Re: [ccp4bb] Bio-rad DuoFlow

[Dima Klenchin]

(FPLC is a trademark. The marketing hype has been so effective that many
people think that FPLC is a method.)


Well, it is, in a way. The FPLC thingie was a pure marketing genius that 
bundled the remarkable technology of Monobeads (AFAIK, there is still no 
other company that offers comparable size dispersion) with an inefficent 
but lower cost alternative to HPLC. It worked. When the market was taken, 
the "technology" reverted back to the standard HPLC under a new marketing 
name.


Dima

Re: [ccp4bb] Bio-rad DuoFlow

[Daniel Anderson]

It still seems to me strange that Bio-Rad would build a machine that can
reach pressures suitable for reverse-phase chromatography, but then not
include software control for gradual pump acceleration. I tried to
communicate to BioRad corporate suits that many HPLC columns are too
fragile for abrupt pump acceleration, but it was like speaking Swahili.

Having typed that, I'm not up to date with the latest DuoFlow software.

For HPLC, I'm still very fond of Waters pumps and their gentle handling of
columns. I tried to communicate to Waters corporate suits that what the
academic world could use is their Breeze system with non-corroding pump
heads, but it was like speaking Swahili.

(FPLC is a trademark. The marketing hype has been so effective that many
people think that FPLC is a method.)

-Dan

On Wed, 14 Feb 2007, William Clemons wrote:

> In my old lab everyone was slowly converting to Bio-rad for
> chromatography. We had an Akta and subsequently bought two Bio-rad
> DuoFlow. I actually never made the conversion then but those that had
> didn't want to use the Akta anymore.
>
> Upon starting my own lab I got quotes for both an Akta and a DuoFlow
> and the cost difference was striking. As Tamir said, the DuoFlow
> really is plug and play and you can build up the system you want so
> just buying the basic may not get you far but relatively easily you
> can get all of the features of a mid-range Akta (mutiple buffer
> valves, column valves, multiwavelength (4)). I should add that in all
> my interaction with equipment reps at GE Healthcare I generally came
> away with the feeling that they don't care that much about academics.
> They have a real air of superiority which is enough for me to not buy
> from them (although I get all my columns from them!).
>
> There are a few downsides to the DuoFlow. The software is not as nice
> as that for the Akta but it is fairly easy to train on and all of my
> people have gotten along fairly easily with it. The pumps for the
> standard DuoFlow are rated for much higher pressures than we
> biochemists typically use so sometimes they can struggle with
> pressures below 40 PSI. We got around this by adding a pressure
> inducer past the pump and have had no problems since. The only other
> downside that I'd mention is that the service reps aren't very well
> trained so this may not be the best system if it is the first time
> you've seen an FPLC. We had a Service Rep come in who forgot to turn
> off the pump after his test runs. This happened on a Friday and no
> one noticed the pump was running until the following Tuesday. This
> killed the pump but they quickly came and replaced all the parts and
> we haven't had a problem since.
>
> My final point is that Bio-rad is really great (at least here in LA)
> with academics and we were able to bundle in all of our protein gel
> parts, DNA gel parts, PCR machines, Gel Doc etc for less than the
> quote for the equivalent Akta. In fact, I just had a second Duo-Flow
> installed yesterday and was able to again bundle in a lot more
> equipment for my slowly growing lab. Bio-Rad isn't perfect but they
> get at least a B+ from me for general support and in the end my
> experience continues to be a positive one. It is probably the best
> purchasing experience I had in my start up and the only one I haven't
> had some major regret on.
>
> Just my 2 cents,
>
> Bil
>
> On Feb 14, 2007, at 8:41 AM, Tamir Gonen wrote:
>
> > I beg to differ.
> >
> > I have been an AKTA explorer user for about 5 years and switched to
> > DuoFlow about 4 yrs ago and now have one in my own lab. The BioRad
> > DuoFlow is awesome. It never ever breaks. I never had any problems
> > with this machine at all, it takes any column (pharmacia or
> > otherwise) given the right adapters. The AKTA are really cumbersome
> > and complicated to use and teach on - its all inside a big black
> > box that looks (and feels) like a tank, while the DuoFlow has a
> > really simple design, and is basically "plug and play".
> >
> > The AKTA is really good for analytical applications when you have
> > very small amounts of your protein and of course you can detect
> > multiple wave lengths at a time (you can add special unit for multi
> > wavelengths on the biorad). The DuoFlow struggles  with very small
> > protein concentrations (<0.05mg/ml) and the void volume on its
> > tubing further dilutes the sample. If you know what you are doing,
> > it is easy to optimize the setup in such a way that you minimize
> > the void volume on the DuoFlow.
> >
> > Finally, the AKTA has an in line filter which always gets clogged
> > up when you have buffer with detergent. The DuoFlow does not have a
> > filter at all which means if your students and postdocs are not
> > careful, the filters in the column will get clogged. But all you
> > need to do is filter your sample prior to injection.
> >
> > BioRad service is not so great but if you take care of your machine
> > you really dont need to worry. It

Re: [ccp4bb] Multi-copies in one assymetric unit

[Yanming Zhang]

Dear All,

After I send out the 'SOS' for my multi-copy problem, I have received many 
good suggestions and tips. Many thanks to all of you.


Now my problem has been solved:
1, There are only 4 molecules in a.u, even the solvent containt is high, 
it is not uncommon for a data with low resolution and high symmetry.
2, CNS anneal can do the magic work to get rid of un-even density 
distribution among all 4 chains.
3, Now my R-value is 36% R-free is 41% around. Few turns fiting can finish 
my structure up, I think


Crystallographers in the world is like one family. One difficulty, many 
helps! Thank you all for your kind replies and your times.


