Re: [ccp4bb] Align linux version

[mesters]

Back in 2003 I wrote an email to Gerson Cohen concerning ALIGN and he 
told me to contact Boaz Shaanan.


Boaz was so kind to send me his linuxified fortran code of the align 
program (reading of a prealigment could not be implemented) that is 
still working on our linux machines! We use it a lot, great program.


Ask Boaz (but not all at once please :-) )!!

- J. -


Am 10.11.13 22:09, schrieb Tim Gruene:


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Mintu Chandra,

Do you mean by 'has linux compiled align version', that 'align' is a
program you use for the alignment? I wonder because I have not heard
of it.

If you would be happy with any alignment software, you could use coot
(graphical) or lsqkab (command line). Both programs areavailable once
you installed ccp4.

Regards,
Tim Gruene




--

Dr. Jeroen R. Mesters

Gruppenleiter Strukturelle Neurobiologie und Kristallogenese
Institut für Biochemie
Universität zu Lübeck
Zentrum für Medizinische Struktur- und Zellbiologie
Ratzeburger Allee 160, D-23538 Lübeck
Tel: +49-451-5004065
Fax: +49-451-5004068
Http://www.biochem.uni-luebeck.de
Http://www.iobcr.org
Http://www.selfish-brain.org
Http://www.opticryst.org
--
Any intelligent fool can make things bigger and more complex. It takes a 
lot of genius and a lot of courage to move in the opposite direction 
(Albert Einstein, 1879-1955)


Ifyou can look into the seeds of time and say which grain will grow and 
which will not - speak then to me(Macbeth)

--
Disclaimer
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Re: [ccp4bb] Spam:Re: [ccp4bb] Align linux version

[Boaz Shaanan]

Hi Jeroen,


Indeed, I did write to the original poster about this, asking him if he really meant Gerson Cohen's align program in his post, in which case I would be happy to send it to him. I still have the linux version but, as others have pointed out, there are new
 kids on the block that do the job. In fact, I myself don't use align these days, nor am I sure that the version I have will handle the v3 pdb's properly.


  Cheers,


            Boaz





 
 
Boaz Shaanan, Ph.D.

Dept. of Life Sciences  
Ben-Gurion University of the Negev  
Beer-Sheva 84105    
Israel  
    
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan  
Fax:   972-8-647-2992 or 972-8-646-1710
 
 








From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of mesters [mest...@biochem.uni-luebeck.de]
Sent: Monday, November 11, 2013 11:19 AM
To: בעז שאנן
Subject: Spam:Re: [ccp4bb] Align linux version




Back in 2003 I wrote an email to Gerson Cohen concerning ALIGN and he told me to contact Boaz Shaanan.

Boaz was so kind to send me his linuxified fortran code of the align program (reading of a prealigment could not be implemented) that is still working on our linux machines! We use it a lot, great program.


Ask Boaz (but not all at once please :-) 
)!!

- J. -


Am 10.11.13 22:09, schrieb Tim Gruene:



-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Mintu Chandra,

Do you mean by 'has linux compiled align version', that 'align' is a
program you use for the alignment? I wonder because I have not heard
of it.

If you would be happy with any alignment software, you could use coot
(graphical) or lsqkab (command line). Both programs areavailable once
you installed ccp4.

Regards,
Tim Gruene





-- 


Dr. Jeroen R. Mesters

Gruppenleiter Strukturelle Neurobiologie und Kristallogenese
Institut für Biochemie
Universität zu Lübeck
Zentrum für Medizinische Struktur- und Zellbiologie
Ratzeburger Allee 160, D-23538 Lübeck
Tel: +49-451-5004065
Fax: +49-451-5004068
Http://www.biochem.uni-luebeck.de
Http://www.iobcr.org
Http://www.selfish-brain.org
Http://www.opticryst.org
--
Any intelligent fool can make things bigger and more complex. It takes a lot of genius and a lot of courage to move in the opposite direction (Albert Einstein, 1879-1955)
If
you can 
look into the 
seeds of time and 
say which grain will
grow and 
which will not - speak then
to me  
(Macbeth)
--
Disclaimer
* Employees of 
the Institute are expressly
required not to 
make defamatory statements
and not to 
infringe or authorize
any infringement 
of copyright or 
any other legal right
by email communications. 
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policy and outside the
scope of 
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the individual concerned. The Institute will not
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communication, and 
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be personally 
liable for any 
damages or other 
liability arising. Employees
who receive such an email must
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supervisor immediately. 
* This message contains 
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[ccp4bb] Senior Scientist / Group leader Position (tenure-track); Institute of Biochemistry, Biocenter, Goethe-University Frankfurt

