Re: [ccp4bb] Rfactor and Rfree not coming below 0.4

[Dale Tronrud]

   The R value is basically a sum of all the Fourier coefficients of the
difference map relative to their Fobs amplitude.  If your R value is in
the 40% range you MUST have a difference map with a lot of stuff in it.
The only way you can have a clean difference map with an R value so
large is if there is a mistake either in the calculation of the R value
or the map.

   I think you need to double-check your work.

Dale Tronrud

P.S. Are you contouring your difference map at a reasonable level?
Think e/A^3 not "sigma"s.  When I look at a difference map I start at a
level of 0.18 e/A^3 and then think about other levels.  There is nothing
magical about that number but looking at all maps the same way helps you
lean what a map should look like.  If you want an internal calibration,
you can leave out one, well ordered, water molecule.  Then you can see
what the difference density due to an absent atom looks like in YOUR
map, and compare that to the other features you see.

   Remember, if you have stuff EVERYWHERE in your difference map, you
will see NOTHING at a 3 rmsd contour because the rmsd of the map is huge!

On 1/20/2017 10:45 PM, ameya benz wrote:
> I am trying to refine my data set collected at 1.9A. The density appears
> clean and the fit is also good. In coot, all residues are in green zone
> in density fit analysis. Also in Ramachandran plot 89% residues are in
> allowed region. Few residues in loop region do not have good density for
> side chains. My protein contains about 61% loops and remaining beta
> sheets , no alpha helices (predicted from homology model). What could be
> done to improve the Rfree and Rfactor?

[ccp4bb] Rfactor and Rfree not coming below 0.4

[ameya benz]

I am trying to refine my data set collected at 1.9A. The density appears
clean and the fit is also good. In coot, all residues are in green zone in
density fit analysis. Also in Ramachandran plot 89% residues are in allowed
region. Few residues in loop region do not have good density for side
chains. My protein contains about 61% loops and remaining beta sheets , no
alpha helices (predicted from homology model). What could be done to
improve the Rfree and Rfactor?

Re: [ccp4bb] on how to use pdbset to get the symmetry mate coordinate

[Bernhard Rupp]

Well, as my weblet was used here, maybe I should explain.

 

This is actually not so easy to understand, and I have seen many students 
having problems here.

 

First, generating symmetry mates in the vicinity of a given copy does not mean 
they are aligned with the generating operator’s axis (which I believe is what 
you want to show).

A program that does that right needs to expand the cell around the object and 
also consider the translational neighbors. Afaik, Pymol does it right.

 

The second problem is, that you need to understand the generator 6sub5. What 
does it do?

If you read the definition of a screw axis (I might suggest a certain textbook, 
p 221):

An operator N(s) rotates the motif by 360/N degrees and shifts it along the 
operator axis by a fraction of s/N, N times.

The moment s>1, you will eventually end up outside the unit cell, and you need 
to translate the generated copies back into

the unit cell. That is what these listed operators (equipoint transformations) 
mean.

 

Example:

 

say 6sub5, first generation: rotate by 60, shift by 5/6 = translation is 0.833 
on z. Check. 

Next, again take this copy, rotate by 60, shift by 5/6 = already 0.833, then 
another 0.833 = 1.666 

aha! outside, so we translate back -1.0 :  0.666 Check.

 

the rest you can figure out easily.

 

The important thing to realize and remember is that when you change the axis to 
its enantiomorphic mate, say 6sub5 -> 6sub1, you

get at the first sight similar looking operators, but the handedness of the 
screw operation is reversed. Some programs invert the

coordinates automatically for you if you know only the point group during 
structure solution but are unsure about the space group.

Our you just try them all (in MR).