Yanming

On Wed, 14 Feb 2007, Petrus H Zwart wrote:


This isnt any real help but I cant solve a ferritin structure in
SG I432
- it probably forms a cage like the other feritins around the
origin,
but every solution I get clashes with others..
After listening to a lecture by a small molecule crystallographer
I
wondered whether there isnt some crystal defect but I am not sure
how to
monitor it..
Eleanor



Hi Elenaor,

Your problem reminds me of this paper:

http://journals.iucr.org/a/issues/2004/04/00/lc0065/index.html

Not sure if it is related (probably not), but the phenomenon itself is 
interesting

Cheers

Peter

Re: [ccp4bb] Bio-rad DuoFlow

[William Clemons]

In my old lab everyone was slowly converting to Bio-rad for  
chromatography. We had an Akta and subsequently bought two Bio-rad  
DuoFlow. I actually never made the conversion then but those that had  
didn't want to use the Akta anymore.


Upon starting my own lab I got quotes for both an Akta and a DuoFlow  
and the cost difference was striking. As Tamir said, the DuoFlow  
really is plug and play and you can build up the system you want so  
just buying the basic may not get you far but relatively easily you  
can get all of the features of a mid-range Akta (mutiple buffer  
valves, column valves, multiwavelength (4)). I should add that in all  
my interaction with equipment reps at GE Healthcare I generally came  
away with the feeling that they don't care that much about academics.  
They have a real air of superiority which is enough for me to not buy  
from them (although I get all my columns from them!).


There are a few downsides to the DuoFlow. The software is not as nice  
as that for the Akta but it is fairly easy to train on and all of my  
people have gotten along fairly easily with it. The pumps for the  
standard DuoFlow are rated for much higher pressures than we  
biochemists typically use so sometimes they can struggle with  
pressures below 40 PSI. We got around this by adding a pressure  
inducer past the pump and have had no problems since. The only other  
downside that I'd mention is that the service reps aren't very well  
trained so this may not be the best system if it is the first time  
you've seen an FPLC. We had a Service Rep come in who forgot to turn  
off the pump after his test runs. This happened on a Friday and no  
one noticed the pump was running until the following Tuesday. This  
killed the pump but they quickly came and replaced all the parts and  
we haven't had a problem since.


My final point is that Bio-rad is really great (at least here in LA)  
with academics and we were able to bundle in all of our protein gel  
parts, DNA gel parts, PCR machines, Gel Doc etc for less than the  
quote for the equivalent Akta. In fact, I just had a second Duo-Flow  
installed yesterday and was able to again bundle in a lot more  
equipment for my slowly growing lab. Bio-Rad isn't perfect but they  
get at least a B+ from me for general support and in the end my  
experience continues to be a positive one. It is probably the best  
purchasing experience I had in my start up and the only one I haven't  
had some major regret on.


Just my 2 cents,

Bil

On Feb 14, 2007, at 8:41 AM, Tamir Gonen wrote:


I beg to differ.

I have been an AKTA explorer user for about 5 years and switched to  
DuoFlow about 4 yrs ago and now have one in my own lab. The BioRad  
DuoFlow is awesome. It never ever breaks. I never had any problems  
with this machine at all, it takes any column (pharmacia or  
otherwise) given the right adapters. The AKTA are really cumbersome  
and complicated to use and teach on - its all inside a big black  
box that looks (and feels) like a tank, while the DuoFlow has a  
really simple design, and is basically "plug and play".


The AKTA is really good for analytical applications when you have  
very small amounts of your protein and of course you can detect  
multiple wave lengths at a time (you can add special unit for multi  
wavelengths on the biorad). The DuoFlow struggles  with very small  
protein concentrations (<0.05mg/ml) and the void volume on its  
tubing further dilutes the sample. If you know what you are doing,  
it is easy to optimize the setup in such a way that you minimize  
the void volume on the DuoFlow.


Finally, the AKTA has an in line filter which always gets clogged  
up when you have buffer with detergent. The DuoFlow does not have a  
filter at all which means if your students and postdocs are not  
careful, the filters in the column will get clogged. But all you  
need to do is filter your sample prior to injection.


BioRad service is not so great but if you take care of your machine  
you really dont need to worry. It is really robust. Plus, for the  
price of an explorer you could buy two top-of-the-line DuoFlow  
systems together with columns.


Tamir.


__
Dr Tamir Gonen

Department of Biochemistry
Box 357350
University of Washington
Seattle, WA 98195

Tel: (206) 616 7565 (Office)
(206) 616 8529 (Lab)
Fax: (206) 685 1792
[EMAIL PROTECTED]

http://faculty.washington.edu/tgonen/




On Feb 14, 2007, at 8:19 AM, Frank Lee wrote:



Dear all,

Thanks a lot for all the feedbacks on AKTA prime. They are so  
helpful that I have abandoned the idea of buying one. Now it is a  
choice between AKTA FPLC and Bio-rad DuoFlow. I heard that DuoFlow  
is not as robust as AKTA and that its parts break down often. The  
question is whether quality difference is worth price difference (~ 
$10K). Any feebacks on DuoFlow would be highly appreciated!


Best,
Frank

Food fight? Enjoy some healthy debate
in the Yahoo! Answer

Re: [ccp4bb] REFMAC5 and Shannon factor

[Billy Poon]

Garib,

Yes!  That clears it up.  The documentation says the default is 1.5 and I
found 1.5 in the source code, so I automatically assumed that was true.