[Martin Pos]

Dear all, 

I am posting an advertisement for a tenure-track group leader position for
structural biology on membrane proteins on behalf of Prof. Dr. Robert Tampé,
Institute of Biochemistry, Biocenter, Goethe-University Frankfurt. Please
reply to  
applicat...@biochem.uni-frankfurt.de for questions and/or application.
Deadline is November 30th, 2013.

With kind regards,

Martin Pos

Senior Scientist / Group leader Position (tenure-track)

Structural Biology on Membrane Proteins

Institute of Biochemistry, Biocenter, Goethe-University Frankfurt

 

A senior scientist position is available to join a research group interested
in investigating the structure and mechanism of membrane transport complexes
involved in immunity, viral and tumor immune evasion. The position funded
for two years (with a renewal for long-term carrier perspective as
tenure-track group leader position) is embedded in a lively and
international competitive research environment, including the Cluster of
Excellence on Macromolecular Complexes ( 
www.cef-mc.de) and the Collaborative Research Center on Membrane Transport
and Communication (  www.sfb807.de).

Candidates having proved their outstanding commitment to science by a prior
experimental thesis in biochemistry, molecular biology, structural biology,
or a closely related field are encouraged to apply. The successful candidate
should have significant experience in x-ray crystallography and present a
strong publication record in quality peer-reviewed journals. The position
also includes radiation survey, supervision of the central isolab, of the
central gene technical security S1, and of the S2/S3 lab together with the
organization and mentoring of the practical courses. Parallel to previously
mentioned scientific tasks, the successful candidate will be given
opportunity to promote her/his own scientific career and to acquire further
qualifications.

Very good IT skills, teaching experience, creative thinking, the ability to
work independently as well as collaboratively so as to lead a small team of
(under)graduate students are required.

Interested applicants are to send till November 30th 2013 an application
containing CV, summary of past research experience and accomplishments
together with names/contact information of two references to: Robert Tampé,
Institute of Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9,
60438 ( 
applicat...@biochem.uni-frankfurt.de).

Reference: 
Hulpke S &Tampé R (2013) Trends Biochem Sci 38, 412-20.
Parcej D & Tampé R (2010) Nature Chem Biol 6, 572-580.

 

 

 

[ccp4bb] Postdoctoral Position – EMBL Heidelberg

[Christoph Mueller]

Dear Colleagues,

A Postdoctoral position is available in the group of Christoph Müller, 
EMBL Heidelberg, Germany to structurally and functionally characterize 
multi-protein complexes involved in RNA polymerase I transcription using 
the combination of X-ray crystallography, electron microscopy and 
biochemistry. The successful candidate will join the Christoph Müller 
group at the Structural and Computational Biology Unit at EMBL 
Heidelberg. EMBL is a leading international research organization with a 
collaborative and interdisciplinary atmosphere (see http://www.embl.de). 
The Müller group studies molecular mechanisms of eukaryotic 
transcriptional regulation. Further details are available at 
http://www.embl.de/research/units/scb/mueller_christoph/index.html.


The position requires an outstanding candidate with strong interest in 
the characterization of challenging multi-protein complexes using 
integrated structural biology approaches. The successful candidate holds 
a PhD in structural biology or biochemistry. Previous experience in the 
purification and biochemical analysis of multi-protein complexes and/or 
previous experience in X-ray crystallography or single-particle electron 
microscopy would be an advantage. The position requires exceptional 
motivation and commitment, the ability to work independently as well as 
in a team and excellent technical, organizational and management skills. 
Further details regarding work in the laboratory and details of the 
projects can be directly obtained from Christoph W. Müller 
(cmuel...@embl.de). EMBL is an inclusive, equal opportunity employer 
offering attractive conditions and benefits appropriate to an 
international research organisation. Please apply online through 
http://www.embl.org/jobs


--

Dr. Christoph W. Müller
Joint Head of Structural and Computational Biology Unit

EMBL
Meyerhofstrasse 1
69117 Heidelberg, Germany

email: cmuel...@embl.de
phone: 0049-6221-387-8320
fax: 0049-6221-387-519
http://www.embl.de
-

[ccp4bb] molprobity

[SD Y]

Hi,
I was wondering if molprobity server is down 
(http://molprobity.biochem.duke.edu/index.php) or its just my files or our 
network has problem because I cant upload my files (some times it gave error).
ThanksSDY 

[ccp4bb] molprobity

[Tanner, John J.]

