[ccp4bb] Open postdoc positions in the Gonen lab

[Johan Hattne]

Dear all;

We would like to draw your attention to two HHMI-funded postdoc 
positions in the laboratory of Tamir Gonen at the University of 
California, Los Angeles.  The first position concerns the biochemistry 
of membrane proteins, the second is focused on computational methods 
development. For further information, as well as application 
instructions, see the links below.


Biochemistry
https://hhmi-openhire.silkroad.com/epostings/index.cfm?fuseaction=app.jobinfo=23=1194_id=16908=2=ONLINE=992841=levelid1=36316=2

Programming
https://hhmi-openhire.silkroad.com/epostings/index.cfm?fuseaction=app.jobinfo=23=1195_id=16908=2=ONLINE=992841=levelid1=36316=2

// Best wishes; Johan



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Re: [ccp4bb] {Disarmed} Re: [ccp4bb] CCP4 7.1 problems

[Andrew Purkiss-Trew]

I had a similar problem with the beta. Do the different systems have  
different processor manufacturers? At that point, a couple of weeks  
ago, the relevant code then ran fine on Intel processors, but crashed  
on AMD. However, this was part of the CCP4Cloud software, I2 seemed to  
work fine after some limited testing.


Andy


Quoting Edward Lowe :

I have also experienced the exact problem below on trying to launch  
ccp4i2 - but only on one of the four Ubuntu systems I have installed  
ccp4-7.1 on.



Running CCP4i2 browser from: /home/rob/CCP4/ccp4-7.1/share/ccp4i2
Python 2.7.16 (default, Apr 22 2020, 09:15:14)
[GCC 4.9.1 20140922 (Red Hat 4.9.1-10)]
Qt version 4.8.7
Illegal instruction

Then, back to the prompt.




Dr. E.D. Lowe
edward.l...@bioch.ox.ac.uk

Department of BiochemistryTel: ++44 (0)1865 275392
University of Oxford
Oxford UK, OX1 3QU

From: CCP4 bulletin board  On Behalf Of  
Robert S Phillips

Sent: 24 April 2020 14:01
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CCP4 7.1 problems

I installed CCP4 7.1 yesterday, and I have problems.  On an Ubuntu  
18.04 LTS system, I get the following:


rob@rob-SA76R4:~$ ccp4i2
Running CCP4i2 browser from: /home/rob/CCP4/ccp4-7.1/share/ccp4i2
Python 2.7.16 (default, Apr 22 2020, 09:15:14)
[GCC 4.9.1 20140922 (Red Hat 4.9.1-10)]
Qt version 4.8.7
Illegal instruction

Then, back to the prompt.

Similarly, with COOT:

rob@rob-SA76R4:~$ coot
INFO:: Reading coordinate file:  
/home/rob/CCP4/ccp4-7.1/share/coot/standard-residues.pdb
INFO:: file /home/rob/CCP4/ccp4-7.1/share/coot/standard-residues.pdb  
has been read.

Spacegroup: P 1
/home/rob/CCP4/ccp4-7.1/bin/coot: line 333: 13382 Illegal  
instruction $coot_bin "$@"
;;; note: source file  
/home/rob/CCP4/ccp4-7.1/share/guile/1.8/ice-9/boot-9.scm
;;;   newer than compiled  
/usr/lib/x86_64-linux-gnu/guile/2.2/ccache/ice-9/boot-9.go

Uncaught exception:
Throw to key syntax-error with args ("memoization" "In file ~S, line  
~S: ~A ~S." ("/home/rob/CCP4/cc
p4-7.1/share/guile/1.8/ice-9/boot-9.scm" 103 "Bad define placement"  
(define (syntax) (error "syntax

error in eval-case"))) #f)

I upgraded the system to Ubuntu 20.04 LTS (also released yesterday),  
and have the same problems.


However, ccp4i starts normally.

Rob

Robert S. Phillips
Professor of Chemistry and of Biochemistry and Molecular Biology
University of Georgia
Athens, GA 30602
Phone: (706) 542-1996
Fax: (706) 542-9454
E-mail: rsphill...@chem.uga.edu
Web:   
http://tryptophan.net




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Re: [ccp4bb] CCP4 7.1 problems

[Edward Lowe]

I have also experienced the exact problem below on trying to launch ccp4i2 - 
but only on one of the four Ubuntu systems I have installed ccp4-7.1 on.

> Running CCP4i2 browser from: /home/rob/CCP4/ccp4-7.1/share/ccp4i2
> Python 2.7.16 (default, Apr 22 2020, 09:15:14)
> [GCC 4.9.1 20140922 (Red Hat 4.9.1-10)]
> Qt version 4.8.7
> Illegal instruction
>
> Then, back to the prompt.



Dr. E.D. Lowe   
edward.l...@bioch.ox.ac.uk
Department of BiochemistryTel: ++44 (0)1865 275392
University of Oxford
Oxford UK, OX1 3QU

From: CCP4 bulletin board  On Behalf Of Robert S Phillips
Sent: 24 April 2020 14:01
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CCP4 7.1 problems

I installed CCP4 7.1 yesterday, and I have problems.  On an Ubuntu 18.04 LTS 
system, I get the following:

rob@rob-SA76R4:~$ ccp4i2
Running CCP4i2 browser from: /home/rob/CCP4/ccp4-7.1/share/ccp4i2
Python 2.7.16 (default, Apr 22 2020, 09:15:14)
[GCC 4.9.1 20140922 (Red Hat 4.9.1-10)]
Qt version 4.8.7
Illegal instruction

Then, back to the prompt.

Similarly, with COOT:

rob@rob-SA76R4:~$ coot
INFO:: Reading coordinate file: 
/home/rob/CCP4/ccp4-7.1/share/coot/standard-residues.pdb
INFO:: file /home/rob/CCP4/ccp4-7.1/share/coot/standard-residues.pdb has been 
read.
Spacegroup: P 1
/home/rob/CCP4/ccp4-7.1/bin/coot: line 333: 13382 Illegal instruction 
$coot_bin "$@"
;;; note: source file /home/rob/CCP4/ccp4-7.1/share/guile/1.8/ice-9/boot-9.scm
;;;   newer than compiled 
/usr/lib/x86_64-linux-gnu/guile/2.2/ccache/ice-9/boot-9.go
Uncaught exception:
Throw to key syntax-error with args ("memoization" "In file ~S, line ~S: ~A 
~S." ("/home/rob/CCP4/cc
p4-7.1/share/guile/1.8/ice-9/boot-9.scm" 103 "Bad define placement" (define 
(syntax) (error "syntax
error in eval-case"))) #f)

I upgraded the system to Ubuntu 20.04 LTS (also released yesterday), and have 
the same problems.

However, ccp4i starts normally.

Rob

Robert S. Phillips
Professor of Chemistry and of Biochemistry and Molecular Biology
University of Georgia
Athens, GA 30602
Phone: (706) 542-1996
Fax: (706) 542-9454
E-mail: rsphill...@chem.uga.edu
Web:  
http://tryptophan.net



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