-Billy

On Wed, 14 Feb 2007 18:33:59 +, Garib Murshudov <[EMAIL PROTECTED]>
wrote:

>There re two places where FSHANN is set. One when keyword is read and
>one default initial value. The second value is the default.
>The first set is when you make mistake with the keyword and the
>second one is the default. Is this what you have?
>
>
>/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/
>rcard_tor1.f:cRead shannon factor for grid spacing. Fshann is
>factor by which
>/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/
>rcard_tor1.f:FSHANN = 1.5
>/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/
>rcard_tor1.f:  CALL GTNREA(2,1,FSHANN,NTOK,ITYP,FVALUE)
>/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/
>rcard_tor1.f:  IF(FSHANN.LE.0.0) THEN
>/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/
>rcard_tor1.f:FSHANN = 1.5
>/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/
>rcard_tor1.f:  ELSEIF(FSHANN.LE.1.0) THEN
>/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/
>rcard_tor1.f:FSHANN = 1.0/FSHANN
>/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/
>rcard_tor1.f:  FSHANN = 1.4
>
>
>Garib
>P.S. That is for version 5.2.0005. For the next version it will be
>1.5 (it seemed to give consistent results).
>
>
>On 14 Feb 2007, at 18:24, Billy Poon wrote:
>
>> Thanks both for your quick replies!
>>
>> Bernie,
>>
>> I didn't use the WEIGHT keyword because I'm not doing any
>> refinement.  I only want to calculate the R values for a structure
>> without any minimization.  And it seems that setting the
>> SHANnon_factor keyword to the default value gives different R
>> values than not setting the SHANnon_factor keyword at all (the
>> program will use the default value in the source code).
>>
>> And Garib,
>>
>> In rcard_tor1.f in the $CCP4/src/refmac5_/ directory, the default
>> shannon factor seems to be set to 1.5.  I'm using version 5.2.0019
>> of REFMAC.  Is the default something else in the newer version?
>>
>> -Billy
>>
>> Santarsiero, Bernard D. wrote:
>>> You didn't say anything about the "weighting term" between the F's
>>> and
>>> geometrical parameters. That will substantially affect the R's,
>>> and the
>>> default value of 0.3 in REFMAC isn't appropriate for all
>>> structures. In
>>> CNS, it's adjusted to a more reasonable value during refinement.
>>>
>>> Bernie Santarsiero
>>>
>>>
>>> On Wed, February 14, 2007 10:36 am, Billy Poon wrote:
>>>
 Dear all,

 I have been using REFMAC5 to calculate the R values of several
 structures
 from
 the PDB and was confused by the behavior of the SHANnon_factor
 keyword.
 When I
 leave it at the default (set at 1.5 in the source code), I get
 one set of
 R
 values.  But when I manually set the value to 1.5 (SHANnon_factor
 1.5) in
 the
 script, I get a different set of values.  Usually, it's off at
 the third
 or
 fourth decimal place, but for one case (PDB code 2OAU), I get a
 difference
 of
 about 0.0116 (0.28416 for default, 0.27258 for manual setting)
 for the R
 value
 and 0.0184 (0.31653 for default, 0.29818 for manual setting) in
 the Free
 R.

 I have tested this on the following architectures and they all
 behave the
 same
 way:

 Intel Xeon (32-bit Linux, REFMAC 5.2.0019, compiled with Intel
 compilers
 9.1)
 Intel Itanium2 (64-bit Linux, REFMAC 5.2.0019, compiled with Intel
 compilers
 9.1)
 AMD Opteron (64-bit Linux, REFMAC 5.2.0019, compiled with GNU
 compilers
 3.3.3)
 SGI MIPS (IRIX 6.5, REFMAC 5.2.0003, pre-compiled binaries)

 I am not doing any refining of the structures.  I just wanted to
 see what
 the R
 values are when calculated with REFMAC5 (the structures I was
 looking at
 were
 refined in CNS or X-PLOR) and was confused by the different
 results with
 the same setting.  Also, should changing the SHANnon_factor
 affect the R
 values much?  Thanks in advance for your help!

 -Billy

 And the script I use is pasted below:

 #
 # Refmac
 #
 refmac:
 refmac5 \
 HKLIN ./fo.mtz \
 XYZIN ./2oau.pdb \
 XYZOUT ./test.pdb \
 << eor
 #
 # Do not add hydrogens
 #
 MAKE HYDR N
 MAKE LINK N
 MAKE CHECK NONE
 #
 # Input mtz labels
 #
 LABIN FP=FP SIGFP=SIGFP FREE=FREE
 #
 # Set resolution
 #
 REFI RESOlution 3.7 50.00
 #
 # Define NCS
 #
 NCSR NCHAI 7 CHAI A B C D E F G NSPANS 1 1 254 4
 #
 # Refine overall B factor
 #
 REFI BREF OVERall
 #
 # Set Free flag
 #
 FREE 0
 #
 # Number of refinement cycles
 #

Re: [ccp4bb] Bio-rad DuoFlow

[Daniel Anderson]

That was cryptic.

My point was that the BioRad pumps are very reliable given some basic
care. Its users quickly learn how to use it, as mentioned previously.


