[ccp4bb] Announcement of the Sixth International Workshop on X-ray Radiation Damage to Biological,Crystalline Samples. SSRL 11-13th March 2010.

2009-08-24 Thread Elspeth Garman

The Sixth International Workshop on X-ray Radiation Damage to Biological
Crystalline Samples will be held at the Stanford Synchrotron Radiation 
Laboratory from

13:00 March 11th to 13:00 March 13th 2010.

This series of workshops was originally concerned with the effects of
radiation damage during investigation of protein structures by X-ray
crystallography. Other techniques of structural biology are now being
included to ensure greater information exchange. The workshop will
therefore be of interest to all those using ionising radiation to
examine biological structures at the molecular and cellular level.

Topics under discussion will include:
1: Reducing and Mitigating Radiation Damage
2: Radiation chemistry and radiolysis of biological molecules
3: Progress in the understanding of radiation damage in MX
4: Correcting for the effects of radiation damage
5: Reduction of metalloproteis and study of protein function
6: Radiation Damage in Electron Microscopy and Electron Crystallography
7: Pulsed Sources: Radiation damage issues.
8: Complementary (or non-crystallographic) methods to study radiation 
damage


The organizers are Ana Gonzales, Elspeth Garman, Colin Nave,
Sean McSweeney, Raimond Ravelli, Gerd Rosenbaum, Soichi Wakatsuki, and 
Martin Weik.


Anyone who would like to participate should e-mail Elspeth Garman
(elspeth.gar...@bioch.ox.ac.uk mailto:elsp...@biop.ox.ac.uk) who will 
forward further information to

interested parties once it is available.

--
**NOTE NEW E-MAIL ADDRESS AND PHONE NUMBER

 Elspeth F. Garman,
 President, British Crystallographic Association
 Professor of Molecular Biophysics, University of Oxford
 Postal address:
 Laboratory of Molecular Biophysics,
 Department of Biochemistry,
 University of Oxford,  Tel: (44)-1865-613297
 South Parks Road,  FAX: (44)-1865-613201
 OXFORD, OX1 3QU, U.K. E-mail: elspeth.gar...@bioch.ox.ac.uk
http://www.biop.ox.ac.uk/www/garman/gindex.html 
-


[ccp4bb] Request for def.site for HKL2000 for ESRF-BM14 MAR 225 CCD

2009-08-24 Thread S. Karthikeyan
Dear All,

I am looking for def.site file for HKL2000 used in ESRF-BM14 beam line. We
collected the data using MAR 225 CCD detector. The following link does not seem
to work for me.

http://www.esrf.fr/exp_facilities/BM14/runexperiment/bm14-def.site

We need this file to process our data in the home lab. If anybody has one, can
you please share with us.

Thanking you

With regards
S.Karthikeyan


*
Dr.Karthikeyan Subramanian, Ph.D
Scientist
Institute of Microbial Technology (CSIR)
Sector 39-A, Chandigarh - 160036, INDIA
email:skart...@imtech.res.in, skarthi...@gmail.com
*


Re: [ccp4bb] Request for def.site for HKL2000 for ESRF-BM14 MAR 225 CCD

2009-08-24 Thread S. Karthikeyan
Dear All,

I got the file. Thanks a lot for the same. I apologize for posting a 'non-CCP4'
question to the CCP4BB.

With regards
S.Karthikeyan


 Dear All,

 I am looking for def.site file for HKL2000 used in ESRF-BM14 beam line. We
 collected the data using MAR 225 CCD detector. The following link does not
 seem
 to work for me.

 http://www.esrf.fr/exp_facilities/BM14/runexperiment/bm14-def.site

 We need this file to process our data in the home lab. If anybody has one,
 can
 you please share with us.

 Thanking you

 With regards
 S.Karthikeyan


 *
 Dr.Karthikeyan Subramanian, Ph.D
 Scientist
 Institute of Microbial Technology (CSIR)
 Sector 39-A, Chandigarh - 160036, INDIA
 email:skart...@imtech.res.in, skarthi...@gmail.com
 *



[ccp4bb] Linux flavour and hard disks

2009-08-24 Thread Claudia Scotti

 

Dear List,

 

I'm planning to migrate soon from Red Hat Linux 7.0 on an HP xw6000 workstation 
with dual Xeon processor.

