[ccp4bb] OSX 10.9.2

[Cygler, Miroslaw]

Hi,
Does the ccp4 suite work with the latest OSX 10.9.2 operating system? Are there 
any known problems?

Mirek

[ccp4bb] PyMol and Schrodinger

[Cygler, Miroslaw]

Hi,
I have inquired at Schrodinger about the licensing for PyMol. I was surprised 
by their answer. The access to PyMol is only through a yearly licence. They do 
not offer the option of purchasing the software and using the obtained version 
without time limitation. This policy is very different from many other software 
packages, which one can use without continuing licensing fees and additional 
fees are only when an upgrade is needed. At least I believe that Office, 
EndNote, Photoshop and others are distributed this way.
I also remember very vividly the Warren’s reason for developing PyMol, and that 
was the free access to the source code. He later implemented fees for 
downloading binary code specific for one’s operating system but there were no 
time restrictions on its use.
As far as I recollect, Schrodinger took over PyMol distribution and development 
promising to continue in the same spirit.  Please correct me if I am wrong.
I find the constant yearly licensing policy disturbing and will be looking for 
alternatives. I would like to hear if you have had the same experience and what 
you think about the Schrodinger policy.
Best wishes,

Mirek

[ccp4bb] shelxCDE in ccp4i

[Cygler, Miroslaw]

Hi,
I have shelx programs installed  on my computer but only shelxs shows as active 
on the ccp4i interface. How to activate shelxCDE?
Thanks,

Mirek

[ccp4bb] Coot labels

[Cygler, Miroslaw]

Hi,
I just started using coot 0.9 and see some differences in behaviour from 
version 0.8. When I move to the next residue using space bar the residue name 
of the residue does not appear. How can I make appear automatically?
Best,

Mirek






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[ccp4bb] OS X yosemite

[Cygler, Miroslaw]

Hi,
I am thinking of upgrading the os on my mac to Yosemite. Are there any known 
issues for crystallographic software that I should pay attention to?
Thanks,

Mirek

[ccp4bb] Tenure Track position in Structural Biology at the University of Saskatchewan

[Cygler, Miroslaw]

Tenure Track Position in the College of Medicine
at the University of Saskatchewan
 The College of Medicine invites applications for a tenure track faculty 
position at the Assistant, Associate or Full Professor level in the area of 
structural biology of membrane proteins, or in the application of NMR 
spectroscopy to explore protein dynamics, for example of intrinsically unfolded 
proteins. Strong preference will be given to candidates whose research is 
related to human diseases and who have a track record in research 
collaboration. The position will be affiliated with the Department of Anatomy 
and Cell Biology, Biochemistry, or Microbiology and Immunology, according to 
the best fit of the candidate’s profile.
The successful candidate will join the Molecular Design Cluster in the College 
of Medicine, which currently includes seven principal investigators in the 
areas of protein X-ray crystallography, NMR spectroscopy and single molecule 
techniques. The mandate of this cluster is to conduct fundamental research on 
the molecular basis of human disease. The College would like to strengthen the 
expertise in structural biology by expanding into the field of membrane 
proteins and protein dynamics. The cluster has just moved into a new laboratory 
space with excellent equipment for protein research.  Facilities for protein 
crystallography and NMR spectroscopy are available at the Canadian Light Source 
(CLS) synchrotron and the Saskatchewan Structural Sciences Center (SSSC), 
respectively, both located on the University campus. The proximity to the 
synchrotron beamlines, ample access time and the existing collaborations with 
the scientists of the Canadian Macromolecular Crystallographic Facility (CMCF) 
at the CLS offer outstanding opportunities for research in structural biology 
of membrane proteins, while future SAXS capability at the synchrotron will 
complement the four NMR spectrometers at the SSSC for research in protein 
dynamics and protein-protein interactions. Additional collaborations are 
available through the Center for Proteomics Research in Interactions and 
Structure of Macromolecules (PRISM).
The University of Saskatchewan is a research-intensive institution with 22,000 
students and 7,000 faculty and staff, and a strong reputation for innovation 
and excellence (www.usask.ca). In addition to the 
Canadian Light Source synchrotron 
(www.lightsource.ca) it is also a home to the 
Vaccine and Infectious Disease Organization / International Vaccine Centre 
(www.vido.org), as well as a University-related Research 
Park at the Innovation Place 
(www.innovationplace.com). The beautiful U of 
S campus is located on the shores of the South Saskatchewan River in Saskatoon, 
a city with a diverse and thriving economic base and vibrant cultural life 
(www.tourismsaskatoon.com).
The successful candidate is expected to attract major external research 
funding, to lead a vigorous research program involving graduate students and 
postdoctoral fellows, and to contribute to teaching in graduate and 
undergraduate academic programs of the College of Medicine.
Review of applications will begin on March 31, 2013 and will continue until the 
position is filled. Preferred starting dates for this position are July 1 to 
September 1, 2013. Please submit (1) curriculum vita, (2) a cover letter 
outlining research interests and experience, (3) description of your proposed 
research and (4) the names of three referees, preferably electronically, to:
Dr. Mirek Cygler
PRISM Selection Committee
College of Medicine,
University of Saskatchewan,
107 Wiggins Road,
Saskatoon, Saskatchewan S7N 5E5
Canada
Email: biomed-sci.supp...@usask.ca
 The University of Saskatchewan is strongly committed to a diverse and 
inclusive workplace that empowers all employees to reach their full potential. 
All members of the university community share responsibility for developing and 
maintaining an environment in which differences are valued and inclusiveness is 
practiced. The university welcomes applications from those who will contribute 
to the diversity of our community. All qualified candidates are encouraged to 
apply; however, Canadian citizens and permanent residents will be given 
priority.