I encountered the same problem last night.   The server won't upload the PDB 
file.  I didn't check this morning.


On Nov 11, 2013, at 10:02 AM, SD Y wrote:

Hi,

I was wondering if molprobity server is down 
(http://molprobity.biochem.duke.edu/index.php) or its just my files or our 
network has problem because I cant upload my files (some times it gave error).

Thanks
SDY



John J. Tanner
Professor of Biochemistry  and Chemistry
University of Missouri-Columbia
125 Chemistry Building
Columbia, MO  65211
email: tanne...@missouri.edu
phone: 573-884-1280
fax: 573-882-2754
web: http://www.chem.missouri.edu/tannergroup/tanner.html

[ccp4bb] Cyro cooling system

[Uday Kumar]

Hello

We are planning to buy a small cryo cooling unit for protein crystal cooling 
which can manage 100 K temp. 

we are limited with space and only small units like Oxford cryosystem Desktop 
cooler or any of that dimensions can fit.

Does anybody has some suggestions in this regard.

Would be nice if someone has some information regarding the use of  Oxford 
cryosystem Desktop cooler for protein crystals.

Thank you

Re: [ccp4bb] Cyro cooling system

[Mark van der Woerd]

Hi Uday,

I would simply ask Oxford for advice, I have never regretted asking them (or 
most others) for advice. On their web site it is written that the Desktop 
Cooler only goes down to 170K, so that will not do, I don't think. In fact, 
they only make two suggestions when you go through their product selection 
process and neither one of those is very small.

We are very happy with our Oxford system (used for protein crystallography) but 
small it is not.

Mark


 

 

 

-Original Message-
From: Uday Kumar 
To: CCP4BB 
Sent: Mon, Nov 11, 2013 10:22 am
Subject: [ccp4bb] Cyro cooling system


Hello

We are planning to buy a small cryo cooling unit for protein crystal cooling 
which can manage 100 K temp. 

we are limited with space and only small units like Oxford cryosystem Desktop 
cooler or any of that dimensions can fit.

Does anybody has some suggestions in this regard.

Would be nice if someone has some information regarding the use of  Oxford 
cryosystem Desktop cooler for protein crystals.

Thank you

 

Re: [ccp4bb] molprobity

[SD Y]

It works now. Thanks for fixing.
Sincerely,SDY
Date: Mon, 11 Nov 2013 16:13:52 +
From: tanne...@missouri.edu
Subject: [ccp4bb] molprobity
To: CCP4BB@JISCMAIL.AC.UK







I encountered the same problem last night.   The server won't upload the PDB 
file.  I didn't check this morning. 





On Nov 11, 2013, at 10:02 AM, SD Y wrote:



Hi,



I was wondering if molprobity server is down 
(http://molprobity.biochem.duke.edu/index.php) or its just my files or our 
network has problem because I cant
 upload my files (some times it gave error).



Thanks
SDY












John
 J. Tanner

Professor of Biochemistry  and Chemistry
University
 of Missouri-Columbia

125 Chemistry Building

Columbia, MO  65211

email: tanne...@missouri.edu

phone: 573-884-1280

fax: 573-882-2754

web: http://www.chem.missouri.edu/tannergroup/tanner.html







  

[ccp4bb] lib32gfortran3 needed for 64-bit ccp4?

[Roger Rowlett]

Just ran into an error running SORTMTZ in CCP4-6.4.0. Looks like SORTMTZ 
requires libgfortran.so.3 32-bit version. I get an error message of the 
missing library if I do not install lib32gfortran3 (32-bit fortran 
libraries). Should this still be necessary for the 64-bit CCP4? I'll 
keep this package on my client workstation install list for now.