 

Please, any suggestion for the best Linux flavour to get the most out of 
today's crystallographic software? I've seen that both Ubuntu and Fedora are 
quite common.

 

Also I'm in doubt about the following: will it be safer to use two mirror hard 
disks (as I'm doing now) or to use one HD for the software and one for the data?

And, finally, please, what HD size is today most reasonable (big, but still 
fast enough)?

 

Thanks a lot,

 

Claudia

 

 

 



Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia 
Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 
0382 986335/8/1 Facs 0039 0382 303673



_
More than messages–check out the rest of the Windows Live™.
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Re: [ccp4bb] Linux flavour and hard disks

2009-08-24 Thread Roger Rowlett




I've used both Fedora (RH 9 through Fedora 8) and
Ubuntu 9.04 for crystallogrpahy. Both are fine distros. Ubuntu was a
little better working out of the box with all the hardware, and
maintenance of the restricted Nvidia drivers is simpler. For some
reason, Wine compatibility was better, too. Those are the principal
reasons I switched from Fedora to Ubuntu. On the other hand, I had
fewer problems with managing NFS shares with my Fedora boxes, but that
may just be familiarity with the required commands. Both Fedora and
Ubuntu seem to be supported by the major crystallographic software
folks.

Personally, I put the OS on a smaller HD, and the home directories for
the lab on a larger HD. Data resides on a separate Linux server with a
large HD. Currently, I'm running the OS on the master and client
workstations on 200-300 Gbyte HDs (overkill--they are only using 4-30
Gbyte, you could go smaller), and the home directory is on a 400 Gbyte
HD (about 30% full). The data server has a 500 Gbyte HD (and should
probably be upgraded to 1 Tbyte). The home directories, data, and
crystallographic software directories are all backed up to a backup
server (500 Gbyte) daily via rsync, with the currrent and last three
versions available. Quite frankly, HDs are so cheap right now, it
doesn't cost much to install big drives for data storage. I could use
RAID, but my system is pretty simple and seems to provide sufficient
protection.

Cheers.

Claudia Scotti wrote:

   
Dear List,
 
I'm planning to migrate soon from Red Hat Linux 7.0 on an HP xw6000
workstation with dual Xeon processor.
 
Please, any suggestion for the best Linux flavour to get the most out
of today's crystallographic software? I've seen that both Ubuntu and
Fedora are quite common.
 
Also I'm in doubt about the following: will it be safer to use two
mirror hard disks (as I'm doing now) or to use one HD for the software
and one for the data?
And, finally, please, what HD size is today most reasonable (big, but
still fast enough)?
 
Thanks a lot,
 
Claudia
 
 
 
  
  
Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di
Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia
Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673
  
  
  
  check out the rest of the Windows Live™.
More than mail–Windows Live™ goes way beyond your inbox. More
than messages
-- 

Roger S. Rowlett
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] Linux flavour and hard disks

2009-08-24 Thread Adam Ralph
Dear Claudia,

I use Ubuntu and I am happy with it, cannot say if it is
the best. It is relatively easy to maintain which is what you
want.

As for HD, try and determine how much space a typical project
would need and how many concurrent projects there might be. Data
from images would be the most space consuming, software would
probably not amount to much. This then gives you a minimum size
of HD. The speed of the disk is perhaps less important because writing
to disk is always slow. It is important to have enough memory so that
programs can be held entirely in memory. Having to use swap space slows
the whole machine.

   Disk partitions (of the same disk) is something worth discussing. If
you have everything on one partition there is a danger that it will be
filled and that this will impact on the performance. I always have
the / partition separate which need only be 5-10GB, a /usr partition
which could contain most of the software (30GB on the machine here) and
a /home partition (for user accounts). You also need a swap partition,
this should be 2 to 3 times the memory size. Maybe somebody knows the
optimum size.

   The most important thing which is easily overlooked is backups. Having
a mirrored disk or a RAID array is one way of reducing corrupted data.
Hot swapable RAID arrays can protect you against disk failure. However
if the building burns down and there is no offsite backup then you are
screwed. Certainly having a second disk on which hourly/daily backups
are done is a good idea. Getting some offsite backups, whether tapes or
networked disks, is a must.


