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On 9/29/2021 12:24 PM, James Holton wrote:
Greetings all,
This year I have the honor of co-organizing the ALS Colloquium Seminar
series. This is normally a
Dear all,
I downloaded the latest mac version of CCP4 suite for installation on a new
Mac (macOS Big Sur Version 11.5.2). The package was downloaded using
Chrome. After unpacking and moving the folder to its destination
/Applications/ccp4-7.1, the set up using
./BINARY.setup
gives error
Greetings all,
This year I have the honor of co-organizing the ALS Colloquium Seminar
series. This is normally a local but broad-audience forum for users of
the Advanced Light Source to learn more about what other users are
doing. But, now that its gone virtual you can all join in and listen
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
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?
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:
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
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
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
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
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?)
Hi all,
We have an exciting new position for a software developer to participate in
the development of the new feature for serial crystallography experiments
in the MXCuBE3. MXCuBE is the experiment control software to perform data
collection and control the MX beamlines and it is part of a large
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