). An advantage is that instead of coming up 
with approximate restraints sourced from AM1 then the actual method itself 
is used.



Regards,

Oliver 
| Dr Oliver Smart |

| Global Phasing Ltd., Cambridge UK   |
| http://www.globalphasing.com/people/osmart/ |

Re: [ccp4bb] reliable/unreliable maps? (Deposition of map coefficients)

[Oliver Smart]

Including the final map coefficients as part of the structure factor file
deposited and then archived by the PDB provides a means to directly
see the actual map as interpreted by the crystallographer. EDS is useful 
in providing a third party view but the actual map is really better.


We think map deposition is a good idea and are working on tools to make it 
easy to do with BUSTER. There are already a few recent (REFMAC) 
depositions with map coefficients in the pdb (for instance 3u57). 
Displaying the maps is currently a bit difficult, see ccp4bb

message (Wed, 21 Dec 2011):

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;325e1870.1112

Cheers,

Oliver

| Dr Oliver Smart |
| Global Phasing Ltd., Cambridge UK   |
| http://www.globalphasing.com/people/osmart/ |

On Tue, 10 Jan 2012, Robbie Joosten wrote:


Hi Frank,

EDS already does that. Even so, reproducing the R-factor does not prove that
the map is reliable. See for instance 3frk for which the deposited dataset
is much smaller and less complete than the one used for refinement. The map
from EDS is therefore completely model biased.
I only recently started looking for this problem of lower-than-reported
completeness with. I have not found a lot of cases, but already too many.
Fortunately, at least a few depositors deposited the rest of the dataset
after I sent a bug report to the PDB (e.g. 3mbs).

Cheers,
Robbie


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Frank von Delft
Sent: Tuesday, January 10, 2012 16:23
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] reliable/unreliable maps?

Or just print both Rfactors...?


On 10/01/2012 15:21, Luca Pellegrini wrote:

Hi Paul,



What would you rather it say, I'm happy to change the message. The EDS

does not think that this is a reliable map, in that it is or may be

inconsistent

with what the authors were looking at during deposition?

How about Warning: the R-factor calculated for this map differs

significantly from the published R-factor?


Then we can discuss what is significant ;-)

Luca

Luca Pellegrini
Department of Biochemistry
University of Cambridge
80 Tennis Court Road
Cambridge CB2 1GA - UK

Email: lp...@cam.ac.uk
Tel: 0044-1223-760469
Fax: 0044-1223-766002
Sanger building, room 3.59

[ccp4bb] How to patch CCP4 cif2mtz so it can handle PDB entries with Map Coefficients

[Oliver Smart]

Some recently released PDB entries (for instance 3u57) have structure 
factor files that contain map coefficients. We think this is a really good 
idea because it means that final maps as interpreted by the 
crystallographer will then be archived and available.


But there is a problem converting such files to mtz with the current 
cif2mtz program; indeed we raised this on the bb in September:

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;6be4044e.1109

To get around this we produced a quick-fix patch for cif2mtz that is 
available at:


http://www.globalphasing.com/buster/wiki/index.cgi?CCP4cif2mtzPatchToHandleMapCoefficients


Regards,

Oliver

| Dr Oliver Smart |
| Global Phasing Ltd., Cambridge UK   |
| http://www.globalphasing.com/people/osmart/ |