Adam




On Mon, 24 Aug 2009, Claudia Scotti wrote:




 Dear List,



 I'm planning to migrate soon from Red Hat Linux 7.0 on an HP xw6000
workstation with dual Xeon processor.



 Please, any suggestion for the best Linux flavour to get the most out of
today's crystallographic software? I've seen that both Ubuntu and Fedora
are quite common.



 Also I'm in doubt about the following: will it be safer to use two
mirror hard disks (as I'm doing now) or to use one HD for the software and
one for the data?

 And, finally, please, what HD size is today most reasonable (big, but still
fast enough)?



 Thanks a lot,



 Claudia









 Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia 
 Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 
 0382 986335/8/1 Facs 0039 0382 303673



 _
 More than messages?check out the rest of the Windows Live?.
 http://www.microsoft.com/windows/windowslive/


Re: [ccp4bb] Linux flavour and hard disks

2009-08-24 Thread artem
I've just set up two home computers for crystallographic work. I decided
to play around, and set one up with Ubuntu and the other one with Fedora
core 11. Both did OK but I'd say that I had to perform marginally less
tweaking with Fedora than with Ubuntu.

As far as disk space - you can cram together almost any number of hard
drives using Logical Volume Management. And then there are numerous RAID
versions - both hardware and software (my two cents: don't get involved in
nerdy discussions of which one is 'better' - just get the one that is
easier for you). As long as you're backed up it really does not matter
which hard drive configuration you choose. I recommend running updates
with whatever you like for software - and also cloning your hard drives
using CloneZilla or any other tool so that in the event of system drive
failure you can just literally swap a cloned drive in and your computer
won't know the difference!

Artem




 Dear List,



 I'm planning to migrate soon from Red Hat Linux 7.0 on an HP xw6000
 workstation with dual Xeon processor.



 Please, any suggestion for the best Linux flavour to get the most out of
 today's crystallographic software? I've seen that both Ubuntu and Fedora
 are quite common.



 Also I'm in doubt about the following: will it be safer to use two mirror
 hard disks (as I'm doing now) or to use one HD for the software and one
 for the data?

 And, finally, please, what HD size is today most reasonable (big, but
 still fast enough)?



 Thanks a lot,



 Claudia









 Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia
 Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel.
 0039 0382 986335/8/1 Facs 0039 0382 303673



 _
 More than messages–check out the rest of the Windows Live™.
 http://www.microsoft.com/windows/windowslive/


Re: [ccp4bb] Linux flavour and hard disks

2009-08-24 Thread William G. Scott

On Aug 24, 2009, at 7:49 AM, ar...@xtals.org wrote:


my two cents: don't get involved in nerdy discussions


Here's a useful summary:

http://bandcamp.tv/linux-demotivators/


Re: [ccp4bb] Linux flavour and hard disks

2009-08-24 Thread Ian Tickle
 -Original Message-
 From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
 Behalf Of Adam Ralph
 Sent: 24 August 2009 15:25
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] Linux flavour and hard disks

 You also need a swap partition,
 this should be 2 to 3 times the memory size. Maybe somebody knows the
 optimum size.

Hi, here: https://help.ubuntu.com/community/SwapFaq
it explains that 1 to 2 times memory size is optimal.  However note that
this calculation assumes you are going to use the hibernate to disk
feature which allows you to restart the machine in exactly the state it
was when you last hibernated (and which obviously needs to use an amount
of disk space equal to the memory size).  First, this assumes that you
are actually going to use hibernate to disk (it's clearly very handy
for laptops, but probably irrelevant for servers which are rarely turned
off).  Second it assumes that the hibernate to disk feature does
actually use the swap partition for this purpose: I believe some systems
use a dedicated hibernate partition, so then you wouldn't need to
allocate extra swap space.  So in some cases you could reduce the swap
partition to 1 times memory size.

It's hardly worth arguing about anyway, the difference in disk usage is
likely to be  1% of the total, so probably most people won't even
consider the options and just go with the default!

Cheers

-- Ian


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[ccp4bb] phaser troubles

2009-08-24 Thread Sylvia Fanucchi
  

Hi

This is probably an obvious one but I'm having trouble getting Phaser to
run. It simply says the status is starting and will not give me more
information in the log file. I suspect the problem has to do with the F
and Sigma F values but I am not sure what to assign them as?

