Re: [ccp4bb] Correcting 3-letter codes based on protonation states in a PDB file

[Briggs, David C]

I believe the ProPka or Pdb2pqr webservers can do this.

ProPka.org

http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/

HTH,

Dave

--
Dr David C Briggs
Hohenester Lab
Department of Life Sciences
Imperial College London
UK
http://about.me/david_briggs


From: CCP4 bulletin board  on behalf of Sampson, Jared 

Sent: Wednesday, June 28, 2017 11:34:05 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Correcting 3-letter codes based on protonation states in a 
PDB file

Dear all -

I'm working with a PDB file with explicit hydrogens where many of the 
histidines are in protonated form due to crystallization at low pH.  
Unfortunately, although the additional protons are present in the model for the 
positively charged histidines, the residues in question are indicated in both 
the SEQRES and the ATOM records as 3-letter code `HIS` regardless of 
protonation state (i.e. instead of `HIP` for positively charged, and `HID` or 
`HIE` for the neutral tautomers).

Are there existing tools available to determine the proper 3-letter residue 
code for titratable amino acid residues based on which hydrogens are present, 
and output a corrected PDB file?

Thank you in advance for your suggestions.

Cheers,

Jared Sampson
Ph.D. Candidate
Columbia University

[ccp4bb] Correcting 3-letter codes based on protonation states in a PDB file

[Sampson, Jared]

Dear all - 

I'm working with a PDB file with explicit hydrogens where many of the 
histidines are in protonated form due to crystallization at low pH.  
Unfortunately, although the additional protons are present in the model for the 
positively charged histidines, the residues in question are indicated in both 
the SEQRES and the ATOM records as 3-letter code `HIS` regardless of 
protonation state (i.e. instead of `HIP` for positively charged, and `HID` or 
`HIE` for the neutral tautomers).  

Are there existing tools available to determine the proper 3-letter residue 
code for titratable amino acid residues based on which hydrogens are present, 
and output a corrected PDB file?

Thank you in advance for your suggestions.

Cheers,

Jared Sampson
Ph.D. Candidate
Columbia University

[ccp4bb] Job Opportunities on the DL_POLY project theme "Beyond Classical Molecular Dynamics"

[Ilian Todorov]

Hello,

Two EPSRC postdoctoral research positions, one at the University of Bristol 
(UK) and one at STFC Daresbury Laboratory (UK), are available funded by the 
EPSRC Software Infrastructure grant DL_POLY_4: Beyond Classical Molecular 
Dynamics.  This project is a collaboration between the School of Chemistry at 
Bristol and STFC Daresbury Laboratory, working also with a number of 
stakeholders around the country who are major users of the DL_POLY molecular 
dynamics package.

We look for Computational Scientists with a strong background in Materials and 
Mathematics sciences (at a PhD level) complemented by excellent research 
software engineer skills with experience in algorithmic and methodology 
development in the Physics and Chemistry domains.  The two positions and 
associated development opportunities are:

Position 1 @Bristol: To develop Density Functional Tight Binding (DFTB) in 
DL_POLY_4 (the CCP5 flagship code for classical molecular dynamics, written in 
Fortran).  The post-holder will design and implement DFTB functionality, 
including energies, forces, and excited states.  The project offers a 30 month 
post-doctoral position based at the University of Bristol under the supervision 
of Profs. Neil Allan and Fred Manby.  For further information and applications 
(only accepted on-line) - follow the link 
http://www.bristol.ac.uk/jobs/find/details.html?nPostingId=6196&nPostingTargetId=23569&id=Q50FK026203F3VBQBV7V77V83&LG=UK&mask=uobext
 .

Position 2 @STFC: To develop forward flux sampling (FFS) methodology in the 
framework of DL_POLY_4 (the CCP5 flagship code for classical molecular 
dynamics, written in Fortran).  The post-holder will design and implement FFS 
functionality, including testing and verifying the functionality in studies of 
rare events.  The project offers a 30 month post-doctoral position based at 
STFC Daresbury Laboratory under the supervision of Drs. Ilian Todorov and Alin 
Elena.  For further information and applications (only accepted on-line) follow 
the link - http://www.topcareer.jobs/Vacancy/irc241494_7253.aspx .

Both positions will deliver outputs required from this Flagship Software 
Infrastructure project, developing research papers research papers, training 
material, workshops, talks, tests, examples and documentation that will ensure 
that the software will be well-known, sustainable, and readily available to the 
wide modelling community.  The post holders will help develop and deliver 
training workshops both in the UK and worldwide, and will work with the project 
team and users around the UK to ensure that the developed software is robust, 
trustable and correct, reproducible and performance portable.

Essential: Knowledge of modern Fortran, python, experience with distributed 
linear algebra libraries, knowledge of statistical physics, knowledge of 
electronic structure methods, experience as a researcher or of working closely 
with researchers and contributing to research through software development, 
previous experience of software development best practice, and of contributing 
to collaborative software projects, or delivering software used by other people.

Highly desirable: Previous experience of computational chemistry/physics 
algorithms eg DFTB, experience of developing/enhancing models for 
particle-based simulation methods, experience of developing and applying 
sampling techniques, working knowledge of non-equilibrium MD techniques, 
experience of teaching or mentoring researchers and/or scientific software 
developers, experience of analysing, researching and solving complex 
programming problems, knowledge of parallel programming, working knowledge of 
MPI.

Regards,

Ilian Todorov

[ccp4bb] CCP4 series 7.0 update 042

[Charles Ballard]

Dear All 

updates 042 has been release.  This contains

DIALS 1.6.0 (2017-06-02):
• dials/xia2: dynamic masking of diamond anvil cells for DLS I19-2 high 
pressure experiments
• JMP improvements to mosaic spread estimate (#342, #119)
xia2 0.5.319:
• xia2: new xia2.html
• xia2 fixed for I23 data with distance != 0; xia2/xia2#124 & friends

DIALS 1.6.1 includes xia2 0.5.325 (2017-06-14):
• dials.image_viewer: respect kernel_size parameter (#354)
• Rayonix TIFF format fixes (#370)
• xia2: XDS compatibility fixes (xia2/xia2#131)
• xia2: Trap non-fatal fatal error (xia2/xia2#115)
• xia2: respect batch_range parameter in resolution determination
• xia2: silence xtriage output

DIALS 1.6.2 includes xia2 0.5.328 (2017-06-20):
• cctbx algorithmic stability fixes (cctbx/cctbx_project#43)
• dials.export_mtz: improved error messages (#357)
• xia2: Generate .p4p files in small molecule mode (xia2/xia2#134)

plus associated changes to ccp4i2.

All the best

CCP4 Core team and DIALS developers.