On Wed, 14 Feb 2007, Daniel Anderson wrote:

> My direct experience is with the old "HR" pumps, but my remarks apply to
> the newer "DuoFlow".
>
> On Day Zero, I disassemble the pump heads in the order specified in the
> manual. I re-assemble with grease on the threads, thus preventing
> expensive repairs due to corrosion of the bolts caused by salty buffers.
> The pistons and seals MUST BE wet with ethanol or methanol for
> re-assembly.
>
> The daily maintenance consists of washing behind the pump heads, before
> and after use.
>
> The daily maintenance is an absolute. Personnel with not even that much
> discipline should not be allowed in the lab. (but I'm not faculty, so my
> opinions don't matter)
>
> (there are good reasons why HPLC training classes cost kilobucks)
>
> My one complaint about BioRad chromatography pumps is that the solenoid
> valves can be damaged by particulates, or by buffers and salts drying
> inside the valves.
> BioRad (probably) won't repair them. So filter, filter, filter, and flush
> with 10% methanol or 20% ethanol. Do not allow the valves to dry.
>
> -Dan
>
> On Wed, 14 Feb 2007, Frank Lee wrote:
>
> >
> > Dear all,
> >
> > Thanks a lot for all the feedbacks on AKTA prime. They are so helpful that 
> > I have abandoned the idea of buying one. Now it is a choice between AKTA 
> > FPLC and Bio-rad DuoFlow. I heard that DuoFlow is not as robust as AKTA and 
> > that its parts break down often. The question is whether quality difference 
> > is worth price difference (~$10K). Any feebacks on DuoFlow would be highly 
> > appreciated!
> >
> > Best,
> > Frank
> >
> >
> > -
> > Food fight? Enjoy some healthy debate
> > in the Yahoo! Answers Food & Drink Q&A.
>

[ccp4bb] Fwd: Re: [ccp4bb] AKTA prime

[Frank Lee]

"David R. Cooper" <[EMAIL PROTECTED]> wrote: From: "David R. Cooper" <[EMAIL 
PROTECTED]>
Subject: Re: [ccp4bb] AKTA prime
To: Frank Lee <[EMAIL PROTECTED]>
Date: Wed, 14 Feb 2007 15:13:18 -0500

 Hello, Frank.
I seem to be having trouble posting directly to the bulletin board. 
 Perhaps you could forward this for me.

We have two AKTA Primes. They came with an external pressure regulator 
attached that gave the system ~ 0.25 Mpa system pressure that Artem 
mentioned (Hi Artem). It can be removed with no loss in performance and the 
pressure will drop to ~ 0.05 for an empty system. We run XK 10/30 Superdex 
columns (~30 ml) at .5 ml/min.

In my opinion, the largest drawback of the Prime is that it lacks a good 
computer interface for programming. The default is that you have to push the 
buttons on the front to program it. Our systems are in refrigerated 
cabinets, so writing a more complex program means you have to have the door 
open for a long time.

To circumvent this, I have written a web server that allows you to generate 
programs for you. The forms generate a text file that can be saved in the 
C:\UNICORN\Bin\Prime directory and then run using the "Run stored program / 
from PC" option. My page has sections for writing generic programs 
"break-point by break-point" or performing size exclusion or desalting 
loops.

Anyone with a prime is welcome to use my "Akta Prime Program Generator" and 
contact me if you need help.
See http://ginsberg.med.virginia.edu/akta.html

Overall, these are not ideal systems.  If this is the only system that you 
will have, consider a more robust system.  If you are looking for something 
to do affinity purrifications, size exclusion, desalting and even simple ion 
exchange, it is a pretty good choice.

Regards,
David

---
David Cooper, Ph.D.
University of Virginia
Molecular Physiology and Biological Physics
Jordan Hall, Box 800736
1300 Jefferson Park Ave
Charlottesville, VA 22908-0736
Phone: (434) 982-3151
Fax: (434) 982-1616


On Tue, 13 Feb 2007 14:16:33 -0800
  Frank Lee  wrote:
> 
> Dear all,
> 
> I need to decide between buying an AKTA prime and an AKTA FPLC from GE 
>health care. I understand AKTA prime is a low-pressure system, but because 
>it is too much cheaper than AKTA FPLC, it is still very attractive to me.
> 
> I will mainly use it for Nickel columns and gel filtration columns, and I 
>am worried about the latter. Is it true that using AKTA prime, you can only 
>run the 24 ml Superdex 200 column at 0.1 or 0.2 ml/min?
> 
> Could anyone who has used AKTA prime give me some feedbacks? I would 
>appreciate it.
> 
> Best,
>Frank
> 
> 
> -
> Need Mail bonding?
> Go to the Yahoo! Mail Q&A for great tips from Yahoo! Answers users.

.
---
David Cooper, Ph.D.
University of Virginia
Molecular Physiology and Biological Physics
Jordan Hall, Box 800736
1300 Jefferson Park Ave
Charlottesville, VA 22908-0736
Phone: (434) 982-3151
Fax: (434) 982-1616


 
-
Don't get soaked.  Take a quick peak at the forecast 
 with theYahoo! Search weather shortcut.

Re: [ccp4bb] x86-64

[Lynn Ten Eyck]

Dear Phil,

Good luck . . . I have been fighting an x86_64 system for some time, and
have just figured out what some of the problems are.  I am running Fedora
Core 5.

I believe that if you use the -m32 flag for gcc you can compile 32-bit code
for 32-bit libraries.  The default is to compile 64-bit and link 64-bit.
The real joker in the deck is the file system layout:

/usrDefault root prefix
/usr/includeUsed for both 32 and 64 bit systems
/usr/libLibraries for 32-bit code
/usr/lib64  Libraries for 64-bit code
/usr/binFor both -- the operating environment is encoded in the file

This breaks the standard prefix scheme for prefix/{include,lib,src,...}
because it is not easy to tell when you need lib and when you need lib64.

I was unable to compile Coot from source until the last day or so because
the linker kept putting the 32-bit libGL.so in the search path.  This is a
fatal error.