[ccp4bb] Glutathione rsin

[Cygler, Miroslaw]

Hi,
I would like to ask the bb faithful for their experience with the glutathione 
affinity resins. We have been using so far the Glutathione Sepharose fast flow 
from GE but the price is getting steeper. We found Glutathione Superflow resin 
from Clontech to be significantly less expensive and Glutathione agarose from 
Fisher somewhere in-between. We have no experience with the latter two resins 
and I wonder what is the experience of other people with these resins? Do they 
have decent binding capacity? Can they be efficiently regenerated or are they a 
single use only?
Thanks for your help,

Mirek

Re: [ccp4bb] Problem with Mg2+ binding site refinement

[Cygler, Miroslaw]

Sent from my Bell Samsung device.


 Original message 
From: Clemens Vonrhein 
Date: 2017-06-16 4:43 AM (GMT-06:00)
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Problem with Mg2+ binding site refinement

Hi,

On Fri, Jun 16, 2017 at 10:47:20AM +0530, Prem Prakash wrote:
> Hi Mubinur,
> I got the same situation while refining my protein complex with Lanthanum
> ion complex, reducing the occupancy while refining solved the problem.

That might have not been the whole story through. You still want to
use the correct formfactor (as Eleanor said) for each atom in your
model. The formfactors we usually use in refinement
(e.g. $CCP4/lib/data/atomsf) are for CuKa wavelength - and the data
might have been collected at a different wavelength. Therefore those
formfactors might not be correct in that case.

For most atoms in your model that won't matter that much, since f'
doesn't change very much with resolution:

0.8A   0.9A   1.0A   1.1A   1.2A   1.3A   1.4A   1.5A   1.6A   1.7A   
1.8A   1.9A   2.0A
 

  C :   0.00   0.00   0.00   0.01   0.01   0.01   0.01   0.02   0.02   0.02   
0.02   0.02   0.03
  N :   0.00   0.01   0.01   0.01   0.02   0.02   0.02   0.03   0.03   0.03   
0.04   0.04   0.05
  O :   0.01   0.01   0.02   0.02   0.03   0.03   0.04   0.04   0.05   0.05   
0.06   0.07   0.07
  P :   0.11   0.13   0.16   0.18   0.21   0.23   0.25   0.27   0.29   0.31   
0.33   0.34   0.35
  S :   0.13   0.16   0.19   0.22   0.24   0.27   0.29   0.31   0.33   0.34   
0.36   0.37   0.37

(S and P do have a small change though). However, for other atoms that
can be much more extreme:

