Re: [ccp4bb] H atoms in refined structure

2022-05-19 Thread Rob Nicholls - MRC LMB 
Hi Luca,

You should find that the hydrogens in the mmCIF file output by Refmac are 
flagged as riding hydrogens, not as an explicit part of the model. This 
behaviour is as intended, and should not pose a problem for deposition. They 
are not in the output PDB file because there is no way to flag hydrogens as 
riding (as opposed to refined parameters) in PDB format, so you'll only see the 
riding hydrogens in the mmCIF file.

Best regards,
Rob



> On 19 May 2022, at 11:38, Christian Roth  wrote:
> 
> Hi, 
> just to clarify one point on the GUI. You can click or unclick the option 
> "use hydrogens during refinement" on the first tab in i2 GUI in the options 
> field. As indicated it used it only during refinement and does not put it 
> into the output pdb. In the output tab you can choose what should happen with 
> the output of hydrogens, e.g. in file, not in file or default. The default 
> should be actually no, but changing it explicitly to no should do the trick, 
> otherwise there is a bug.
> 
> Best
> Christian
> 
> On Tue, May 17, 2022 at 9:59 AM Luca Mazzei  > wrote:
> Hello,
> 
> just to clarify, I do not use H atoms for refinement, but as idealised riding 
> H atoms. In the old-style GI of Refmac one could use riding hydrogens during 
> refinement without adding them in the output coordinate file. I do not find 
> this option in the new GI of the CCP4i2 window. As a result from a a REFMAC 
> job, the ouput PDB file does not contain H atoms, while the mmcif output file 
> does. At the end of the story, I ran pdbx/mmcif to convert the PDB in a mmcif 
> file that does not contain H atoms anymore. It seems to work.
> 
> Best regards
> 
> Luca Mazzei
> 
> 
> Luca Mazzei - PhD
> Laboratory of Bioinorganic Chemistry
> Department of Pharmacy and Biotechnology (FaBiT)
> Alma Mater Studiorum - University of Bologna
> Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy
> Tel: +39 0512096235
> 
> 
> 
> 
>> Il giorno 16 mag 2022, alle ore 15:43, Luca Mazzei > > ha scritto:
>> 
>> Dear CCP4 people,
>> 
>> Refining a 1.7 Angstroem structure with REFMAC (CCP4i2) using hydrogens 
>> during refinements by generating riding hydrogens I obtain a PDB file that 
>> does not contain H atoms. However, the corresponding mmcif file that I 
>> should use for deposition contains their coordinates and give them either 
>> full or zero occupancy. Do you know how I can safely delete H atoms from the 
>> mmcif file prior deposition? Would this affect Rwork and Rfree calculated 
>> upon validation on the wwPDB?
>> 
>> Thanks in advance,
>> 
>> Luca Mazzei
>> 
>> 
>> Luca Mazzei - PhD
>> Laboratory of Bioinorganic Chemistry
>> Department of Pharmacy and Biotechnology (FaBiT)
>> Alma Mater Studiorum - University of Bologna
>> Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy
>> Tel: +39 0512096235
>> 
>> 
>> 
>> 
> 
> 
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Re: [ccp4bb] Double covalent ligand

2021-09-16 Thread Rob Nicholls - MRC LMB 
Dear Rens,

CCP4i2 now contains a CIF dictionary accumulator, which should help with 
handling such problems (note it's also available as standalone to be used via 
command line if that's useful). This is used automatically when providing 
multiple ligand CIF dictionaries to the Refinement interface. You might want to 
check out this article, which gives an overview of the various options for 
dealing with covalent linkages within the CCP4 suite, along with advice and 
discussion to help you decide which solution is best in your case: 
https://scripts.iucr.org/cgi-bin/paper?ir5021

Regards,
Rob



> On 16 Sep 2021, at 15:53, Vries, Rens de  wrote:
> 
> Dear all,
> 
> I was wondering if there was a good way to generate a restraint file for 
> ligands that are covalently bound to two sites of the same protein. Just to 
> clarify, the ligand can be viewed as a "bridge" between two residues of the 
> same protein monomer. 
> 
> At present, I use JLigand to prepare the separate links (so two separate 
> files). However, you can't combine both CIF files without software running 
> into errors. If I use either the ligand CIF (without links) or the CIF of the 
> singly covalent version, the refinement will still work fine, because the 
> LINK in the PDB file is present. But I'm wondering if there is no better way 
> to do this.
> 
> Thanks in advance,
> 
> Rens
> 
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Re: [ccp4bb] help needed with link description

