Re: [ccp4bb] How to rebuild a molecular only

[Eleanor Dodson]

On 07/09/2011 03:49 AM, weifeng wrote:
> 
> Dear All,
> There are 8 moleculars in an asymmetry unit, but only one molecular should be 
> rebulit, what can I do ?
> Thanks a lot!
> Wei Feng
>   


Use coot - average maps over your best molecule, rebuild that - save
coordinates, then refit those cordinayes over theins and expor other
chains and export them again
Eleanor

Re: [ccp4bb] Potential Space Group Issuetely..

[Eleanor Dodson]

If there is no indication of twinning and your Rmerge is sensible then 
it is probably point group P222


Run pointless - that gives you the quality of each of the 2 folds sepera 
tely..


Deciding on the spacegroup is a bit trickier.

That depends on absences along h00 0k0  and 00l, and if there is a 
non-crystallographic-translation with a 1/2 translation along a b or c 
then they can mislead you.


Eg if the pseudo-translation was (0.5,0.3,0.1) then the h00 would  have 
all h=odd weak and the spacegroup could be P212121 or P 2 21 21


truncate tells you whether there is non-crystallographic translation.

On 07/08/2011 04:30 AM, Raji Edayathumangalam wrote:

Hello Everyone,

I have a 3.1 Ang dataset for which I'd like to get to the bottom of what the
correct space group is.

The current unit cell in p212121 is 98.123   101.095   211.20190.000
90.00090.000
I fed the reflection data into Xtriage to look for twinning and
pseudotranslational NCS and there is no indication for either issue in the
Xtriage output. Also, all odd 00h, 00k, 00l reflections are systematically
absent as they should be for p212121.

However, my colleague who is also working on the same dataset recently
reprocessed the data in P21. Here's the cell in p21:
98.010  100.940  210.470  90.00  90.04  90.00 p21

I am not sure if BETA=90.04 is significant enough to treat as p21 (0.04%
deviation of beta angle from ideal lattice for p212121). I don't think so
but I could be wrong. Could someone please clarify?

Also, what kind of twinning and twinning operators can relate a p212121 cell
to a p21 cell with almost identical unit cell parameters as that of the
p212121 cell and leave all systematic absences intact?

Thanks much.
Raji


---
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University

[ccp4bb] How to rebuild a molecular only

[weifeng]

Dear All,
There are 8 moleculars in an asymmetry unit, but only one molecular should be 
rebulit, what can I do ?
Thanks a lot!
Wei Feng
  

Re: [ccp4bb] How to evaluate Fourier transform ripples

[conan仙人指路]

Dear All, Thank you so much for the help and suggestions on the issue 
of Fourier Transform Ripples. They are really helpful.
Best,ConanUniversity of California, Riverside   
  

[ccp4bb] peptide docking

[crystal]

Hi all,
   As I'm a newbie in peptide docking, I was wondering what programs/servers
people would suggest for generating the peptide PDB (keeping all the proper
stereochemistry)?
Is it possible to extract a file from the PDB database?
All comments will be much appreciated!

Re: [ccp4bb] Off Topic: PDB validation server

[Katherine Sippel]

Hi again,

I have an update. The nice people at the PDB have gotten in touch and they
think it might be a bug. They are looking into it.

Thank you for all the off-board replies and I hope you all have a wonderful
weekend.

Katherine

On Fri, Jul 8, 2011 at 1:13 PM, Katherine Sippel  wrote:

> Hi all,
>
> I am putting the finishing touches on a structure and as a good little
> crystallographer I am running it through Molprobity and PDB validation to
> make sure everything clears before deposition. Everything was looking
> alright until I threw the file into the PDB validation server and suddenly
> there are a significant number of solvents that violate the 3.5 angstrom
> rule. Concerned that something had gone wrong I put an older file that I had
> run through the server in April. I was shocked to discover that the file
> with only one "questionable solvent" in April now has 173 of them.
>
> I know that the PDB updated its validation server in May as described in
> their news link but it seemed to indicate an increase in output options
> rather than a change in criteria. Is anyone aware of  what changes were made
> to the validation server in regards to the preferred geometrical and
> stereochemical features?
>
> Thanks for your time,
>
> Katherine
>

[ccp4bb] Position for a crystallographer at the Pfizer Connecticut location

[Kurumbail, Ravi G]

We are looking for an enthusiastic crystallographer to join our
structural biology and biophysics group at the Pfizer Connecticut
location. The successful candidate for this position will join Groton
Structural Biology and Biophysics (SB&B), a multi-disciplinary group
with well-established expertise in molecular biology, protein
biochemistry, biological mass spectrometry, NMR, biophysics,
crystallography & computational sciences. Our mission is to provide
integrated molecular insights into drug target mechanism and
target-ligand interactions to impact discovery efforts across important
therapeutic areas, such as Immunology & Autoimmune Diseases,
Inflammation & Remodeling, Neuroscience, Cardiovascular, Metabolic &
Endocrine Diseases and Oncology.