I finally tracked this to a bug in libtool, which figures out about the
32/64 bit issues *nearly* all of the time.  Sigh.

Short answer:  get the latest, bleeding-edge Autoconf package from the GNU
web site and install it.  It is alpha, but seems to work, and the configure
scripts once generated can be run almost anywhere.  (Oh, you may also have
to upgrade M4.)

*Note* I got Autoconf 2.61, but the real key seems to be the version number
on the libtool macros.  Version 1.2248 does not work, but Version 1.2381
does work on my system.  Unfortunately the latest versions are also more
picky about the macros, so if autoupdate can't fix them, you have to do some
hand editing.

I will be happy to follow up on this off-line, and expect to post a summary
on the Coot bulletin board once I have some loose ends tidied up.  I suspect
this may be why I have had problems trying to build ccp4mg from source on
this machine, as well.

Overall the machine runs really well, but you do hit the occasional package
that is not 64-bit clean.

Best regards,
Lynn Ten Eyck


On 2/14/07 10:00 AM, "Phil Evans" <[EMAIL PROTECTED]> wrote:

> I'm just starting to use a 64-bit Linux machine (running some sort of
> RedHat Enterprise system) as a development machine
> 
> Our general CCP4 installation is from the binary download (redHat
> option) (presumably built on a 32-bit machine), which seems to run OK
> on a range of different Linux machines
> 
> However if I compile on the 64-bit machine & try to link with these
> libraries, it doesn't work
> 
> r/bin/ld: skipping incompatible /public/xtal/ccp4-6.0/ccp4-6.0.2-
> linux/lib/libccp4f.a when searching for -lccp4f
> /usr/bin/ld: cannot find -lccp4f
> collect2: ld returned 1 exit status
> make: *** [scala] Error 1
> 
> 
> Is it possible to set compile flags to produce something (.o) which
> will link with th distributed libraries, and produce an executable
> which will run on other (32-bit) Linux machines?
> 
> In the mean time, I'm doing a complete source build on the 64-bit
> machine
> 
> Phil

-- 
Lynn F. Ten Eyck[EMAIL PROTECTED]
San Diego Supercomputer Center  (858) 534-5141 (Voice)
University of California, San Diego (858) 822-3610 (Fax)
9500 Gilman Drive #0444 Office: 3131 Atkinson Hall
La Jolla, CA 92093-0444

Re: [ccp4bb] mtz to hkl conversion

[Kumar, Abhinav]

Hi Vineet,

 

The following script should output the required CNS data file:

 

mtz2various hklin Fobs.mtz HKLOUT Fobs.xpl << EOL

LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag HLA=HLA HLB=HLB HLC=HLC HLD=HLD

OUTPUT XPLOR 

END

EOL

 

Thanks 
Abhinav 

 



From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Vineet Gaur
Sent: Wednesday, February 14, 2007 11:32 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] mtz to hkl conversion

 

Hi all

i am trying to solve a structure using MIR by solve/resolve. With Solve/Resolve 
i have got FOM of 0.70 (3.3A) after density modification n we have got 
reasonable model as well, but most of it is without side chain. using this 
model we have determined the NCS rotation n translation matrices but we r not 
able to utilize the NCS information fully with solve/resolve n thus we have 
decided to shift to CNS. 
while shifting to CNS i need to convert mtz file to hkl format. i m using 
mtztovarious option of ccp4 for format conversion but in doing so the 
information related to HL coeff, which is there in MTZ file as well as the 
information abt FOBS and SIGMA is getting lost. 
is there any other  other way of converting mtz file to hkl while retaining all 
the necessary information?

 

Although i have native data up to 2.2A but i m unable to extend the phases 
beyond 3.0 with reasonable FOM. Is there any programme for model building which 
can work at resolution as low as 3.0.


thanks in advance

vineet gaur

Re: [ccp4bb] mtz to hkl conversion

[Raji Edayathumangalam]

Hi Vineet,

Try using TEXTAL for model building at your resolution. I heard
that this is optimized for 2.8Ang or so resolution.

For MTZ to HKL with HL's intact, read the Tutorial section on the
CNS webpage with example scripts. Go to section 'Data Conversion'
and look at 'Converting a CCP4 MTZ reflection file'.

Hope that helps.
Raji



-Included Message--
>Hi all
>i am trying to solve a structure using MIR by solve/resolve. With
>Solve/Resolve i have got FOM of 0.70 (3.3A) after density
modification n we
>have got reasonable model as well, but most of it is without
side chain.
>using this model we have determined the NCS rotation n
translation matrices
>but we r not able to utilize the NCS information fully with
solve/resolve n
>thus we have decided to shift to CNS.
>while shifting to CNS i need to convert mtz file to hkl format.
i m using
>mtztovarious option of ccp4 for format conversion but in doing
so the
>information related to HL coeff, which is there in MTZ file as
well as the
>information abt FOBS and SIGMA is getting lost.
>is there any other  other way of converting mtz file to hkl
while retaining
>all the necessary information?
>
>Although i have native data up to 2.2A but i m unable to extend
the phases
>beyond 3.0 with reasonable FOM. Is there any programme for model
building
>which can work at resolution as low as 3.0.
>
>thanks in advance
>vineet gaur
>
>
-End of Included Message--

[ccp4bb] mtz to hkl conversion

[Vineet Gaur]

Hi all
i am trying to solve a structure using MIR by solve/resolve. With
Solve/Resolve i have got FOM of 0.70 (3.3A) after density modification n we
have got reasonable model as well, but most of it is without side chain.
using this model we have determined the NCS rotation n translation matrices
but we r not able to utilize the NCS information fully with solve/resolve n
thus we have decided to shift to CNS.
while shifting to CNS i need to convert mtz file to hkl format. i m using
mtztovarious option of ccp4 for format conversion but in doing so the
information related to HL coeff, which is there in MTZ file as well as the
information abt FOBS and SIGMA is getting lost.
is there any other  other way of converting mtz file to hkl while retaining
all the necessary information?