 

here the operator set for 6sub 1

 

| 6 equipoint transformations (X)'=[R]*(X)+(T) :  | 

 
+-+ 

 | R(11) R(12) R(13) R(21) R(22) R(23) R(31) R(32) R(33)   T(1)   T(2)   T(3)  
| 

 | 1.0   0.0   0.0   0.0   1.0   0.0   0.0   0.0   1.00.000  0.000  0.000  
| 

 | 1.0  -1.0   0.0   1.0   0.0   0.0   0.0   0.0   1.00.000  0.000  0.167  
| 

 | 0.0  -1.0   0.0   1.0  -1.0   0.0   0.0   0.0   1.00.000  0.000  0.333  
| 

 |-1.0   0.0   0.0   0.0  -1.0   0.0   0.0   0.0   1.00.000  0.000  0.500  
| 

 |-1.0   1.0   0.0  -1.0   0.0   0.0   0.0   0.0   1.00.000  0.000  0.667  
| 

 | 0.0   1.0   0.0  -1.0   1.0   0.0   0.0   0.0   1.00.000  0.000  0.833  
| 

 
+-+ 

 

see the difference?

 

An example for 31 vs 32 is given here

http://www.ruppweb.org/Garland/gallery/Ch5/pages/Biomolecular_Crystallography_Fig_5-33.htm

http://www.ruppweb.org/Garland/gallery/Ch5/thumbnails/Biomolecular_Crystallography_Fig_5-34.jpg

 

So your question what to do depends on what you want to show, and that is not 
quite clear. But you should

be able to figure it out by now.

 

BR

 

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Smith Lee
Sent: Friday, January 20, 2017 6:05 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] on how to use pdbset to get the symmetry mate coordinate

 

Dear All,

 

I have a pdb with P 65 space group. 

 

6 equipoint transformations (X)'=[R]*(X)+(T) :  | 
 
+-+ 
 | R(11) R(12) R(13) R(21) R(22) R(23) R(31) R(32) R(33)   T(1)   T(2)   T(3)  
| 
 | 1.0   0.0   0.0   0.0   1.0   0.0   0.0   0.0   1.00.000  0.000  0.000  
| 
 | 1.0  -1.0   0.0   1.0   0.0   0.0   0.0   0.0   1.00.000  0.000  0.833  
| 
 | 0.0  -1.0   0.0   1.0  -1.0   0.0   0.0   0.0   1.00.000  0.000  0.667  
| 
 |-1.0   0.0   0.0   0.0  -1.0   0.0   0.0   0.0   1.00.000  0.000  0.500  
| 
 |-1.0   1.0   0.0  -1.0   0.0   0.0   0.0   0.0   1.00.000  0.000  0.333  
| 
 | 0.0   1.0   0.0  -1.0   1.0   0.0   0.0   0.0   1.00.000  0.000  0.167  |
 
6 equipoint transformations decoded into atom coordinate format :   | 
 
+-+ 
 |  X   ,  Y   ,  Z
| 
 |  X -Y,  X   ,5/6 +Z 
| 
 | -Y   ,  X -Y,2/3 +Z 
| 
 | -X   , -Y   ,1/2 +Z 
| 
 | -X +Y, -X   ,1/3 +Z 
| 
 |  Y   , -X +Y,1/6 +Z 
Will you please show me step by step (what exactly to input in the black in the 
graphical pdbset interface) by pdbset how can I get the symmetry mate pdb, for 
example how to get the pdb for 1 of 6 equipoint transformation X -Y,  X   ,5/6 
+Z?
 
I am looking forward to getting a reply from you.
 
Smith

[ccp4bb] on how to use pdbset to get the symmetry mate coordinate

[Smith Lee]

Dear All,
I have a pdb with P 65 space group. 
6 equipoint transformations (X)'=[R]*(X)+(T) :  | 
 
+-+ 
 | R(11) R(12) R(13) R(21) R(22) R(23) R(31) R(32) R(33)   T(1)   T(2)   T(3)  
| 
 | 1.0   0.0   0.0   0.0   1.0   0.0   0.0   0.0   1.00.000  0.000  0.000  
| 
 | 1.0  -1.0   0.0   1.0   0.0   0.0   0.0   0.0   1.00.000  0.000  0.833  
| 
 | 0.0  -1.0   0.0   1.0  -1.0   0.0   0.0   0.0   1.00.000  0.000  0.667  
| 
 |-1.0   0.0   0.0   0.0  -1.0   0.0   0.0   0.0   1.00.000  0.000  0.500  
| 
 |-1.0   1.0   0.0  -1.0   0.0   0.0   0.0   0.0   1.00.000  0.000  0.333  
| 
 | 0.0   1.0   0.0  -1.0   1.0   0.0   0.0   0.0   1.00.000  0.000  0.167  |
6 equipoint transformations decoded into atom coordinate format :   | 
 