 

As a Principal Scientist - Protein Crystallography, you will apply
expert knowledge to determine the atomic structures of novel drug target
proteins and protein-ligand complexes by protein crystallographic
methods and extract novel and relevant structural insights to drive drug
discovery efforts. You will need to collaborate with other scientists in
our multidisciplinary SB&B teams to deliver high impact results from the
laboratory, and partner with scientists across Medicinal Chemistry,
Biology and other platform lines to impact project decisions. You will
also use your deep knowledge in protein crystallography and other
related techniques to drive the development of cutting-edge technologies
and external collaborations in structural sciences.

 

Responsibilities

Primary Duties:

- Determine the atomic structures of novel drug target proteins and
protein-ligand complexes using protein crystallographic methods

- Expert analysis of relevant data and literature to extract novel
structural insights and drive drug discovery efforts.

- Contribute to the design and execution of other experiments (e.g.
construct design, purification, crystallization) and laboratory duties
(e.g. synchrotron trips) when needed

- Mentor junior scientists and contribute to vigorous experimental
design and execution as well as high level of scientific engagement

 

Qualifications

Training & Education:

- Doctoral degree or equivalent in Biochemistry, Chemistry or related
field

- Postdoctoral or industry training in Protein Crystallography

- Established track record in solving novel protein structures and
applying innovative methods throughout the gene-to-structure process

Prior Experience:

- 3-5 years of additional research experience (after postdoctoral
training) in using structural information to impact drug discovery
efforts, preferably in an industrial setting and through collaborative
efforts

 

Please submit your application online via the link, 

 

https://jobs.pfizer.com/psc/recruit/EMPLOYEE/EMPL/S/WEBLIB_HRS_HROI.HRS_
ISCRIPT.FieldFormula.IScript_JobBoard?PostingId=88951

 

With best wishes, 

 

Ravi 

 

Ravi G Kurumbail

Pfizer Global Research & Development

Research Fellow 

Mailstop: 8118W-235

Groton, CT

email:ravi.g.kurumb...@pfizer.com

 

 

Re: [ccp4bb] Potential Space Group Issue

[Pavel Afonine]

Hi,

yes, that would be my preferred strategy: often (but not always), sampling
space by trying plausible options saves you more time than thinking hard
first... and then still ending up trying -:)

All the best,
Pavel.


On Fri, Jul 8, 2011 at 1:07 PM, Van Den Berg, Bert <
lambertus.vandenb...@umassmed.edu> wrote:

> I'd say its very likely to be orthorhombic. Refinement should tell
> you.its the best way to determine the space group anyway. Why do you
> doubt its orthorhombic? Is Vm reasonable?
> It could be monoclinic and merohedrally winned with the beta angle very
> close to 90 degrees, but my money is on orthorhombic. if refinement fails I
> would try monoclinic plus/minus twinning. As for the operators,
> xx.triage will tell you and xx.refine will apply them for you during
> refinement;-)
>
> Bert
> 
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Raji
> Edayathumangalam [r...@brandeis.edu]
> Sent: Friday, July 08, 2011 3:24 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Potential Space Group Issue
>
> Oops sorry for the slippery fingers. I meant h00, 0k0 and 00l in my
> original email and NOT "00h, 00k, 00l". Note the correction especially if
> you are a first-year graduate student trying to learn stuff from these
> emails :)
>
> Raji
>
>
>
> On Thu, Jul 7, 2011 at 11:30 PM, Raji Edayathumangalam  > wrote:
> Hello Everyone,
>
> I have a 3.1 Ang dataset for which I'd like to get to the bottom of what
> the correct space group is.
>
> The current unit cell in p212121 is 98.123   101.095   211.20190.000
>  90.00090.000
> I fed the reflection data into Xtriage to look for twinning and
> pseudotranslational NCS and there is no indication for either issue in the
> Xtriage output. Also, all odd 00h, 00k, 00l reflections are systematically
> absent as they should be for p212121.
>
> However, my colleague who is also working on the same dataset recently
> reprocessed the data in P21. Here's the cell in p21:
> 98.010  100.940  210.470  90.00  90.04  90.00 p21
>
> I am not sure if BETA=90.04 is significant enough to treat as p21 (0.04%
> deviation of beta angle from ideal lattice for p212121). I don't think so
> but I could be wrong. Could someone please clarify?
>
> Also, what kind of twinning and twinning operators can relate a p212121
> cell to a p21 cell with almost identical unit cell parameters as that of the
> p212121 cell and leave all systematic absences intact?
>
> Thanks much.
> Raji
>
>
> ---
> Raji Edayathumangalam
> Instructor in Neurology, Harvard Medical School
> Research Associate, Brigham and Women's Hospital
> Visiting Research Scholar, Brandeis University
>
>
>
>
> --
>
> --
> Raji Edayathumangalam
> Instructor in Neurology, Harvard Medical School
> Research Associate, Brigham and Women's Hospital
> Visiting Research Scholar, Brandeis University
>