Although i have native data up to 2.2A but i m unable to extend the phases
beyond 3.0 with reasonable FOM. Is there any programme for model building
which can work at resolution as low as 3.0.

thanks in advance
vineet gaur

Re: [ccp4bb] Bio-rad DuoFlow

[Daniel Anderson]

My direct experience is with the old "HR" pumps, but my remarks apply to
the newer "DuoFlow".

On Day Zero, I disassemble the pump heads in the order specified in the
manual. I re-assemble with grease on the threads, thus preventing
expensive repairs due to corrosion of the bolts caused by salty buffers.
The pistons and seals MUST BE wet with ethanol or methanol for
re-assembly.

The daily maintenance consists of washing behind the pump heads, before
and after use.

The daily maintenance is an absolute. Personnel with not even that much
discipline should not be allowed in the lab. (but I'm not faculty, so my
opinions don't matter)

(there are good reasons why HPLC training classes cost kilobucks)

My one complaint about BioRad chromatography pumps is that the solenoid
valves can be damaged by particulates, or by buffers and salts drying
inside the valves.
BioRad (probably) won't repair them. So filter, filter, filter, and flush
with 10% methanol or 20% ethanol. Do not allow the valves to dry.

-Dan

On Wed, 14 Feb 2007, Frank Lee wrote:

>
> Dear all,
>
> Thanks a lot for all the feedbacks on AKTA prime. They are so helpful that I 
> have abandoned the idea of buying one. Now it is a choice between AKTA FPLC 
> and Bio-rad DuoFlow. I heard that DuoFlow is not as robust as AKTA and that 
> its parts break down often. The question is whether quality difference is 
> worth price difference (~$10K). Any feebacks on DuoFlow would be highly 
> appreciated!
>
> Best,
> Frank
>
>
> -
> Food fight? Enjoy some healthy debate
> in the Yahoo! Answers Food & Drink Q&A.

Re: [ccp4bb] REFMAC5 and Shannon factor

[Garib Murshudov]

There re two places where FSHANN is set. One when keyword is read and  
one default initial value. The second value is the default.
The first set is when you make mistake with the keyword and the  
second one is the default. Is this what you have?



/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/ 
rcard_tor1.f:cRead shannon factor for grid spacing. Fshann is  
factor by which
/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/ 
rcard_tor1.f:FSHANN = 1.5
/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/ 
rcard_tor1.f:  CALL GTNREA(2,1,FSHANN,NTOK,ITYP,FVALUE)
/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/ 
rcard_tor1.f:  IF(FSHANN.LE.0.0) THEN
/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/ 
rcard_tor1.f:FSHANN = 1.5
/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/ 
rcard_tor1.f:  ELSEIF(FSHANN.LE.1.0) THEN
/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/ 
rcard_tor1.f:FSHANN = 1.0/FSHANN
/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/ 
rcard_tor1.f:  FSHANN = 1.4



Garib
P.S. That is for version 5.2.0005. For the next version it will be  
1.5 (it seemed to give consistent results).



On 14 Feb 2007, at 18:24, Billy Poon wrote:


Thanks both for your quick replies!

Bernie,

I didn't use the WEIGHT keyword because I'm not doing any  
refinement.  I only want to calculate the R values for a structure  
without any minimization.  And it seems that setting the  
SHANnon_factor keyword to the default value gives different R  
values than not setting the SHANnon_factor keyword at all (the  
program will use the default value in the source code).


And Garib,

In rcard_tor1.f in the $CCP4/src/refmac5_/ directory, the default  
shannon factor seems to be set to 1.5.  I'm using version 5.2.0019  
of REFMAC.  Is the default something else in the newer version?


-Billy

Santarsiero, Bernard D. wrote:
You didn't say anything about the "weighting term" between the F's  
and
geometrical parameters. That will substantially affect the R's,  
and the
default value of 0.3 in REFMAC isn't appropriate for all  
structures. In

CNS, it's adjusted to a more reasonable value during refinement.

Bernie Santarsiero


On Wed, February 14, 2007 10:36 am, Billy Poon wrote:


Dear all,

I have been using REFMAC5 to calculate the R values of several  
structures

from
the PDB and was confused by the behavior of the SHANnon_factor  
keyword.

When I
leave it at the default (set at 1.5 in the source code), I get  
one set of

R
values.  But when I manually set the value to 1.5 (SHANnon_factor  
1.5) in

the
script, I get a different set of values.  Usually, it's off at  
the third

or
fourth decimal place, but for one case (PDB code 2OAU), I get a  
difference

of
about 0.0116 (0.28416 for default, 0.27258 for manual setting)  
for the R

value
and 0.0184 (0.31653 for default, 0.29818 for manual setting) in  
the Free

R.

I have tested this on the following architectures and they all  
behave the

same
way:

Intel Xeon (32-bit Linux, REFMAC 5.2.0019, compiled with Intel  
compilers

9.1)
Intel Itanium2 (64-bit Linux, REFMAC 5.2.0019, compiled with Intel
compilers
9.1)
AMD Opteron (64-bit Linux, REFMAC 5.2.0019, compiled with GNU  
compilers

3.3.3)
SGI MIPS (IRIX 6.5, REFMAC 5.2.0003, pre-compiled binaries)

I am not doing any refining of the structures.  I just wanted to  
see what

the R
values are when calculated with REFMAC5 (the structures I was  
looking at

were
refined in CNS or X-PLOR) and was confused by the different  
results with
the same setting.  Also, should changing the SHANnon_factor  
affect the R

values much?  Thanks in advance for your help!