Any help would be appreciated

Sylvia

 


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Witwatersrand, Johannesburg. All agreements between the University and 
outsiders are subject to South African Law unless the University agrees in 
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image001.jpg

Re: [ccp4bb] phaser troubles

2009-08-24 Thread Mark Brooks
Hi,

 is the problem related to one of the problems listed below?
(taken from the CCP4i troubleshooting page
http://www.ccp4.ac.uk/ccp4i/trouble_shooting.html ):

If I recall correctly, once I saw similar behaviour when my
$CCP4I_TCLTK/tclsh was pointing to an incorrect directory.

I hope that helps,

Mark

Jobs run but are reported as STARTING in the Job Window
=

When CCP4i runs a job it starts a separate process and this process
reports back to the main CCP4i on progress - returning the status
RUNNING, REMOTE,FINISHED or FAILED. However sometimes after jobs are
reported as STARTING, the status never gets updated (even though the
job runs or fails).

There are several known problems which cause this to happen:

On Windows systems, this may be a symptom of having spaces in
directory or file names. Having spaces causes a variety of problems,
and is best avoided.

In older versions of the gui (pre CCP4 4.1) the communication between
the two processes used the Tcl/Tk command send which didn't not work
in Tcl/Tk built with the default options. As of CCP4 4.1 send is no
longer used so this problem shouldn't arise.

Check your version of CCP4 and upgrade, if necessary.

When running jobs, CCP4i needs to be able to find the tclsh command in
the directory pointed to by the CCP4I_TCLTK environment variable. For
Unix/Linux systems this is set when you source the ccp4.setup file. If
tclsh is not present then jobs may start but never actually run.

Check that $CCP4I_TCLTK/tclsh exists, and edit your ccp4.setup file to
point to the correct directory if it doesn't.

This problem will also be observed if localhost is not defined in the
system /etc/hosts. In this case a number of other symptoms will also
be observed, for example 1) a warning message about running scripts
being unable to connect to the server port; 2) neither the Run and
view com file nor the Kill job options work.

The fix is to make sure that localhost is defined in the /etc/hosts file.

2009/8/24 Sylvia Fanucchi sylvia.fanuc...@wits.ac.za

 Hi

 This is probably an obvious one but I’m having trouble getting Phaser to run. 
 It simply says the status is “starting” and will not give me more information 
 in the log file. I suspect the problem has to do with the F and Sigma F 
 values but I am not sure what to assign them as?

 Any help would be appreciated

 Sylvia



 This communication is intended for the addressee only. It is confidential. If 
 you have received this communication in error, please notify us immediately 
 and destroy the original message. You may not copy or disseminate this 
 communication without the permission of the University. Only authorized 
 signatories are competent to enter into agreements on behalf of the 
 University and recipients are thus advised that the content of this message 
 may not be legally binding on the University and may contain the personal 
 views and opinions of the author, which are not necessarily the views and 
 opinions of The University of the Witwatersrand, Johannesburg. All agreements 
 between the University and outsiders are subject to South African Law unless 
 the University agrees in writing to the contrary.


--
Mark Brooks, IBBMC, UMR8619 - Bâtiment 430,
Université de Paris-Sud, 91405 Orsay, France.
Tel: (33) 169157968
Fax: (33) 169853715
Skype: markabrooks


Re: [ccp4bb] Linux flavour and hard disks

2009-08-24 Thread mjvdwoerd

 Hi Claudia,

There is an option that has not been mentioned yet and has a very obvious 
advantage: CentOS. I am mentioning this because it is identical in 
functionality to Red Hat and therefore it will take the least of your time to 
move to a new system. We like CentOS because it is derived from Red Hat, no 
surprises, no unexpected bugs. And unlike Red Hat, it is completely free and 
you don't need to talk to the Red Hat people (which I found to be completely 
impossible). 

As far as configuration goes, this is what we do:
- Each workstation has a small (100GB or less) drive for the OS. Nothing else.
- We have a network-attached disk farm that holds X-ray images on one share, 
programs on another, and personal data on a third. The advantage is that you 
need to maintain everything only in one place and it does not matter where you 
are working - the data and programs are transparently available to all 
workstations. 
- We have two storage devices, one primary, one backup. All data get backed up 
hourly (X-ray images) or daily (user data) or weekly (Programs). We currently 
have 2TB of space and probably will go to 4TB soon.