Re: [ccp4bb] Potential Space Group Issue

[Van Den Berg, Bert]

I'd say its very likely to be orthorhombic. Refinement should tell you.its 
the best way to determine the space group anyway. Why do you doubt its 
orthorhombic? Is Vm reasonable?
It could be monoclinic and merohedrally winned with the beta angle very close 
to 90 degrees, but my money is on orthorhombic. if refinement fails I would try 
monoclinic plus/minus twinning. As for the operators, xx.triage will tell 
you and xx.refine will apply them for you during refinement;-)

Bert

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Raji 
Edayathumangalam [r...@brandeis.edu]
Sent: Friday, July 08, 2011 3:24 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Potential Space Group Issue

Oops sorry for the slippery fingers. I meant h00, 0k0 and 00l in my original 
email and NOT "00h, 00k, 00l". Note the correction especially if you are a 
first-year graduate student trying to learn stuff from these emails :)

Raji



On Thu, Jul 7, 2011 at 11:30 PM, Raji Edayathumangalam 
mailto:r...@brandeis.edu>> wrote:
Hello Everyone,

I have a 3.1 Ang dataset for which I'd like to get to the bottom of what the 
correct space group is.

The current unit cell in p212121 is 98.123   101.095   211.20190.000
90.00090.000
I fed the reflection data into Xtriage to look for twinning and 
pseudotranslational NCS and there is no indication for either issue in the 
Xtriage output. Also, all odd 00h, 00k, 00l reflections are systematically 
absent as they should be for p212121.

However, my colleague who is also working on the same dataset recently 
reprocessed the data in P21. Here's the cell in p21:
98.010  100.940  210.470  90.00  90.04  90.00 p21

I am not sure if BETA=90.04 is significant enough to treat as p21 (0.04% 
deviation of beta angle from ideal lattice for p212121). I don't think so but I 
could be wrong. Could someone please clarify?

Also, what kind of twinning and twinning operators can relate a p212121 cell to 
a p21 cell with almost identical unit cell parameters as that of the p212121 
cell and leave all systematic absences intact?

Thanks much.
Raji


---
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University




--

--
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University

Re: [ccp4bb] Potential Space Group Issue

[Raji Edayathumangalam]

Oops sorry for the slippery fingers. I meant h00, 0k0 and 00l in my original
email and NOT "00h, 00k, 00l". Note the correction especially if you are a
first-year graduate student trying to learn stuff from these emails :)

Raji



On Thu, Jul 7, 2011 at 11:30 PM, Raji Edayathumangalam wrote:

> Hello Everyone,
>
> I have a 3.1 Ang dataset for which I'd like to get to the bottom of what
> the correct space group is.
>
> The current unit cell in p212121 is 98.123   101.095   211.20190.000
> 90.00090.000
> I fed the reflection data into Xtriage to look for twinning and
> pseudotranslational NCS and there is no indication for either issue in the
> Xtriage output. Also, all odd 00h, 00k, 00l reflections are systematically
> absent as they should be for p212121.
>
> However, my colleague who is also working on the same dataset recently
> reprocessed the data in P21. Here's the cell in p21:
> 98.010  100.940  210.470  90.00  90.04  90.00 p21
>
> I am not sure if BETA=90.04 is significant enough to treat as p21 (0.04%
> deviation of beta angle from ideal lattice for p212121). I don't think so
> but I could be wrong. Could someone please clarify?
>
> Also, what kind of twinning and twinning operators can relate a p212121
> cell to a p21 cell with almost identical unit cell parameters as that of the
> p212121 cell and leave all systematic absences intact?
>
> Thanks much.
> Raji
>
>
> ---
> Raji Edayathumangalam
> Instructor in Neurology, Harvard Medical School
> Research Associate, Brigham and Women's Hospital
> Visiting Research Scholar, Brandeis University
>
>