+-+ 
 |  X   ,  Y   ,  Z
| 
 |  X -Y,  X   ,5/6 +Z 
| 
 | -Y   ,  X -Y,2/3 +Z 
| 
 | -X   , -Y   ,1/2 +Z 
| 
 | -X +Y, -X   ,1/3 +Z 
| 
 |  Y   , -X +Y,1/6 +Z Will you please show me step by step (what exactly 
to input in the black in the graphical pdbset interface) by pdbset how can I 
get the symmetry mate pdb, for example how to get the pdb for 1 of 6 equipoint 
transformation X -Y,  X   ,5/6 +Z?
I am looking forward to getting a reply from you.

Smith

[ccp4bb] POINTLESS error: "NormaliseInRuns::apply Unused run 0"

[Joseph Brock]

Dear ccp4 experts,

I am trying to use the ccp4i Pointless, Aimless, Ctruncate application to 
convert a XDS.HKL file. This usually works fine, however I suddenly have the 
task immediately fail with the error message below pasted from the bottom of 
the logfile.

If anyone can translate this error message for me I would be very grateful.

I am running up to date ccp4 (7.0.027) on Ubuntu 14.04.



***
* Information from CCP4Interface script
***
The program run with command: /usr/local/bin/ccp4-7.0/bin/pointless HKLOUT 
"/tmp/joe/jsb_32_2_mtz.tmp"
has failed with error message
NormaliseInRuns::apply Unused run 0
***


#CCP4I TERMINATION STATUS 0 "NormaliseInRuns::apply Unused run 0"
#CCP4I TERMINATION TIME 21 Jan 2017  00:18:31
#CCP4I MESSAGE Task failed


Thanks in advance for the help.

Cheers,
Joe.

Joseph Brock | PhD
Division of Physiological Chemistry II
Department of Medical Biochemistry and Biophysics
Karolinska Institutet
Scheeles väg 2
SE-171 77 Stockholm, Sweden

[ccp4bb] Diploma thesis in biomolecular crystallography

[Bernhard Rupp]

Hi Fellows,

 

A (frugally) paid diploma/master thesis position is available in my small
Austrian team at the Medical University in Innsbruck. The position is
ideally suited for candidates with biochemistry, bioscience or biomedical
background enlisted in a local program (MUI, MCI, LFU, etc.) but other
affiliations are also welcome. 

 

More here:

https://www.dropbox.com/s/hgryqyb2r0hio6q/Diploma_thesis.pdf?dl=0

 

Best, BR

--

Bernhard Rupp

  http://www.hofkristallamt.org/

  b...@hofkristallamt.org

+1 925 209 7429

+43 767 571 0536

--

All models are wrong

but some are useful.

--

 

Re: [ccp4bb] Pocket identification and substrate tunnelling

[Kabasakal, Burak V]

Dear Mohamed,

There is a software called CAVER to calculate tunnels in the protein for a 
given pdb file. ( http://caver.cz/)

It has also a PyMol plugin which you can find from its web site.

Burak

Sent from my iPhone

On 20 Jan 2017, at 18:45, Mohamed Noor 
> wrote:

Dear all

I think this was discussed before on this board but I can't find the relevant 
thread(s), so apologies.

I have a crystal structure on an enzyme with the NAD+ cofactor bound but no 
substrate, despite trying both co-crystallization and soaking methods and 
collecting datasets from 20-30 crystals.

Is there a way of identifying the approximate path that the substrate takes 
from the outside into the active site computationally using electrostatics, 
residue chemistry etc.?

Thanks
Mohamed

[ccp4bb] Pocket identification and substrate tunnelling

[Mohamed Noor]

Dear all

I think this was discussed before on this board but I can't find the relevant 
thread(s), so apologies.

I have a crystal structure on an enzyme with the NAD+ cofactor bound but no 
substrate, despite trying both co-crystallization and soaking methods and 
collecting datasets from 20-30 crystals.