0.8A   0.9A   1.0A   1.1A   1.2A   1.3A   1.4A   1.5A   1.6A   1.7A   
1.8A   1.9A   2.0A
 

 Br :  -1.05  -3.12  -2.23  -1.62  -1.31  -1.11  -0.95  -0.82  -0.71  -0.61  
-0.52  -0.45  -0.37
 Cl :   0.15   0.19   0.22   0.25   0.27   0.30   0.32   0.34   0.35   0.36   
0.37   0.37   0.37
 Ca :   0.23   0.27   0.30   0.33   0.34   0.35   0.35   0.35   0.32   0.29   
0.25   0.19   0.11
 Mg :   0.05   0.06   0.08   0.09   0.11   0.13   0.14   0.16   0.17   0.19   
0.20   0.22   0.23
 La :  -0.47  -0.37  -0.34  -0.38  -0.50  -0.72  -1.04  -1.50  -2.11  -2.93  
-4.06  -5.75  -8.32
 Se :  -0.64  -1.62  -3.48  -1.96  -1.52  -1.26  -1.08  -0.94  -0.81  -0.71  
-0.62  -0.53  -0.46

(running CROSSEC will give you those numbers).

When refining against your data at a wavelength different than CuKa,
you need to adjust your formfactors accordingly (see e.g. [1]). So if
you collected your Lanthanum dataset at slightly longer wavelengths
than CuKa, you should tell your refinement program to adjust its
scattering factors - and since f' is lower, this might already
remove that negative density without the need to fudge it via a
reduction in occupancy. Of course, you could still have a partially
occupied ion, but with the correct formfactor you will at least have
the chance to get the occupancy adjustment right.

I always thought that the very common approach of adjusting SE atom
occupancy down to 0.75 or 0.80 in Se-MET (MSE) structures deposited in
the PDB is not necessarily due to only partial incorporation of Se-MET
(versus S-MET) during expression, but can sometimes be attributed to
using the wrong formfactor during refinement.

Of course, it is very helpful if data processing packages keep the
wavelength information in the MTZ file correct. Then one can at
least compute theoretical f' values for a given wavelength. Using
measured f' values from a good fluorescence scan when collecting data
close to the edge is obviously even better.

Cheers

Clemens

[1] 
https://www.globalphasing.com/buster/wiki/index.cgi?AutoBusterExampleFormfactor
(slightly out-of=date, but gives the idea). Assuming the
wavelength in the MTZ header is correct (e.g. from autoPROC,
www.globalphasing.com/autoproc/) 
and you are away from the edge,
using AutomaticFormfactorCorrection=yes is all you need to add to
the command-line. Otherwise one can use
e.g. FormfactorCorrection="Se:-6.5 Ca:0.27" or such).


> Good luck
> P.P
>
> On Thu, Jun 15, 2017 at 11:17 PM, Pavel Afonine  wrote:
>
> > Hi Mubinur,
> >
> > try without "metal restraints" and see if that helps. As others suggested,
> > make sure 2+ is present in rightmost column of PDB file. The side may be
> > partially occupied, so refining occupancy of Mg2+ is not a bad idea.
> >
> > Pavel
> >
> > On Wed, Jun 14, 2017 at 2:44 PM, Mohammad Rahman 
> > wrote:
> >
> >> Dear All,
> >>
> >> I am trying to refine a tetrameric enzyme structure that was determined
> >> at 2.7 Å. The structure contains a Mg2+  binding site in each monomer.
> >> After refinement,   in Mg2+ binding site  negative density (red) has been
> >> found as in pictures. I am us

[ccp4bb] XQuartz problems

[Cygler, Miroslaw]

Hello Mac Gurus,
I have run today into a problem with XQuartz on my iMac. No problems till now. 
Now, any application that uses X11 does not start. It invokes XQuartz but that 
is it. What is more, when running, XQuartz can not be stopped; after an attempt 
to quit the application XQuartz immediately restarts. I cannot restart the 
computer the normal way but have to hold the power button to power down the 
computer. I deleted XQuartz and installed it from the depository but to no 
avail.
This behaviour might be related to me plugging in today someone else hard drive 
and transferring files to my own hard drive. Something else could have been 
transferred to my iMac. I would like to avoid reinstalling the operating system 
from scratch and restoring the files from backup
Any advice what to try? Thanks for your help,

