Re: [ccp4bb] C-terminal amide

[Bernhard Lechtenberg]

HI Abhisek,

I had the same problem a few years back. Here is the solution I came up with 
thanks to help from the CCP4bb:

1) Add pointer atom in Coot NH2 and create link to C-terminal residue (Coot: 
Extensions -> Modeling -> Make link)
2) create cif file with correct link description (see below)
3) modify LINK record in PDB file to correct residues/ link name (TYR-NH2 if 
you use the file below with modifications for your case)
4) refine in Refmac with cif as LIB in

Augie Pioszak sent me the cif file copied below. you will have to change PHE to 
TYR for your particular case.

Hope that helps.

Best,
Bernhard

---

Bernhard,
You need a link record in the pdb file to link the NH2 amino group to your last 
peptide residue.  When I did this a few years back I had to include a .cif 
library file describing the link for use with Refmac.  See pdb entry 3c4m and 
below for the lib description I used.  I still use O, so not sure how coot 
handles it, but I would guess it will recognize the NH2 group just fine.  Hope 
this helps.
Regards,
Augie Pioszak

# ---   LIST OF LINKS ---
#
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
PHE-NH2  PHE  ..NH2  ..
bond_PHE-C_=_NH2-N
# --
#
# --- DESCRIPTION OF LINKS ---
#
data_link_PHE-NH2
#
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
PHE-NH2  1 C   2 N single  1.3290.020
loop_
_chem_link_angle.link_id
_chem_link_angle.atom_1_comp_id
_chem_link_angle.atom_id_1
_chem_link_angle.atom_2_comp_id
_chem_link_angle.atom_id_2
_chem_link_angle.atom_3_comp_id
_chem_link_angle.atom_id_3
_chem_link_angle.value_angle
_chem_link_angle.value_angle_esd
PHE-NH2  1 O   1 C   2 N   122.0001.600
PHE-NH2  1 CA  1 C   2 N   118.2002.000
loop_
_chem_link_plane.link_id
_chem_link_plane.plane_id
_chem_link_plane.atom_comp_id
_chem_link_plane.atom_id
_chem_link_plane.dist_esd
PHE-NH2plane11 CA0.020
PHE-NH2plane11 C 0.020
PHE-NH2plane11 O 0.020
PHE-NH2plane12 N 0.020
# --

-
> On Oct 12, 2017, at 2:53 PM, Abhishek Anan  wrote:
> 
> Dear all,
> 
> I am trying to solve the structure of a peptide with C-terminal amide. In 
> order to add the amide group to the c-terminal TYR, I substituted TYR with 
> TYC (tyrosinamide) and created a link between the preceding GLY and TYC. When 
> refined in refmac, the pdb inserts a TER card between GLY and TYC and no 
> covalent bond is created between them. How do I fix this? I have also tried 
> to add NH2 pointer atom to TYR in coot and create a link between them but in 
> vain. I also imported the NH2.cif file into coot and tried to make a link but 
> of no use. I also tried to import NH2.cif into Jligand so I could get a link 
> record but it refuses to open the NH2.cif file. 
> 
> I would greatly appreciate any help!
> 
> Best regards,
> Abhishek

[ccp4bb] C-terminal amide

[Abhishek Anan]

Dear all,

I am trying to solve the structure of a peptide with C-terminal amide. In
order to add the amide group to the c-terminal TYR, I substituted TYR with
TYC (tyrosinamide) and created a link between the preceding GLY and TYC.
When refined in refmac, the pdb inserts a TER card between GLY and TYC and
no covalent bond is created between them. How do I fix this? I have also
tried to add NH2 pointer atom to TYR in coot and create a link between them
but in vain. I also imported the NH2.cif file into coot and tried to make a
link but of no use. I also tried to import NH2.cif into Jligand so I could
get a link record but it refuses to open the NH2.cif file.

I would greatly appreciate any help!