-- 

--
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University

[ccp4bb] Off Topic: PDB validation server

[Katherine Sippel]

Hi all,

I am putting the finishing touches on a structure and as a good little
crystallographer I am running it through Molprobity and PDB validation to
make sure everything clears before deposition. Everything was looking
alright until I threw the file into the PDB validation server and suddenly
there are a significant number of solvents that violate the 3.5 angstrom
rule. Concerned that something had gone wrong I put an older file that I had
run through the server in April. I was shocked to discover that the file
with only one "questionable solvent" in April now has 173 of them.

I know that the PDB updated its validation server in May as described in
their news link but it seemed to indicate an increase in output options
rather than a change in criteria. Is anyone aware of  what changes were made
to the validation server in regards to the preferred geometrical and
stereochemical features?

Thanks for your time,

Katherine

[ccp4bb] Beta test versions of Mosflm & iMosflm

[Harry Powell]

Dear all

New versions of ipmosflm (7.0.8) and the matched iMosflm (1.0.6) are now 
available for beta testing.

http://www.mrc-lmb.cam.ac.uk/harry/mosflm/betas/index.html 

The changes in ipmosflm are of particular relevance to processing very weak 
Pilatus images (with background pixel values of zero), but will also have some 
beneficial effect for any fine sliced data and result in both more stable 
detector parameter refinement and improved intensity estimates. The new version 
is strongly recommended when trying to measure small anomalous differences.

The major change in iMosflm has eliminated the gradual slowing down of the rate 
of data processing when dealing with large datasets (>500 images) that is 
observed with iMosflm 1.0.5. Again, this is a particular issue with fine sliced 
Pilatus datasets.

We would welcome any feedback on the performance of the new release.


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
Cambridge, CB2 0QH

http://www.iucr.org/resources/commissions/crystallographic-computing/schools/mieres2011

Re: [ccp4bb] Unexplained density near cobalt

[Balendu Avvaru]

Hi MM,

Co in its +2 oxidation state typically forms a tetrahedrally coordinated 
species in high pH environment; and pentagonally  coordinated species with five 
ligands at low pH. A Co ion in its +3 oxidation state forms a octahedrally 
coordinated species with six ligands. Co +3 is unusual in biological molecules. 
However it is seen in crystal structures, sometimes with partial occupancy and 
is a likely product of radiation damage caused by the X-ray beam. In the past I 
have found that Co+2 is prone to oxidation in the beam if the crystallizing 
condition has a pH lower than 6.5. Here is a article you might enjoy. 

Comparison of solution and crystal properties of Co(II)-substituted human 
carbonic anhydrase II.
Avvaru BS, Arenas DJ, Tu C, Tanner DB, McKenna R, Silverman DN.

Cheers
Balu

[ccp4bb] Senior Scientist- X-Ray Crystallography & Technology

[Mitch Kocen]

Important: Do *NOT* reply to this e-mail to apply for this position.
Only applications processed through the apply link will be accepted. Any
direct replies to this e-mail will be ignored.

 

Passionate About Science

We're passionate and rigorous about our science. For more than 30 years,
Genentech has been at the forefront of the biotechnology industry, using
innovative science to develop breakthrough medicines that improve the
lives of people with serious or life-threatening diseases.

 

The following opportunity exists in our South San Francisco, CA,
headquarters: 

 

Senior Scientist- X-Ray Crystallography & Technology

 

Responsibilities:

Genentech has an opportunity for an outstanding X-ray crystallographer
to join the Genentech Structural Biology Department as a Senior
Scientist (Technology). The department encompasses protein expression,
purification, crystallography, and NMR spectroscopy, and collaborates
with scientists and project teams throughout the Research organization.
Primary job responsibilities include being an integral member of project
teams, creatively applying crystallography to structure-based drug
design, and providing strategic and managerial oversight of protein
expression, purification and crystallography approaches for projects at
all stages of the drug discovery pipeline. In addition to participation
on project teams, the successful candidate will be expected carry out
innovative research resulting in co- and lead-authored publications on
structures of therapeutic and biological importance.

