Re: [ccp4bb] H atoms in refined structure

[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] H atoms in refined structure

[Christian Roth]

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
>
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] H atoms in refined structure

[Luca Mazzei]

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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[ccp4bb] H atoms in refined structure

[Luca Mazzei]

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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