Mirek

[ccp4bb] gif dictionary for connecting sugars

[Cygler, Miroslaw]

Hi,
I have difficulty with the cif dictionary to connect sugars in a 
tetrasaccharide. The dictionary works well in coot (regularizes as expected) 
but when refined in Phenix, one connection misbehaves. Where can I find 
description of the rules for creating the link? Which residue is taken as '1' 
and which as ‘2'
Thanks for your help,

Mirek

[ccp4bb] PyMol question

[Cygler, Miroslaw]

Hi,
When I loaded the ed map into PyMol v1.8.4.1 and used iso mesh around part of 
the protein all is well until I use the RAY command. In the ray traced image I 
see the unit cell box that does not show on the image in the normal view. How 
can I remove the box from the ray traced image?
Thanks for your help,

Mirek

[ccp4bb] Assistant Professor positions at the U of Saskatchewan, Canada

[Cygler, Miroslaw]

Dear Colleagues,
Our department is recruiting two new faculty. The structural biology is among 
the research areas that are considered. I would be grateful if you could bring 
the attached ad to the attention of qualified candidates.
Many thanks and best wishes,

Mirek

===
Dr. Miroslaw Cygler, FCAHS
Professor, Department of Biochem, Microbiol and Immunol, U. of Saskatchewan
and Adjunct Professor, Department of Biochemistry, McGill University
Canada Research Chair in Molecular Medicine Using Synchrotron Light
Director, Centre for Proteomics Research in Interactions and Structure of 
Macromolecules (PRISM)
Health Sciences Building, 3D30.6 (Box 9)
107 Wiggins Road, Saskatoon SK S7N 5E5 Canada
Email: miroslaw.cyg...@usask.ca
Website: http://www.usask.ca/research-groups/cygler/
Phone: 306-966-4361, cell: 306-203-2317
===









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BMI Advertisement Jan_16 final.pdf
Description: BMI Advertisement Jan_16 final.pdf

[ccp4bb] Comparing two datasets

[Cygler, Miroslaw]

Hi,
I would like to calculate the R-merge for Fs from two datasets processed from 
two different crystals. Tried to use Blend but got the message that Blend 
requires R. Downloaded R but do not know how to tell CCP4 where it is located 
on my Mac. Is there another program that would take two mtg files and merge the 
Fs?
Any help would be greatly appreciated.

Mirek







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Re: [ccp4bb] Comparing two datasets

[Cygler, Miroslaw]

MRC LMB 
mailto:and...@mrc-lmb.cam.ac.uk>> wrote:

I think that POINTLESS works with intensities rather than structure factors 
(I’m not sure if this can be changed). Also, SCALEIT gives a much more detailed 
breakdown (R factors as a function of resolution and differences in terms of 
sigmas etc) than POINTLESS WILL.

Cheers,

Andrew

On 26 Jul 2022, at 09:24, LEGRAND Pierre 
mailto:pierre.legr...@synchrotron-soleil.fr>>
 wrote:

Hello Mirek,

A very quick approach for that is offered by pointless:

pointless HKLREF 1_1_aimless.mtz  HKLIN 2_1_aimless.mtz
or
pointless HKLREF 1_1_aimless.mtz  XDSIN XDS_ASCII.HK

You will obtain a table looking like that, taking into account to possible 
reindexing:

Alternative indexing scores relative to reference
  Alternative reindexingLklhd  CC R(E^2)Number 
Cell_deviation
1  [h,k,l]  0.9930.9620.118 19150  0.08
2  [-k,h,l] 0.0070.0780.512 19150  0.87


Best wishes,

Pierre Legrand
PROXIMA-1 Beamline
Synchrotron SOLEIL

De: "Nicolas Foos" mailto:nicf...@embl.fr>>
À: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Envoyé: Mardi 26 Juillet 2022 08:36:35
Objet: Re: [ccp4bb] Comparing two datasets

Hi Mirek,

I am pretty sure XSCALE will do that for you : 
https://xds.mr.mpg.de/html_doc/xscale_program.html

If not, maybe have a look on SHELXC in SIR mode.

Hope this help.