 

Requirements:

This position requires a PhD in Structural Biology, Biophysics,
Biochemistry or related discipline, relevant post doctoral experience
and at least five years of additional experience as an independent
scientific investigator or group leader. The candidate must have
experience with successfully managing external resource and/or leading
multi-disciplinary project teams and a strong publication record in top
tier journals is required. Technical expertise in solving X-ray crystal
structures including hand-on operation of relevant data collection
devices and software packages is required along with an established
track record as an effective manager. The ideal candidate is a skillful
speaker at high profile internal and external forums.

 

The successful candidate will show evidence of sustained productivity,
creativity and independent contributions to science; and must also be
highly organized, motivated, work independently in a collaborative
team-oriented setting, and have strong managerial and communication
skills. The applicant must be passionate about applying structural
biology to the pursuit of drug discovery including using structure-based
drug design and carrying out cutting edge research on protein complexes
of importance to human diseases. Demonstrated scientific leadership
resulting in significant achievements either in a collaborative academic
setting or in the context of multi-disciplinary projects team in a
biotech/pharmaceutical setting is a must.

 

Passionate About Our People

We recognize that our people are our most important asset. It's why we
foster an inclusive environment that encourages diversity and offer
competitive healthcare and benefits to help you bring the best to the
business and to your personal life.

Join us as we continue to tackle medicine's most challenging problems
and live a life inspired. To apply for this job, visit
https://roche.taleo.net/careersection/test/jobapply.ftl?lang=en&job=0037
7162&src=JB-11480.

 

Now a member of the Roche Group, Genentech has multiple medicines on the
market for cancer and other serious illnesses. We are an equal
opportunity employer.

 

[ccp4bb] EMBO Practical Course on "Computational structural biology - from data to structure to function"

[Gerard DVD Kleywegt]

Hi all,

From 14-18 November, an EMBO Practical Course on "Computational structural 
biology - from data to structure to function" will be held at the EBI in 
Cambridge (UK). The course is organised by James Watson, Rosemary Wilson, 
Gerard Kleywegt, Victor Lamzin, Christine Orengo and Gert Vriend.


The course will address computational aspects of protein structure 
determination, validation and analysis. Students will learn to critically 
examine and validate data from the Protein Data Bank and use a variety of 
analysis tools to identify similarities that can help identify function. The 
course will also provide an introductory session to homology modelling for use 
with proteins less amenable to structure determination. Finally, the 
importance of protein structure to drug development will be illustrated with a 
day focussing on protein interactions, small molecules, chemoinformatics and 
docking. The course is aimed at PhD students and post-docs working on the 
collection and analysis of protein structure data. The goal is to provide them 
with insight into the protein structure determination process, how to 
critically assess the quality of data from models and also provide expertise 
in the analysis of protein structure data with a view to predicting protein 
function.


Registration for the course is now open. For more information, surf to: 
http://www.ebi.ac.uk/training/handson/course_110912_structures.html


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

Re: [ccp4bb] rosetta/ubuntu

[Alexander Batyuk]

Hi Harry,

Recently I successfully compiled rosetta 3.2.1 with gcc 4.5 following these 
hints:


***
from http://morganbye.net/blog/2011/05/rosetta-32-ubuntu-1104

Rosetta 3.2 with Ubuntu 11.04
Rosetta is a very useful program for the prediction of protein structure, 
folding and interactions be that docking with proteins or ligands.

However, the current version of Rosetta (3.2.1) uses SCons to compile itself on 
your system. This is usually fine except that these use gcc libraries 4.1 and 
before.

Ubunutu 11.04 considers anything before gcc v4.4 to be obsolete and you can't 
install them (even with apt-get).

As a result, a small amount of hacking is required.

First get SCons. Open a new terminal window.

sudo apt-get install scons

Check that the file tree has been updated

sudo apt-get update

Now you can unzip your Rosetta download to wherever you like. I personally put 
new software into /opt

Change your terminal window to the correct path. So in my case

cd /opt/rosetta

Now in a perfect world, and according to the installation instructions you 
should be able to type:

scons bin mode=release

And Rosetta will install and compile itself. However, amongst a load of other 
errors you'll see the root of the problem

 

KeyError: "Unknown version number 4.5 for compiler 'gcc'"

Now, the first thing I tried was to specify a fixed gcc version for SCons to run

 

scons bin mode=release cxx=gcc cxx_ver=4.4

But this doesn't work as gcc v4.4 is still too new. And any version before 4.4 
isnt supported by Ubuntu.