Thanks,
___
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu

Re: [ccp4bb] help on preparing EM map for mask generation and molecular replacement

[Viswanathan Chandrasekaran]

Hi Fei:

I once had the same error message when using an EM map as an MR model. To make 
this work, you need to change your map's axis order from XYZ to whatever is 
appropriate (in my case it was ZXY) and also change the spacegroup to P1 using 
the CCP4 program "maputils".

In the CCP4i GUI, you do as follows:
1) Go to maputils: "Map and Mask Utilities" -> "Edit/Rotate Maps & Masks".
2) Choose "Edit a map/mask file" for a "map" file.
3) Choose your map as input and choose an appropriate output file name.
4) Under the "Edit file" section, enter "Space group" as 1 and "Change axis 
order to" ZXY. You can get this from mapman's header when you load the map or 
CCP4 log file header from the failed SFall run. Alternatively, you could try 
all possibilities in the drop-down list.

SFall should run fine using the output map from maputils.

Best,
Vish



-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Fei Li
Sent: Sunday, November 10, 2013 4:33 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] help on preparing EM map for mask generation and molecular 
replacement

Dear experts,

I'm planning to use a EM map to generate a mask for density modification and 
also potentially use it in molecular replacement. But I'm stuck on how to make 
this EM map to behave now.

The original EM map was a reconstruction from 2D helical tube. The file was 
huge (containing several layer of the protein) and ended with .map. Our 
computation collaborator had already cut out a dimer, which is what I'm 
interested in, and put it into a small unit cell just slightly bigger than the 
dimer density. this file is ended with .mrc.  
I can open both file with coot and chimera fine. I tried to convert the dimer 
map into a .mtz file but when I try to use any of the ccp4 program (sfall, 
mapman etc), I always get error message on something like "map and mask grid 
samplings do not match", "Fatal disagreement between input info and map header" 
or "Incorrect sampling grid factors
  40  29  45". I'm thinking it may be the unit cell that it is already in. But 
as I'm not familiar with Chimera, I couldn't figure out how to remove it. Also, 
how to choose and/or specify a proper grid? Any suggestion on how to make this 
EM map to work is high appreciated.  
Thank you very much!

Best regards,

Fei

Fei LI
Graduate Assistant
310 Biochemistry Building
Department of Biochemistry and Molecular Biology Michigan State University East 
Lansing, MI
48824

Re: [ccp4bb] help on preparing EM map for mask generation and molecular replacement

[Edward A. Berry]

You may also have to change your grid for the fft ("resampling" in photoshop parlance). 
From the sfall documentation:

 Different spacegroups have special requirements
   for factorisation. No prime factors higher than 19 are permitted (The
   `atom map' generated on this grid has the asymmetric unit defined for
   this spacegroup. See table below .).

   The following general restrictions must be observed:
   >= 2 * HMAX + 1
   >= 2 * KMAX + 1
   >= 2 * LMAX + 1

   In addition there are further space group dependent conditions as
   follows (where `n' is an integer, i.e.  must be even, for
   instance):

 P1-2n   2n
 P21   2n   4n   2n
 P212124n   4n   4n
 P21212a   ''   ''   ''
 P212121   ''   ''   ''
 P4122/P4322   4n   4n   8n
 P41212/P43212 ''   ''   ''
 P31/P32   6n   6n   6n
 P3/R3 ''   ''   ''
 P3121/p3221   ''   ''   ''
 P61/P65   6n   6n  12n


Viswanathan Chandrasekaran wrote:

Hi Fei:

I once had the same error message when using an EM map as an MR model. To make this work, 
you need to change your map's axis order from XYZ to whatever is appropriate (in my case 
it was ZXY) and also change the spacegroup to P1 using the CCP4 program 
"maputils".

In the CCP4i GUI, you do as follows:
1) Go to maputils: "Map and Mask Utilities" -> "Edit/Rotate Maps & Masks".
2) Choose "Edit a map/mask file" for a "map" file.
3) Choose your map as input and choose an appropriate output file name.
4) Under the "Edit file" section, enter "Space group" as 1 and "Change axis order 
to" ZXY. You can get this from mapman's header when you load the map or CCP4 log file header from the 
failed SFall run. Alternatively, you could try all possibilities in the drop-down list.

SFall should run fine using the output map from maputils.

Best,
Vish



-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Fei Li
Sent: Sunday, November 10, 2013 4:33 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] help on preparing EM map for mask generation and molecular 
replacement

Dear experts,

I'm planning to use a EM map to generate a mask for density modification and 
also potentially use it in molecular replacement. But I'm stuck on how to make 
this EM map to behave now.