Best regards,
Abhishek

Re: [ccp4bb] CCP4 series 7.0 update 045

[Andrey Lebedev]

Dear CCP4 users

There were two mistakes in my previous e-mail announcing the update 7.0.045:
- an incorrect list of platforms for which the new version of shelxe
is provided and
- an out-of-date reference to SHELX web-site.

The correct statement is as follows:

shelxe (Mac OS X, Linux 64 bits, Windows 32 and 64 bits)
• update to 2017_1
• improved chain tracing at lower than 2A resolution
• further details at http://shelx.uni-goettingen.de/changes.php

Best wishes
Andrey

On 4 October 2017 at 22:16, Andrey Lebedev  wrote:
> Dear All
>
>
> updates 045 has been release.  This contains
>
>
> shelxe (Mac, Linux 64 bit)
> • update to 2017_1
> • improved chain tracing at lower than 2A resolution
> • further details at http://shelx.uni-ac.gwdg.de/SHELX/changes.php
>
> coot (Mac, Linux)
> • correctsions to some typos
>
> molrep
> • fix for bug in map read
>
> sfcheck
> • removed bug in reading ccp4 map
>
> pointless
> • 1.11.4 increase number of images from Scalepack file
>
> lorestr
> • fixed CCP4i2 compatibility issue with -p2 file names
>
> ctruncate
> • bug fixes, protect 0 value diagonal elements in hessian
>
> hklfile
> • bug fixes
>
> acedrg
> • bug fixes
>
> ccp4i2
> • new nautilus interface
> • lorestr: fixed difference map import
> • crank2: fixes for specific space groups
> • arpwarp: added output xyz with dummy atoms removed
> • added task interface for morda-mp
>
> ccp4i
> • jsrview set as the default viewer for crank2
> • fixed termination of subprocesses
>
> morda-mp (Mac, Linux)
> • released python wrapper and i1 interface
>
> crank2
> • disabling ccp4i jsrview pop-up
> • prasa fine-tuning
> • fixes for specific space groups
> • fixed flip-mem variant of charge flipping
>
>
> All the best
>
> CCP4 Core team

Re: [ccp4bb] ccp4 website not secure

[Ville Uski]

Dear all

yes, the cert should be valid, but let me know if some of you continue
having problems with it. I had an error last week on Android, complaining
about unknown certificate authority, but this error went away for some
reason, possibly thanks to a system update.

As Michael said, https is only enforced on ccp4online so that the user
credentials not be passed unencrypted. On www.ccp4.ac.uk it's
optional.

best wishes
Ville

On Thu, Oct 12, 2017 at 12:10:07AM +0200, Tim Gruene wrote:
> Dear Markus, dear Michael,
> 
> the certificate from ccp4 appears to be signed by QuoVadis Ltd. 
> If I understand correctly, this is a trusted company, as of Firefox Version 
> 32, according to the information at https://wiki.mozilla.org/CA/
> Included_Certificates
> 
> Maybe you need to UPdate, not DOWNdate your browser?
> 
> Regards,
> Tim
> 
> On Wednesday, October 11, 2017 12:50:13 PM CEST R. Michael Garavito wrote:
> > Markus,
> > 
> > I had that problem for a short while with slightly older versions of
> > Firefox, but more recently (v54 - v56) it has not impacted any of the CCP4
> > sites.  Whether it is a Firefox correction, I don’t know, but it is fine
> > for me.  Note that CCP4online is https://www.ccp4.ac.uk/ccp4online/
> > , which requires logins, but ccp4 is
> > http://www.ccp4.ac.uk/  still.  I had it mostly
> > when connecting from home.
> > 
> > Michael

[ccp4bb] A clearer 3D view of sugars

[John Berrisford]

Dear CCP4BB

Carbohydrates, even when formed from very few sugar units, can often be 
hard to interpret in three dimensions when all their atoms are shown. 
This week, PDBe have updated the 3D structure viewer (LiteMol) on our 
web pages to add a simpler representation of common pyranose sugars.


for example pdbe.org/5ezi

Approximately 10% of entries in the PDB archive contain some form of 
carbohydrate - that’s around 13.5 thousand PDB entries! We hope that 
adding this new feature will help users to see them more clearly.