2021-06-03 Thread Rob Nicholls - MRC LMB 
Dear Gerlind,

I'm glad that we were of help! I should point out that the "Make link (click 2 
atoms)" is dangerous as it only generates a LINK record but not a full link 
dictionary - it should only be used for common known links that are present in 
the monomer library. This issue is discussed in section 4.4 of the article I 
posted earlier 
(https://journals.iucr.org/d/issues/2021/06/00/ir5021/index.html). I'd ignore 
Coot's "Make link" tool unless you really know what you're doing. Otherwise, 
I'd favour the AceDRG interfaces as recommended in that article.

Regards,
Rob


> On 3 Jun 2021, at 20:13, Gerlind Sulzenbacher 
>  wrote:
> 
> Dear David and Rob,
> 
> thanks a lot for your help and your suggestions.
> Following your suggestions I found in Coot the very neat solution "Make link 
> (click 2 atoms ...): Much better than my previous dinosaur approach.
> Thanks again and all the best,
> Gerlind
> 
> 
> On 03/06/2021 20:17, David Briggs wrote:
>> Hi Gerlind,
>> 
>> Rob Nicholls gave a talk on how to deal with covalent linkages using AceDrg 
>> at CCP4 study weekend in 2020.
>> 
>> https://youtu.be/p4oTJ0bjD3M 
>> 
>> And Paul Emsley has written up a guide about it...
>> 
>> https://pemsley.github.io/coot/blog/2020/06/30/make-a-link.html 
>>  
>> 
>> Hopefully these will be useful for you.
>> 
>> Good luck,
>> 
>> Dave
>> 
>> --
>> Dr David C. Briggs
>> Senior Laboratory Research Scientist
>> Signalling and Structural Biology Lab
>> The Francis Crick Institute
>> London, UK
>> ==
>> about.me/david_briggs
>> 
>> From: CCP4 bulletin board  
>>  on behalf of Gerlind Sulzenbacher 
>>  
>> Sent: Thursday, June 3, 2021 7:10:12 PM
>> To: CCP4BB@JISCMAIL.AC.UK  
>>  
>> Subject: [ccp4bb] help needed with link description
>>  
>> 
>> External Sender: Use caution.
>> 
>> 
>> Dear all,
>> 
>> I am going litteraly mad (or just old).
>> 
>> I would like to make a covalent link between a carbohydrate moiety and
>> and ASP of my well-cheered protein.
>> 
>> The identifier for the carbohydrate moiety is MAD, chain C, res number 1.
>> 
>> The link is established between C5 of MAD and OD2 of ASP 518, chain A.
>> 
>> In the mad_monlib.cif I added the following:
>> 
>> data_link_list
>> loop_
>> _chem_link.id
>> _chem_link.comp_id_1
>> _chem_link.mod_id_1
>> _chem_link.group_comp_1
>> _chem_link.comp_id_2
>> _chem_link.mod_id_2
>> _chem_link.group_comp_2
>> _chem_link.name
>> ASP-MAD  ASP  ..MAD  ..
>>   bond_ASP-OD2_=_MAD-C5
>> #
>> data_link_ASP-MAD
>> #
>> loop_
>> _chem_link_bond.link_id
>> _chem_link_bond.atom_1_comp_id
>> _chem_link_bond.atom_id_1
>> _chem_link_bond.atom_2_comp_id
>> _chem_link_bond.atom_id_2
>> _chem_link_bond.type
>> _chem_link_bond.value_dist
>> _chem_link_bond.value_dist_esd
>>   ASP-MAD  1 OD2 2 C5.   1.3700.040
>> 
>> In the entry PDB file I added the line:
>> 
>> LINKOD2  ASP A 518C5  MAD C 1
>> 
>> The log file of REFMAC tells me
>> 
>> INFO: link is found (not be used) dist=   1.370 ideal_dist= 1.370
>>  ch:AAA  res: 518  ASP  at:OD2 .->ch:CCC  res:
>> 1  MAD  at:C5  .
>> 
>> And the expression "not be used" is certainly the case, as the distance
>> of the covalent bond changes from 1.37 to 1.6 Å.
>> 
>> The data resolution is 1.8 Å.
>> 
>> If somebody could please point out what I am doing wrong, I'd be very
>> grateful.
>> 
>> With best wishes,
>> 
>> Gerlind
>> 
>> 
>> --
>> Gerlind Sulzenbacher
>> Architecture et Fonction des Macromolécules Biologiques
>> UMR7257 CNRS, Aix-Marseille Université
>> Case 932
>> 163 Avenue de Luminy
>> 13288 Marseille cedex 9
>> France
>> Tel +33 491 82 55 66
>> Fax +33 491 26 67 20
>> E-mail: gerlind.sulzenbac...@univ-amu.fr 
>> 
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1data=04%7C01%7C%7C360c620f3de94e6ef46808d926badcf6%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637583406295071625%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=C80B0ezyZ5AAWTgXEeVuLEfSw1QljocDI3Kzz6L9vxU%3Dreserved=0
>>  
>>