You do need to make a careful analysis of what your needs are. We determined at 
the time that network traffic is never a limiting factor. Disk access can be 
somewhat of a limit, say when you have multiple people processing raw X-ray 
images at the same time, but that never happens in our group. So in the end we 
found that our limiting factor was C
PU power and this is where we focused our attention to make an efficient 
system. 

There are slight advantages to each flavor of Linux, but my personal argument 
(as care taker) is that it should take as little time as possible to maintain 
your setup (because maintaining Linux systems is a necessity but not really 
what we wish to do). It should also be very reliable - it should always work 
and you want to make a careful plan to deal with disaster recovery - disks fail 
sooner or later and yes, I have had numerous users who accidentally did 'rm *' 
when they did not mean to do that... That, of course, works equally well in all 
Linux flavors. 

Mark


 


 

-Original Message-
From: Claudia Scotti claudiasco...@hotmail.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Mon, Aug 24, 2009 7:30 am
Subject: [ccp4bb] Linux flavour and hard disks













 

Dear List,

 

I'm planning to migrate soon from Red Hat Linux 7.0 on an HP xw6000 workstation 
with dual Xeon processor.

 

Please, any suggestion for the best Linux flavour to get the most out of 
today's crystallographic software? I've seen that both Ubuntu and Fedora are 
quite common.

 

Also I'm in doubt about the following: will it be safer to use two mirror hard 
disks (as I'm doing now) or to use one HD for the software and one for the data?

And, finally, please, what HD size is today most reasonable (big, but still 
fast enough)?

 

Thanks a lot,

 

Claudia=0
A
 

 

 



Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia 
Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 
0382 986335/8/1 Facs 0039 0382 303673





check out the rest of the Windows Live™.
More than mail–Windows Live™ goes way beyond your inbox.
 More than messages=


 



[ccp4bb] shape complementarity

2009-08-24 Thread amit sharma
Dear All,

Could someone please suggest me program(s)  to get the shape complementarity
index for a protein complex structure of mine?

Many thanks

-- 
Amit Sharma, Ph.D. Research Associate, Department of Biology,
University of York, YO10 5DD UK


Re: [ccp4bb] shape complementarity

2009-08-24 Thread Edward A. Berry

amit sharma wrote:

Dear All,
 
Could someone please suggest me program(s)  to get the shape 
complementarity index for a protein complex structure of mine?
 
Many thanks


sc, by Michael Lawrence:
http://www.ccp4.ac.uk/dist/html/sc.html
(included in ccp4 distro)


Re: [ccp4bb] phaser troubles

2009-08-24 Thread Joseph Ho
Hi, Sylvia:
  Did you also install Phenix in your machine? Phenix contains another
version of phaser and will alias phaser to the phaser in Phenix. Try
to type which phaser. If your command is not aliased to the phaser in
your ccp4 version. Just use runview com file in the ccp4 and type in
the phaser with the ccp4 directory (for example, /your
directory/ccp4-6.1.1/ccp4-6.1.1/ccp4i/bin/phaser/).

Meng-Chiao Joseph Ho
Postdoc
Dept. of Biochemistry
Albert Einstein College of Medicine

On Mon, 2009-08-24 at 18:03 +0200, Sylvia Fanucchi wrote:
 
 Hi
 
 This is probably an obvious one but I’m having trouble getting Phaser
 to run. It simply says the status is “starting” and will not give me
 more information in the log file. I suspect the problem has to do with
 the F and Sigma F values but I am not sure what to assign them as?
 
 Any help would be appreciated
 
 Sylvia
 
  
 
 
 This communication is intended for the addressee only. It is confidential. If 
 you have received this communication in error, please notify us immediately 
 and destroy the original message. You may not copy or disseminate this 
 communication without the permission of the University. Only authorized 
 signatories are competent to enter into agreements on behalf of the 
 University and recipients are thus advised that the content of this message 
 may not be legally binding on the University and may contain the personal 
 views and opinions of the author, which are not necessarily the views and 
 opinions of The University of the Witwatersrand, Johannesburg. All agreements 
 between the University and outsiders are subject to South African Law unless 
 the University agrees in writing to the contrary.
 