The original EM map was a reconstruction from 2D helical tube. The file was 
huge (containing several layer of the protein) and ended with .map. Our 
computation collaborator had already cut out a dimer, which is what I'm 
interested in, and put it into a small unit cell just slightly bigger than the 
dimer density. this file is ended with .mrc.
I can open both file with coot and chimera fine. I tried to convert the dimer map into a .mtz file but 
when I try to use any of the ccp4 program (sfall, mapman etc), I always get error message on something 
like "map and mask grid samplings do not match", "Fatal disagreement between input info 
and map header" or "Incorrect sampling grid factors
   40  29  45". I'm thinking it may be the unit cell that it is already in. But 
as I'm not familiar with Chimera, I couldn't figure out how to remove it. Also, how 
to choose and/or specify a proper grid? Any suggestion on how to make this EM map to 
work is high appreciated.
Thank you very much!

Best regards,

Fei

Fei LI
Graduate Assistant
310 Biochemistry Building
Department of Biochemistry and Molecular Biology Michigan State University East 
Lansing, MI
48824

Re: [ccp4bb] Align linux version

[Dyda]

Please correct me if I'm wrong, but I think lsqman implements G. Cohen's 
operator
improvement in DP_improve. Assuming of course if that was the reason why someone
wanted to use align.

Fred
***
Fred Dyda, Ph.D.   Phone:301-402-4496
Laboratory of Molecular BiologyFax: 301-496-0201
DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov  
Bldg. 5. Room 303 
Bethesda, MD 20892-0560  URGENT message e-mail: 2022476...@mms.att.net
Google maps coords: 39.000597, -77.102102
http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred
***

Re: [ccp4bb] lib32gfortran3 needed for 64-bit ccp4?

[Marcin Wojdyr]

On Mon, Nov 11, 2013 at 03:15:46PM -0500, Roger Rowlett wrote:
> Just ran into an error running SORTMTZ in CCP4-6.4.0. Looks like
> SORTMTZ requires libgfortran.so.3 32-bit version. I get an error
> message of the missing library if I do not install lib32gfortran3
> (32-bit fortran libraries). Should this still be necessary for the
> 64-bit CCP4? I'll keep this package on my client workstation install
> list for now.

Is it Linux? Could you copy the error message?
No 32-bit libraries should be needed.
Could you also copy the output of:

which sortmtz
ldd /path/to/ccp4-6.4.0/bin/sortmtz
md5sum /path/to/ccp4-6.4.0/bin/sortmtz

Regards
Marcin
-- 
Scanned by iCritical.

[ccp4bb] Beamline scientist position at SLS

[Meitian Wang]

Please find the link to the advertised BLS position 
http://www.psi.ch/pa/offenestellen/0601-1.

Beamline Scientist 
Protein Crystallography Beamlines at SLS
Your tasks
As a beamline scientist you will join a team effort to operate, maintain and 
develop protein crystallography beamlines at the SLS. You are expected to 
contribute in some of the current activities of the macromolecular 
crystallography, i.e. micro-focusing beamline upgrade, novel crystallographic 
data acquisition, phasing methods with advanced beamline instrumentation and 
next generation pixel-array detectors, automation of in-situ diffraction 
screening, as well as development of integrated software from beamline control 
to advanced data acquisition and analysis.
Your profile
You hold a PhD degree in physics or (bio-) / chemistry and have extensive 
experience in protein crystallography at synchrotron radiation sources. 
Knowledge in programming is a plus. If you are a good team player with fine 
communication skills and sense of responsibility, this position will offer a 
great opportunity for you to develop your research career in an exciting and 
highly multidisciplinary environment.

For further information please contact Dr Meitian Wang, phone +41 56 310 41 75.

Please submit your application online (including list of publications and 
addresses of referees) for the position as a Beamline Scientist (index no. 
6112-02).

Paul Scherrer Institut, Human Resources, Elke Baumann, 5232 Villigen PSI, 
Switzerland

__
Meitian Wang, Ph.D.
Head of Macromolecular Crystallography Group
Swiss Light Source at Paul Scherrer Institut
CH-5232 Villigen PSI - http://www.psi.ch/sls/
Phone: +41 56 310 4175