Is there a way of identifying the approximate path that the substrate takes 
from the outside into the active site computationally using electrostatics, 
residue chemistry etc.?

Thanks
Mohamed

[ccp4bb] Diamond MX Bag training - 22-23 February 2017

[Pierre Aller]

Dear all,

The Diamond Light Source Macromolecular Crystallography group would like to 
invite both our academic and industrial users to MX beamline training sessions 
on the 22nd and 23rd February 2017.
The aim is to provide MX users with sufficient training to be able to operate 
any of the Diamond MX beamlines efficiently and to get the most benefit from 
their beamtime. The training will involve hands-on sessions on the suite of 
five operational MX beamlines (http://www.diamond.ac.uk/mx-home/) as well as 
optional offline software sessions.
 Sessions include:
22nd February afternoon optional session Hands on software:

  *   Tutorial sessions:
 *   CCP4i2: scaling with Aimless, phasing and refinement (CCP4 team)
 *   Data processing with DIALS and Mosflm

23rd February session on MX beamlines:

  *   Multi-axis goniometry / Anomalous data collection
  *   Sample humidity control (HC1)
  *   I24 new end station/ In-situ diffraction
  *   Experiment database:  ISPyB
  *   MX pipeline / autoprocessing
Registration is free-of-charge with lunch provided on the 22nd and 23rd 
February, and accommodation and dinner for the night of the 22nd February. 
Travelling expenses within the UK will also be provided. The training is 
targeted at all users, and is not limited to students and post docs. It is 
essential that each BAG sends at least one representative per calendar year.

Registration
Places are limited to twenty five participants. The registration deadline is on 
the 8th February.
Registration is now 
open

Regards,

Pierre


Pierre Aller, Ph.D.
Beamline Scientist XFEL Hub
Diamond Light Source Ltd., Diamond House
Harwell Science & Innovation Campus
Didcot, Oxfordshire OX11 0DE

+44 (0) 1235 778183
pierre.al...@diamond.ac.uk


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the message.
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Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

[ccp4bb] AW: [ccp4bb] Salt bridge-hydrogen bonds

[Herman . Schreuder]

Yes, Arg has 3 potential Hbond donor/acceptors and Glu 2. Also a single atom 
can have multiple interactions.
Look in coot at the structures and which atom has which interaction with which 
partner atom.

Best,
Herman

-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Mohamed 
Noor
Gesendet: Freitag, 20. Januar 2017 11:45
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Salt bridge-hydrogen bonds

Dear all

Is it possible for two residues to form a salt bridge between them, and at the 
same time**, each of them form a hydrogen bond with another residue? In other 
words:

Arg1 - Glu10 (salt bridge)

Arg1 - Tyr600 (H bond)

Glu10 - Thr590 (H bond)


** I understand proteins are not static structures, so I am referring to an 
exact time and space here and not something formed and broken throughout a 
sampled period of time.

[ccp4bb] DL_Software Training 3-5 April and Hack Day 6 April @ QMUL

[Ilian Todorov]

Dear all,

There will be a 3-day DL_Software training workshop at Queen Mary University of 
London from 3-5 April 2017, followed by a Hack Day on 6 April 2017.

The events could be of value to the community as it will showcase the CCP5 
software framework and its application for bio-molecule force-field model 
set-up and other general complex and organic molecules such as drugs and 
polymers.  DL_FIELD and DL_POLY offer advantages in setting up multi-component, 
complex systems, including organic-inorganic interfaces, by utilising a wide 
range of force-field schemes and a large selection of MD techniques, not 
commonly available in other traditional, bio-simulation programs.  Access to 
modelling polymer and organic systems on the mesoscale is facilitated by 
DL_MESO via Dissipative Particle Dynamics.

The aim of the training workshop is to provide course material and training to 
the following molecular modelling packages – DL_POLY, DL_FIELD, DL_MESO and 
DL_CGMAP.  DL_MONTE and ChemShell will also be showcased on day 3 (5 April 
2017), however, support for these packages will be limited during the tutorial 
sessions.

The events are an opportunity for current and potential users of DL_Software to 
learn what methodologies and algorithms these programs offer, how to use them 
efficiently and best apply to user specific needs.  The workshop also offers 
demonstrations and hands-on sessions giving users the opportunity to compile, 
run and experiment with the programs as well as interact with their developers.