Re: [ccp4bb] phaser troubles

2009-08-24 Thread Nathaniel Echols
On Mon, Aug 24, 2009 at 12:30 PM, Joseph Ho 
j...@medusa.bioc.aecom.yu.eduwrote:

  Did you also install Phenix in your machine? Phenix contains another
 version of phaser and will alias phaser to the phaser in Phenix.


No, it will be called phenix.phaser.  The Phenix environment scripts
($PHENIX/phenix_env*) do not alias anything; they only add the directory
containing the command-line launchers to PATH.  If used properly, you
shouldn't see any conflicts with CCP4 or anything else.


[ccp4bb] FPLC for sale

2009-08-24 Thread Natalie Roy
Dear All:

Please see attached is an ad for our AKTAprime plus FPLC system which is only 2 years old, used a dozen times and in excellent condition. Thanks,

Natalie Roy


FPLC for sale.doc
Description: MS-Word document


[ccp4bb] Sketcher and Refmac monomer library construction

2009-08-24 Thread Roger Rowlett




CCP4bbers,

I am trying to do a restrained refinement in refmac using a rhenium
tricarbonyl (RTC) fragment similar to the one in PDB 1I53. My
understanding of how to proceed is to take the PDB description of the
file, read it into sketcher, and then run libcheck to create the
various cif and lib files in my local directory. Assuming I can get
this to work (see below), then refmac should recognize the monomer
files in the local directory from the residue name and use the proper
restraints? Or do I need to explicitly read in the lib file(s) (e.g.,
libcheck_RTC.cif) in the LibIn field in CCP4i?

I can read in the RTC PDB file below into sketcher and change the CO
bonds to triple (they come up double on read-in), but then running
libcheck dutifully makes the carbons sp2 and adds riding hydrogens.
Agh. Running libcheck at the command line does the same thing with
or without the HFLAG set. I would be grateful for any
assistance/suggestions. I thought this would be an easy task... :) I
must be missing something obvious. BTW, the RTC monomer in the HIC-UP
server is incorrect: it is meridional instead of (the correct) facial
geometry. THe PDB file below is correct.

ATOM 1976 RE RTC B 905 39.199 36.612 61.900 1.00
20.26 RE 
ATOM 1977 O1 RTC B 905 41.664 36.504 60.063 1.00
20.75 O 
ATOM 1978 O2 RTC B 905 40.911 37.753 64.220 1.00
20.54 O 
ATOM 1979 O3 RTC B 905 39.925 33.794 62.879 1.00
20.49 O 
ATOM 1980 C1 RTC B 905 40.757 36.541 60.750 1.00
20.06 C 
ATOM 1981 C2 RTC B 905 40.269 37.327 63.349 1.00
20.00 C 
ATOM 1982 C3 RTC B 905 39.667 34.827 62.518 1.00
20.04 C 

Cheers,

-- 

Roger S. Rowlett
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...@mail.colgate.edu






[ccp4bb] How to work around strange naming XYZIN convention?

2009-08-24 Thread Ethan Merritt
Not sure this is the right place to ask, but...

I'm trying to chain some ccp4 programs together via a script.
It creates temporary files with arbitrary names based on the process id.
The problem is that when I try to pass one of these files to the
next program in the chain, as in:

   tlsanl XYZIN $tempfile EOF
   ...
   EOF

The ccp4 libraries seem to expand this to be an input file named
   $tempfile.brk

Is there any way to make the programs _not_ append a useless extension
.brk  in a scripted environment?

-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742


Re: [ccp4bb] Linux flavour and hard disks

2009-08-24 Thread James Stroud

On Aug 24, 2009, at 8:32 AM, William G. Scott wrote:

On Aug 24, 2009, at 7:49 AM, ar...@xtals.org wrote:


my two cents: don't get involved in nerdy discussions


Here's a useful summary:


So it's freebsd then?


[ccp4bb] FPLC for sale *PRICE*

2009-08-24 Thread Natalie Roy
Hi everyone,

Thank you for all the replies to the ad I posted about the FPLC for sale, we 
are asking $11,000  CAD for the system and all of its components, but we are 
willing to negotiate price.  The UV lamp is also 2 years old but only been used 
about a dozen times.  Shipping will be discussed with those who are interested 
because it will be dependant on the location of the buyer whether or not it's 
included in the price.  Thanks!

Nat