-Billy

And the script I use is pasted below:

#
# Refmac
#
refmac:
refmac5 \
HKLIN ./fo.mtz \
XYZIN ./2oau.pdb \
XYZOUT ./test.pdb \
<< eor
#
# Do not add hydrogens
#
MAKE HYDR N
MAKE LINK N
MAKE CHECK NONE
#
# Input mtz labels
#
LABIN FP=FP SIGFP=SIGFP FREE=FREE
#
# Set resolution
#
REFI RESOlution 3.7 50.00
#
# Define NCS
#
NCSR NCHAI 7 CHAI A B C D E F G NSPANS 1 1 254 4
#
# Refine overall B factor
#
REFI BREF OVERall
#
# Set Free flag
#
FREE 0
#
# Number of refinement cycles
#
NCYC 0
#
# Monitoring level
#
MONI MEDI
#
# Change Shannon sampling (commented out if testing default  
behavior)

#
SHANNON_FACTOR 1.5
#
# end
#
end
eor

Re: [ccp4bb] REFMAC5 and Shannon factor

[Billy Poon]

Thanks both for your quick replies!

Bernie,

I didn't use the WEIGHT keyword because I'm not doing any refinement.  I 
only want to calculate the R values for a structure without any 
minimization.  And it seems that setting the SHANnon_factor keyword to 
the default value gives different R values than not setting the 
SHANnon_factor keyword at all (the program will use the default value in 
the source code).


And Garib,

In rcard_tor1.f in the $CCP4/src/refmac5_/ directory, the default 
shannon factor seems to be set to 1.5.  I'm using version 5.2.0019 of 
REFMAC.  Is the default something else in the newer version?


-Billy

Santarsiero, Bernard D. wrote:

You didn't say anything about the "weighting term" between the F's and
geometrical parameters. That will substantially affect the R's, and the
default value of 0.3 in REFMAC isn't appropriate for all structures. In
CNS, it's adjusted to a more reasonable value during refinement.

Bernie Santarsiero


On Wed, February 14, 2007 10:36 am, Billy Poon wrote:
  

Dear all,

I have been using REFMAC5 to calculate the R values of several structures
from
the PDB and was confused by the behavior of the SHANnon_factor keyword.
When I
leave it at the default (set at 1.5 in the source code), I get one set of
R
values.  But when I manually set the value to 1.5 (SHANnon_factor 1.5) in
the
script, I get a different set of values.  Usually, it's off at the third
or
fourth decimal place, but for one case (PDB code 2OAU), I get a difference
of
about 0.0116 (0.28416 for default, 0.27258 for manual setting) for the R
value
and 0.0184 (0.31653 for default, 0.29818 for manual setting) in the Free
R.

I have tested this on the following architectures and they all behave the
same
way:

Intel Xeon (32-bit Linux, REFMAC 5.2.0019, compiled with Intel compilers
9.1)
Intel Itanium2 (64-bit Linux, REFMAC 5.2.0019, compiled with Intel
compilers
9.1)
AMD Opteron (64-bit Linux, REFMAC 5.2.0019, compiled with GNU compilers
3.3.3)
SGI MIPS (IRIX 6.5, REFMAC 5.2.0003, pre-compiled binaries)

I am not doing any refining of the structures.  I just wanted to see what
the R
values are when calculated with REFMAC5 (the structures I was looking at
were
refined in CNS or X-PLOR) and was confused by the different results with
the same setting.  Also, should changing the SHANnon_factor affect the R
values much?  Thanks in advance for your help!

-Billy

And the script I use is pasted below:

#
# Refmac
#
refmac:
refmac5 \
HKLIN ./fo.mtz \
XYZIN ./2oau.pdb \
XYZOUT ./test.pdb \
<< eor
#
# Do not add hydrogens
#
MAKE HYDR N
MAKE LINK N
MAKE CHECK NONE
#
# Input mtz labels
#
LABIN FP=FP SIGFP=SIGFP FREE=FREE
#
# Set resolution
#
REFI RESOlution 3.7 50.00
#
# Define NCS
#
NCSR NCHAI 7 CHAI A B C D E F G NSPANS 1 1 254 4
#
# Refine overall B factor
#
REFI BREF OVERall
#
# Set Free flag
#
FREE 0
#
# Number of refinement cycles
#
NCYC 0
#
# Monitoring level
#
MONI MEDI
#
# Change Shannon sampling (commented out if testing default behavior)
#
SHANNON_FACTOR 1.5
#
# end
#
end
eor







  

[ccp4bb] DENSITY MODIFICATION PROGRAM

[GP Poornam]

Dear All,

I am looking for a density modification program called Demon/Angel.

CCP4 manual has an outdated ftp link for the same I guess. Can anyone
provide me the updated link to it please?

Thanks and regards,

GP Poornam

Re: [ccp4bb] electron density maps in Coot vs O / Pymol

[Sue Roberts]

In addition to contouring differences, your  mapmask script asks for  
a border of only 2 A around the pdb file.  If you're looking for  
waters, unbuilt loops, or things on the edge of your pdb file, this  
will need to be larger.  When I used O and created the maps over the  
pdb file of interest I used a border at least 5 A.