The solution

This isnt a short or elegant solution, but it is a solution that got Rosetta to 
install for me. If you have any troubles yourself I recommend you head on over 
to the Rosetta forums.

Install zlib

Install zlib (developer version) to ensure all your necessary libraries are 
installed

sudo apt-get install zlib1g-dev
sudo apt-get update

basic.settings

In /rosetta_path/tools/build there is the file basic.settings

At line 203, I needed to add

 

"gcc, 4.5" : {
"appends" : {
"version"   : [ "4", "5" ],
"flags" : {
"compile"   : [ "-param inline-unit-growth=1000",
"-param large-function-growth=5" ],
},
},
},
I didnt change line 329 but you can for completeness if you so wish.

options.settings

 

In /rosetta_path/tools/build there is the file options.settings

Line 11 and 12 now read

"cxx" : {
"gcc" : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "*" 
],
So as to include v4.4 and 4.5

util.cc

Finally and most importantly, in  /rosetta_path/src/core/conformation/symmetry 
open util.cc. At line 357 there is an if statement. What we need to do is 
change the "else" argument so that the reference is correct (I've commented out 
the old line)

 

#ifdef WIN32
pose::PDBInfoOP pdb_info_src (new pose::PDBInfo( pose.pdb_info() ));
#else
/// pose::PDBInfoOP pdb_info_src = new pose::PDBInfo::PDBInfo( pose.pdb_info() 
);
pose::PDBInfoOP pdb_info_src = new pose::PDBInfo( pose.pdb_info() );
#endif
Apparently this is required as the new versions of gcc are fussier about their 
name references than older versions.
 
After which we can now go back to the terminal and type:

scons bin mode=release cxx=gcc cxx_ver=4.5

After some amount of processing time (~30mins on my dual core 2.8 GHz), you 
should be greeted with the final lines

 

Install file: 
"build/src/release/linux/2.6/64/x86/gcc/4.5/super_aln.linuxgccrelease" as 
"bin/super_aln.linuxgccrelease"
scons: done building targets.
 
 
Credit goes to those on the Rosetta forums for help.


qrsh -cwd ./scons.py bin mode=release cxx=gcc cxx_ver=4.5 extras=static -j16 
doesn't work

the working solution:

qlogin
module load gcc/4.5.0
/scons.py bin mode=release cxx=gcc cxx_ver=4.5 -j16
exit


***


Best wishes,

Alex



On 8 Jul 2011, at 15:21, Harry Xu wrote:

> Hi, everyone on board.
> I want to try mr_rosetta for my project, but I had problem installing rosetta 
> on my computer. My computer is running ubuntu 11.04 with gcc 4.5. Compiling 
> of rosetta 3.2 failed with the message: KeyError: "Unknown version number 4.5 
> for compiler 'gcc'" .
> I want to know whether anybody had any experience install rosetta in ubuntu? 
> Or do I need to change to a different linux distribution? If so, what linux 
> distribution is best for running most of the main stream crystallography 
> software?
> thanks in advance.
>  
> Harry

--
Alex Batyuk
Lab of Prof. Dr. A. Plueckthun
Biochemistry Institute
University of Zurich
Winterthurerstrasse 190
8057 Zurich, Switzerland
Phone: +41 44 635 5574

Re: [ccp4bb] rosetta/ubuntu

[Chris Richardson]

On 8 Jul 2011, at 14:21, Harry Xu wrote:

> I want to try mr_rosetta for my project, but I had problem installing rosetta 
> on my computer. My computer is running ubuntu 11.04 with gcc 4.5. Compiling 
> of rosetta 3.2 failed with the message: KeyError: "Unknown version number 4.5 
> for compiler 'gcc'" .

There's a good summary of the problem and a proposed solution here:

  http://morganbye.net/blog/2011/05/rosetta-32-ubuntu-1104

I haven't tried this myself, but I've done something similar to get it working 
with Intel compilers on an SGI ICE cluster.

Basically, Rosetta uses SCons to compile itself.  SCons has, among its many 
configuration files, one that lists the compiler versions it is prepared to use 
and any compiler-specific options that go with them.  gcc 4.5 is relatively new 
and not in the config files included with rosetta.  Editing the files and 
adding 4.5 as an acceptable compiler should fix the problem.

Note that the author of the blog post also has a fix for a piece of code that 
gcc v4.5 rejects on syntactical grounds.