Re: [ccp4bb] help needed with link description

2021-06-03 Thread Rob Nicholls - MRC LMB 
Dear Gerlind,

Where did you get your mad_monlib.cif file? It shouldn't be neccesary for you 
to be manually modifying such restraint dictionaries (any more). You can 
generate these using AceDRG, either via CCP4i2 or Coot.

Shameless plug:
https://journals.iucr.org/d/issues/2021/06/00/ir5021/index.html
https://journals.iucr.org/d/issues/2021/06/00/ir5022/index.html

Regards,
Rob






Dr Rob Nicholls
Senior Investigator Scientist
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge CB2 0QH



> On 3 Jun 2021, at 19:10, Gerlind Sulzenbacher 
>  wrote:
> 
> Dear all,
> 
> I am going litteraly mad (or just old).
> 
> I would like to make a covalent link between a carbohydrate moiety and and 
> ASP of my well-cheered protein.
> 
> The identifier for the carbohydrate moiety is MAD, chain C, res number 1.
> 
> The link is established between C5 of MAD and OD2 of ASP 518, chain A.
> 
> In the mad_monlib.cif I added the following:
> 
> data_link_list
> loop_
> _chem_link.id
> _chem_link.comp_id_1
> _chem_link.mod_id_1
> _chem_link.group_comp_1
> _chem_link.comp_id_2
> _chem_link.mod_id_2
> _chem_link.group_comp_2
> _chem_link.name
> ASP-MAD  ASP  ..MAD  ..
>  bond_ASP-OD2_=_MAD-C5
> #
> data_link_ASP-MAD
> #
> loop_
> _chem_link_bond.link_id
> _chem_link_bond.atom_1_comp_id
> _chem_link_bond.atom_id_1
> _chem_link_bond.atom_2_comp_id
> _chem_link_bond.atom_id_2
> _chem_link_bond.type
> _chem_link_bond.value_dist
> _chem_link_bond.value_dist_esd
>  ASP-MAD  1 OD2 2 C5.   1.3700.040
> 
> In the entry PDB file I added the line:
> 
> LINKOD2  ASP A 518C5  MAD C 1
> 
> The log file of REFMAC tells me
> 
> INFO: link is found (not be used) dist=   1.370 ideal_dist= 1.370
> ch:AAA  res: 518  ASP  at:OD2 .->ch:CCC  res:   1  
> MAD  at:C5  .
> 
> And the expression "not be used" is certainly the case, as the distance of 
> the covalent bond changes from 1.37 to 1.6 Å.
> 
> The data resolution is 1.8 Å.
> 
> If somebody could please point out what I am doing wrong, I'd be very 
> grateful.
> 
> With best wishes,
> 
> Gerlind
> 
> 
> -- 
> Gerlind Sulzenbacher
> Architecture et Fonction des Macromolécules Biologiques
> UMR7257 CNRS, Aix-Marseille Université
> Case 932
> 163 Avenue de Luminy
> 13288 Marseille cedex 9
> France
> Tel +33 491 82 55 66
> Fax +33 491 26 67 20
> E-mail: gerlind.sulzenbac...@univ-amu.fr
> 
> 
> 
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