Nicolas

On 25/07/2022 21:52, Cygler, Miroslaw wrote:
Hi,
I would like to calculate the R-merge for Fs from two datasets processed from 
two different crystals. Tried to use Blend but got the message that Blend 
requires R. Downloaded R but do not know how to tell CCP4 where it is located 
on my Mac. Is there another program that would take two mtg files and merge the 
Fs?
Any help would be greatly appreciated.


Mirek





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--
Nicolas Foos PhD - ARISE fellow
https://orcid.org/-0003-2331-8399

EMBL Grenoble, McCarthy Team
71 av. des Martyrs,
38000 Grenoble FRANCE

+33 4 57 42 84 67

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* Global Phasing Ltd., Sheraton House, Castle Park
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[ccp4bb] Missing file

[Cygler, Miroslaw]

When I start coot on Mac there are several warnings:

/Applications/ccp4-8.0/coot_py2/bin/coot: line 81: 
/Applications/ccp4-8.0/coot_py2/bin/ccp4.setup-sh: No such file or directory
WARNING:: Coot REFMAC dictionary override COOT_REFMAC_LIB_DIRfailed to find a 
dictionary /Applications/ccp4-8.0/coot_py2/share/coot/lib
WARNING:: COOT_PREFIX set, but no dictionary lib found
WARNING: Failed to read restraints dictionary.
WARNING: in init_refmac_mon_lib, file "/data/monomers/list/mon_lib_list.cif" 
not found.
WARNING: file /data/monomers/a/ALA.cif is not a regular file
WARNING: file /data/monomers/a/ASP.cif is not a regular file
…
WARNING: file /data/monomers/n/NA.cif is not a regular file
WARNING:: energy lib /data/monomers/ener_lib.cif not found.

I cannot find the file ccp4.setup-sh in the ccp4 or coot directories. Where can 
I find this file?
Thanks,

Mirek







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[ccp4bb] Coot issue

[Cygler, Miroslaw]

Hi,
I just upgrade my Mac to Ventura v13.2 from v12.6.3 and run into issue with 
Coot. When I use the delete command it causes the main Coot window disappearing 
while other Coot windows stay open. Has anyone had this issue? Is there a way 
around it? No such problem on v12.6.3.
Best,

Mirek







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[ccp4bb] Tenure track position in Protein Science for Pathogen Defense

[Cygler, Miroslaw]

Dear Colleagues,
I am excited to let you know that the Department of Biochemistry, Microbiology 
and Immunology, College of Medicine, University of Saskatchewan, is searching 
for an exceptional candidate in the area of Protein Science for Pathogen 
Defense, to fill a tenure-track Canada Research Chair (CRC) Tier 2 position. 
The CRC program is the flagship of a national strategy to make Canada one of 
the world's top countries in research and development.
We are looking for an outstanding early career scientist to establish and lead 
a groundbreaking research program in protein science to understand the 
mechanisms of bacterial and viral infection in humans or animals, to 
investigate host-pathogen interactions, or to discover novel mechanisms of 
defense against known and potential future pathogens. Within this broad scope, 
specific areas of interest include synthetic antigen design, the molecular 
basis of immune response to pathogens, mechanisms of antimicrobial resistance, 
and the prediction-guided design of artificial antibodies. We are interested in 
hiring a world-class expert in one or more of the following areas: (i) protein 
structure prediction and structural bioinformatics, (ii) protein design, and 
(iii) cryo-electron microscopy.
A detailed advertisement with instruction how to apply is enclosed and can also 
be viewed here:

Canada Research Chair (CRC) Tier 2 in Protein Science for Pathogen 
Defense
protection.outlook.com
[X]

.
Regards,



Mirek

===
Dr. Miroslaw Cygler, FCAHS
Professor, Dept. Biochem, Microbiol & Immune, U. of Saskatchewan
Canada Research Chair in Molecular Medicine Using Synchrotron Light
Health Sciences Building 3D30.6 (Box 9)
107 Wiggins Road, Saskatoon, SK S7N 5E5 Canada
Email: miroslaw.cyg...@usask.ca
Website: http://research-groups.usask.ca/cyglerlab/
Phone: 306-966-4361, cell: 306-203-2317
===






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