Regards,

Chris
--
Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk


The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

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[ccp4bb] rosetta/ubuntu

[Harry Xu]

Hi,
everyone on board.
I
want to try mr_rosetta for my project, but I had problem installing rosetta on
my computer. My computer is running ubuntu 11.04 with gcc 4.5. Compiling of
rosetta 3.2 failed with the message: KeyError: "Unknown version number 4.5
for compiler 'gcc'" .
I
want to know whether anybody had any experience install rosetta in ubuntu? Or
do I need to change to a different linux distribution? If so, what linux
distribution is best for running most of the main stream crystallography
software?
thanks
in advance.
 
Harry 

Re: [ccp4bb] Potential Space Group Issue

[Ed Pozharski]

Raji,

Assuming that the real space group is P212121, in P21 you will still get
a solution except for the extra NCS which will closely resemble the
extra 2-fold screw.  Then you can probably tell if there are any
significant differences between NCS-related copies that justify lower
symmetry space group.  It's not impossible, as Fred points out, that P21
is the true space group, but I think most people here would agree it may
be less likely.  Did your colleague actually try going orthorhombic?

One possibility is that symmetry breakdown results from lattice
distortion upon cryocooling.  I would expect that shifts/rotations are
small and naturally the effect on the refinement is
resolution-dependent.  I am sure there are more examples in the
literature, but this one should hit close to the hills of Waltham:

http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0040099

which is PDB ID 2PZV - check out that P1 with beta=89.98.  Colonel Pybus
could tell you more (if the brass lets him, of course :), but what I
recall is that most of the time and at lower resolution KSI can be
processed in C2221 without problems.  With that particular dataset (and
the goal was to get as high resolution as possible to discern minute
changes in hydrogen bonds) it processed fine too, except that R-values
stayed a little too high (lower 20s?) for authors comfort.  But they do
go down significantly in P1.

However, you are at much lower resolution.  My own unpublished example
was at 2.4A, processed fine in C2221, gave a clear MR solution, but then
stayed in R~40% zone and had every loop missing in electron density.
Turned out to be P21 with NCS resembling higher symmetry just enough to
confuse denzo (and me).

I guess the message is that everything is P1 and higher symmetry is just
a dream within a dream so you can experience a drop at any time :)

Cheers,

Ed.

On Thu, 2011-07-07 at 23:30 -0400, Raji Edayathumangalam wrote:
> Hello Everyone,
> 
> I have a 3.1 Ang dataset for which I'd like to get to the bottom of
> what the correct space group is.
> 
> The current unit cell in p212121 is 98.123   101.095   211.201
> 90.00090.00090.000
> I fed the reflection data into Xtriage to look for twinning and
> pseudotranslational NCS and there is no indication for either issue in
> the Xtriage output. Also, all odd 00h, 00k, 00l reflections are
> systematically absent as they should be for p212121.
> 
> However, my colleague who is also working on the same dataset recently
> reprocessed the data in P21. Here's the cell in p21:
> 98.010  100.940  210.470  90.00  90.04  90.00 p21
> 
> I am not sure if BETA=90.04 is significant enough to treat as p21
> (0.04% deviation of beta angle from ideal lattice for p212121). I
> don't think so but I could be wrong. Could someone please clarify? 
> 
> Also, what kind of twinning and twinning operators can relate a
> p212121 cell to a p21 cell with almost identical unit cell parameters
> as that of the p212121 cell and leave all systematic absences intact?
> 
> Thanks much.
> Raji
> 
> 
> ---
> Raji Edayathumangalam
> Instructor in Neurology, Harvard Medical School
> Research Associate, Brigham and Women's Hospital
> Visiting Research Scholar, Brandeis University
> 

-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
--   / Lao Tse /

[ccp4bb] Postdoc and PhD student opportunities in multidisciplinary ribosome research

[Maria Selmer]

RiboCORE http://www.icm.uu.se/ribocore/, a newly established center  
for multidisciplinary ribosome studies at Uppsala University, Sweden,  
is looking for a number of outstanding postdoctoral fellows with an  
interest for multidisciplinary research and PhD degrees in for example  
structural biology, molecular biology, single molecule biophysics,  
biochemistry, genetics, microscopy and image analysis, microbiology or  
computational chemistry.  Excellent skills in spoken and written  
English is an absolute requirement.


If you are interested, please send an email to riboc...@icm.uu.se  
including a brief statement of research interests and a CV including  
list of publications before 1 Aug 2011.