For the full workshop description and registration, please, follow the link - 
https://www.ccp5.ac.uk/events/training_workshop.shtml .

The Hack Day is a one-day technical workshop aiming specifically for 
researchers who are interested to modify the supported DL_Software programs 
(DL_POLY, DL_FIELD, DL_MESO, ChemShell, DL_MONTE) and tailor model set up to 
their specific project needs.  For instance: model set-up, software porting, 
addition of new features, modification of the existing features, etc. (please, 
state your needs in the registration page).  In addition, the Hack Day is the 
best opportunity for those who may be interested to seek advice and help in 
simulation set-up and model development, work flow scripting, job submissions, 
etc.

For the Hack Day registration, please, follow the link - 
https://www.ccp5.ac.uk/events/hack_days/hack_days.shtml .

Regards,

Ilian Todorov

Computational Chemistry Group
STFC Daresbury Laboratory
United Kingdom

[ccp4bb] Open position: Professor in Molecular Biochemistry, University of Oulu, Finland

[Tuomo Glumoff]

Please see and navigate using the link:

https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=3230=en



=
Tuomo Glumoff, FT, Dosentti
yliopistonlehtori
koulutusdekaani
/ Lecturer & Adjunct Professor, Dean of Education

Biokemian ja molekyylilääketieteen tiedekunta /
Faculty of Biochemistry and Molecular Medicine
Oulun yliopisto / University of Oulu
PL 5400 / PO Box 5400
90014 Oulun yliopisto
Finland

Käyntiosoite: Aapistie 7 A, 90220 Oulu
Sisäinen posti / internal mail: 5BMTK
Huone/office: L104A
Puh. 0294 481170 / Tel. +358 294 481170
email: tuomo.glum...@oulu.fi
http://www.oulu.fi/fbmm/
=

[ccp4bb] Salt bridge-hydrogen bonds

[Mohamed Noor]

Dear all

Is it possible for two residues to form a salt bridge between them, and at the 
same time**, each of them form a hydrogen bond with another residue? In other 
words:

Arg1 - Glu10 (salt bridge)

Arg1 - Tyr600 (H bond)

Glu10 - Thr590 (H bond)


** I understand proteins are not static structures, so I am referring to an 
exact time and space here and not something formed and broken throughout a 
sampled period of time.

Re: [ccp4bb] help with Buccaneer

[Bellini, Dom]

If you look carefully in the GUI of Buccaneer there has been for quite sometime 
now an option to use Phi and FOM instead of HL coefficients (quickest solution).


Although Buccaneer is optimized to use HL coefficients, getting your ABCD from 
MR solutions will results in CD equal to zero anyway.


D




From: CCP4 bulletin board  on behalf of Carlos 
CONTRERAS-MARTEL 
Sent: 20 January 2017 07:33:28
To: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] help with Buccaneer

You need go first for some density improvement, see

http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=Automated_phase_improvement_with_Parrot
Automated phase improvement with Parrot - Media 
Wiki
ccp4wiki.org
Main Page - Using the CCP4 software - Phase improvement with CCP4 - Automated 
phase improvement with Parrot. Parrot is a program which takes an initial set 
of phase ...




All the best

Carlos


On 01/20/17 05:10, Vikram Dalal wrote:
Hi Everyone,

I want to run the Buccaneer. I need Hendrickson-Lattman coefficients for it. 
How I can find Hendrickson-Lattman coefficients?




Thanks & Regards,











--
 Carlos CONTRERAS MARTEL, Ph.D.
 (CR1 CNRS)

 carlos.contreras-mar...@ibs.fr

 "Bacterial Pathogenesis Group"
Institut de Biologie Structurale
 UMR5075 CEA-CNRS-UGA

  IBS
  Campus EPN
  71, avenue des Martyrs
  CS 10090
  38044 Grenoble CEDEX 9
  FRANCE


 tel : (+33) (0)4 57 42 86 41

http://www.ibs.fr/groupes/groupe-pathogenie-bacterienne/?lang=fr
http://www.ibs.fr/groups/bacterial-pathogenesis-group/?lang=en