See https://www.ebi.ac.uk/pdbe/about/news/clearer-3d-view-sugars for 
further details



John

PDBe


--
John Berrisford
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529

http://www.pdbe.org
http://www.facebook.com/proteindatabank
http://twitter.com/PDBeurope

[ccp4bb] 2018 HERCULES School - Neutron & Synchrotron Radiation Science

[Silvia Onesti]

HERCULES 2018 - European School
28 Years of Neutron & Synchrotron Radiation Science

2018 session:   25 February-30 March, 2018
DEADLINE FOR APPLICATION: 25 October 2017

HERCULES is a European course for PhD students and young researchers using 
Neutrons and Synchrotron Radiation for applications in Biology, Chemistry, 
Physics, Hard & Soft Condensed Matter.

The 1-month school includes lectures (60%), hands-on practicals and tutorials 
at partner institutes (Elettra and FERMI in Trieste, Italy; ESRF, ILL in 
Grenoble; Soleil and LLB in Paris-Saclay; PSI in Villigen, Switzerland) and 
Grenoble Laboratories (CEA, CNRS, EMBL, IBS). (*)
(*)  also, participation of DESY and the European XFEL to be confirmed for 2018 
due to scheduled down-time.

The school  includes a common part and two parallel sessions:
- Biomolecular, soft condensed matter structure & dynamics
- Physics and chemistry of condensed matter


Why join Hercules ?
- to learn new techniques using neutron and synchrotron radiation
- to expand your theoretical and practical knowledge, not only for your present 
research but for your scientific career
- to experiment these techniques on world-class instruments & beamlines
- to build a network of relations with fellow young researchers and experienced 
teachers from all around the World

Bursaries/reduced costs
- A limited number of bursaries will be available either to reduce registration 
fees or cover travel costs.

More information: (see programme overview below)
Hercules website: http://hercules-school.eu/
Full list of lectures: http://hercules-school.eu/24-session-program.htm
Download the full 2017 Booklet (lectures, practicals..)

Contact email: hercu...@hercules-school.eu
---
Silvia Onesti - Head of Structural Biology

Elettra - Sincrotrone Trieste S.C.p.A.
AREA Science Park, 34149 Basovizza, Trieste ITALY

Email: silvia.one...@elettra.eu
Tel. +39 040 3758451  Mob +39 366 6878001

http://www.elettra.trieste.it/People/SilviaOnesti
http://www.elettra.trieste.it/labs/structural-biology
---

Re: [ccp4bb] areaimol missing symmetry mates

[Eleanor Dodson]

Eugene is away but I think the PISA symmetry checking only looks at 2 unit
cells in all directions from the origin, so if the origin chain is far away
you may lose contacts.

..

As someone says - always try to place the molecule reasonably close to the
origin.

There is an old program
pdbset xyzin mol.pdb
end

which tells you the centre of symmetry of the mol.  If it is a long way off
the origin say 1.27 -0.73 0.95 an equally valid molecule could be
repositioned saying
pdbset xyzin mol.pdb xyzout mol-Sym.pdb
symgen x-1,y+1,z-1
end

Then the centre of mass would be 0.27 0.27 -0.05


You may want to split the check to do individual chains

COOT will apply a shift too, once you know what it should be.
Eleanor



On 11 October 2017 at 18:15, Phillip Gregory Gross 
wrote:

> I got a symmetry-related molecule in the ASU (mine was about 400 A off the
> origin) and ran areaimol and the PDBe PISA server, and it worked on both!
> Got all the same contacts as my DIFFMODE COMPARE run. Thanks Paul!
> -Phillip
>
> --
> *From:* CCP4 bulletin board  on behalf of Paul
> Emsley 
> *Sent:* Wednesday, October 11, 2017 12:07:33 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] areaimol missing symmetry mates
>
> Try moving your molecule closer to the origin, by unit cell shift or
> choosing a symmetry-related molecule.
>
> (In Coot, you can do this by using Extensions -> Modelling -> Symm Shift
> Reference Chain Here.
>
> Paul.
>