Re: [ccp4bb] Add hydrogens

[Sam Tang]

Have just tried out some of the options -- done within minutes! Many thanks
for the numerous input!

All the best

Sam


On Wed, 29 Sept 2021 at 19:03, Sam Tang  wrote:

> Dear community
>
> 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. It happens that I cannot locate the
> map coefficients under the entry (am I missing something?) So... is there
> an easy way to do what I want in this case?
>
> Warm regards
>
> Sam
>



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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] [External] [ccp4bb] Add hydrogens

[Srivastava, Dhiraj]

Even pymol and chimera can add hydrogen. Sorry I understand it’s ccp4bb forum 
and i am talking about chimera and pymol.
Depending on you need, you can do energy minimization in chimera as well.

Dhiraj


From: CCP4 bulletin board  on behalf of Sam Tang 

Sent: Wednesday, September 29, 2021 6:03 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [External] [ccp4bb] Add hydrogens

Dear community

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. It happens that I cannot locate the map coefficients 
under the entry (am I missing something?) So... is there an easy way to do what 
I want in this case?

Warm regards

Sam



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Re: [ccp4bb] Add hydrogens

[Tim Gruene]

Dear Sam,

refmac5 has the option of 'geometry optimisation', which doesn't
require data. I would assume that you can ask refmac5 to write out the
hydrogen atoms for the resulting PDB file.

Best regards,
Tim

On Wed, 29 Sep 2021 19:03:47 +0800 Sam Tang 
wrote:

> Dear community
> 
> 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. It happens that
> I cannot locate the map coefficients under the entry (am I missing
> something?) So... is there an easy way to do what I want in this case?
> 
> Warm regards
> 
> Sam
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
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-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

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pgpKgCsmgnogX.pgp
Description: OpenPGP digital signature

Re: [ccp4bb] Add hydrogens

[Marcin Wojdyr]

Dear Sam,

if you want to add hydrogens on "riding" positions in the same way that
Refmac adds them, here is a command that aims to do exactly the same thing:

gemmi h 1cdw.pdb output.pdb

Otherwise, a program called reduce from MolProbity (distributed with both
Phenix and CCP4) is probably the most popular one for adding hydrogens. I
don't know if there are any newer and better programs than reduce as of
today.

Best,
Marcin


On Wed, 29 Sept 2021 at 13:04, Sam Tang  wrote:

> Dear community
>
> 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. It happens that I cannot locate the
> map coefficients under the entry (am I missing something?) So... is there
> an easy way to do what I want in this case?
>
> Warm regards
>
> Sam
>
> --
>
> 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] Add hydrogens

[Wim Burmeister]

Hello, there is for exemple the "addh" command in chimerax to add hydrogens to 
a structure. Wim 


De: "Mark J. van Raaij"  
À: "CCP4BB"  
Envoyé: Mercredi 29 Septembre 2021 13:11:24 
Objet: Re: [ccp4bb] Add hydrogens 

Dear Sam, 

1CDW is from 1996, when it was not obligatory (or common practice) to upload 
structure factors to the PDB. 
So I think you can't do any refinement, just perhaps some optimisation. 

Mark J van Raaij 
Dpto de Estructura de Macromoleculas, lab 20B 
Centro Nacional de Biotecnologia - CSIC 
calle Darwin 3 
E-28049 Madrid, Spain 
tel. +34 91 585 4616 (internal 432092) 
Section Editor Acta Crystallographica F 
[ https://journals.iucr.org/f/ | https://journals.iucr.org/f/ ] 




On 29 Sep 2021, at 13:03, Sam Tang < [ mailto:samtys0...@gmail.com | 
samtys0...@gmail.com ] > wrote: 

Dear community 

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. It happens that I cannot locate the map coefficients 
under the entry (am I missing something?) So... is there an easy way to do what 
I want in this case? 

Warm regards 

Sam 




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 | website ] 

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Re: [ccp4bb] Add hydrogens

[Mark J. van Raaij]

Dear Sam,

1CDW is from 1996, when it was not obligatory (or common practice) to upload 
structure factors to the PDB.
So I think you can't do any refinement, just perhaps some optimisation.

Mark J van Raaij
Dpto de Estructura de Macromoleculas, lab 20B
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. +34 91 585 4616 (internal 432092)
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/

> On 29 Sep 2021, at 13:03, Sam Tang  wrote:
> 
> Dear community
> 
> 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. It happens that I cannot locate the map 
> coefficients under the entry (am I missing something?) So... is there an easy 
> way to do what I want in this case?
> 
> Warm regards
> 
> Sam
> 
> 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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[ccp4bb] Add hydrogens

[Sam Tang]

Dear community

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. It happens that I cannot locate the
map coefficients under the entry (am I missing something?) So... is there
an easy way to do what I want in this case?

Warm regards

Sam



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