We also recruit several PhD students. For more information and  
application procedures see the following link: http://www.personalavd.uu.se/ledigaplatser/1609PhD.html


Best regards
/Maria

Maria Selmer, PhD, docent   
Assistant Professor 
Cell and Molecular Biology, Uppsala University
BMC, Box 596
SE-75124 Uppsala
Sweden

Telephone: +46-(0)18-4714177
Fax: +46-(0)18-536971

[ccp4bb] Postdoctoral position in protein crystallography in Durham (UK)

[POHL E.]

Applications are invited for a Wellcome Trust postdoctoral position for two 
years at the Biophysical Sciences Institute at Durham University.

The aim of the project is to investigate the structure and function of 
phospholipases from the opportunistic pathogen Pseudomonas aeruginosa. 
The successful applicant will be part of a team that uses a combination of 
biophysical and structural methods to establish the molecular basis 
of activity. The primary technique employed will be protein crystallography. 
Protein purification and crystallisation conditions have been already 
been established. The post-holder will be responsible for sample preparation, 
crystallisation and data collections at the synchrotron with the 
ultimate goal of solving the crystal structure of the target proteins and their 
complexes with substrates and inhibitors.  Further information 
can be found here: http://www.dur.ac.uk/jobs/,
informal enquiries should be directed to ehmke.p...@durham.ac.uk.

--
Dr. Ehmke Pohl
Reader in Protein Crystallography
Biophysical Sciences Institute
Durham University
Durham DH1 3LE
United Kingdom

tel: +44 (0)191 334 3619
e-mail: ehmke.p...@durham.ac.uk
--

Re: [ccp4bb] Crystallographic Computing School - Mieres, Spain

[Harry Powell]

Dear all

We still have a few places available, so we have decided to extend the 
registration deadline - so if anyone wants to come who hasn't registered 
already, you still have an opportunity to do so.


http://www.iucr.org/resources/commissions/crystallographic-computing/schools/mieres2011

Unfortunately we have no more bursaries!

On 2 Mar 2011, at 18:24, harry powell wrote:

> Dear all
> 
> The registration website is now live - see
> 
>   
> http://www.iucr.org/resources/commissions/crystallographic-computing/schools/mieres2011
> 
> We had to change venue at a late stage, so although we are still calling it 
> the "Mieres" School, it is now going to take place in Oviedo, about 20km up 
> the road.
> 
> 
> On 8 Jan 2011, at 11:33, harry powell wrote:
> 
>> Dear all
>> 
>> Those of you who attended the CCP4 Study "Weekend" at Warwick University 
>> this week (either in vivo or in silico), and who stayed to the end will 
>> remember Roberto Steiner's suggestion that some of the younger members of 
>> the audience may wish to become involved in software development themselves.
>> 
>> The IUCr Commission on Crystallographic Computing ("CompComm") will be 
>> holding a Computing School immediately before the Madrid IUCr General 
>> Assembly and Congress this August that is intended to expose younger members 
>> of the Crystallographic community to the knowledge and experience of senior 
>> developers across the whole science. CCP4BB readers will possibly be most 
>> interested in those developers in macromolecular crystallography; the 
>> following people in this field have accepted our invitations to speak -
>> 
>>  Paul Emsley
>>  Ralf Grosse-Kunstleve
>>  Garib Murshudov
>>  George Sheldrick
>>  Tom Terwilliger
>> 
>> There are many other speakers who will concentrate on their own specialities 
>> (e.g. powder diffraction, small-molecule crystallography), but who will 
>> offer food for thought for all.
>> 
>> The School is intended for prospective (or current...) developers, not to 
>> help those people who just want to run the programs better. Registration 
>> will be open to all, but priority will be given to postgrads and postdocs; 
>> we hope to have a number of bursaries available for applicants from less 
>> economically favoured regions.
>> 
>> We are still finalising items such as the registration fee, but I expect to 
>> be able to make the website live by the end of January with more 
>> comprehensive details.
>> 
>> Watch this space...
>> 
>> Harry
>> --
>> Dr Harry Powell,
>> MRC Laboratory of Molecular Biology,
>> Hills Road,
>> Cambridge,
>> CB2 0QH
>> 
>> Treasurer British Crystallographic Association
>> Chairman ECA SIG9 (Crystallographic Computing)
>> Acting Chairman IUCr Commission on Crystallographic Computing
> 
> Harry
> --
> Dr Harry Powell,
> MRC Laboratory of Molecular Biology,
> Hills Road,
> Cambridge,
> CB2 0QH

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
Cambridge, CB2 0QH

http://www.iucr.org/resources/commissions/crystallographic-computing/schools/mieres2011