On Feb 14, 2007, at 9:58 AM, mac minista wrote:


Hi,

thank you for your suggestions, the difference I am
seeing in the maps is mainly with the Fo-Fc maps i.e.
what appears in coot does not always appear in
O/Pymol. Here are the scripts for FFT and MAPMASK:

FFT

#!/bin/sh

set -e

fft hklin  model.mtz  mapout fofc_f.map <_ 
___

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Try the free Yahoo! Mail Beta.
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Sue Roberts
Biochemistry & Biopphysics
University of Arizona

[EMAIL PROTECTED]

Re: [ccp4bb] electron density maps in Coot vs O / Pymol

[Soisson, Stephen Michael]

I am guessing it is a difference in normalization, but I would love to hear a 
definitive answer from someone.

Steve


-Original Message-
From: CCP4 bulletin board on behalf of mac minista
Sent: Wed 2/14/2007 10:59 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] electron density maps in Coot vs O / Pymol
 
Dear all,
 
I have noticed that going from refmac 5 (script) to generate fo-fc and 2fo-fc 
maps in O / Pymol once and Coot in the other, the outcome is not exactly the 
same electron density maps-I mean some differences are seen.  I have used the 
following columns in Coot (latest version): FOFCWT, PHFOFCWT and 2FOFCWT, 
PH2FOFCWT.  The .o map file was generated using FFT, MAPMASK and MAPMAN.
I want to know why I am not getting identical maps, and if there is a solution 
to avoid this problem then I would really appreciate your help.
 
With regards
Mac



Finding fabulous fares is fun.
Let Yahoo! FareChase search your favorite travel sites 

  to find flight and hotel bargains.


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Re: [ccp4bb] AKTA prime

[Flip Hoedemaeker]

 Thanks to all who replied so promptly.. What I feared was true, you need
one of those ancient OS/2 computers for the software to run..:(

Luckily I now found a system that comes shipped with software on a working
computer for the same price..:)

Like Heidi Schubert says, I love these old machines, not too many things
that can break, etc. There are more 2nd hand systems around, so this might
be a good alternative for a new Äkta...

Flip

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Flip
Hoedemaeker
Sent: Wednesday, February 14, 2007 15:30
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AKTA prime

 Talking about akta's and beyond... Im offered a 2nd hand Pharmacia FPLC,
but in order to run it with a PC I'd need a copy of FPLCManager. The
software is not sold anymore by Pharmacia --> Amersham --> GE. Would anybody
have a copy lying around by any chance? 

Thx,

Flip

Re: [ccp4bb] electron density maps in Coot vs O / Pymol

[Peter Adrian Meyer]

Hi Mac,

>   I have noticed that going from refmac 5 (script) to generate fo-fc and
> 2fo-fc maps in O / Pymol once and Coot in the other, the outcome is not
exactly the same electron density maps-I mean some differences are seen.
>  I have used the following columns in Coot (latest version): FOFCWT,
> PHFOFCWT and 2FOFCWT, PH2FOFCWT.  The .o map file was generated using
FFT, MAPMASK and MAPMAN.
>   I want to know why I am not getting identical maps, and if there is a
> solution to avoid this problem then I would really appreciate your help.

There could be any number of reasons; which is more likely would depend on
the level of differences between the maps.  In (rough) level of
significance, the ones I can think of are:

1. inputs - are your scripts using the same columns as coot (if I'm
understanding correctly that coot is calculating the maps on the fly for
you)?

2. FFT specific stuff - are both maps being calculated using the same
gridpoints and FFT algorithm?

3. contouring issues - the graphics programs may be using different
contouring algorithms; if you're contouring by sigma/rms deviation, then
this can be affected by the size of the region used for rms determination
(are the maps the same size?).  Map normalization may also be an issue.

4. Computational "noise" - I've been able to get non-identical maps just
by changing the variable precision (identical input files) used by the
programs.  The differences are minimal, but observable.  I'm assuming that
you're using a single system for both maps, otherwise there could be
additional issues (although these should also be relatively minor).

One thing that shouldn't make a difference - O can directly read ccp4
formatted maps, so using FFT with xyzlim asu and reading in O with qmap or
fmap should let you skip over the mapmask/mapman steps.

As far as your specific case, run down the list of things that could have
an effect (there may be other issues that I'm forgetting), and eventually
you should find where the differences are.

Good luck,

Pete

Pete Meyer
Fu Lab
BMCB grad student
Cornell University

Re: [ccp4bb] REFMAC5 and Shannon factor

[Santarsiero, Bernard D.]

You didn't say anything about the "weighting term" between the F's and
geometrical parameters. That will substantially affect the R's, and the
default value of 0.3 in REFMAC isn't appropriate for all structures. In
CNS, it's adjusted to a more reasonable value during refinement.

Bernie Santarsiero


On Wed, February 14, 2007 10:36 am, Billy Poon wrote:
> Dear all,
>
> I have been using REFMAC5 to calculate the R values of several structures
> from
> the PDB and was confused by the behavior of the SHANnon_factor keyword.
> When I
> leave it at the default (set at 1.5 in the source code), I get one set of
> R
> values.  But when I manually set the value to 1.5 (SHANnon_factor 1.5) in
> the
> script, I get a different set of values.  Usually, it's off at the third
> or
> fourth decimal place, but for one case (PDB code 2OAU), I get a difference
> of
> about 0.0116 (0.28416 for default, 0.27258 for manual setting) for the R
> value
> and 0.0184 (0.31653 for default, 0.29818 for manual setting) in the Free
> R.
>
> I have tested this on the following architectures and they all behave the
> same
> way:
>
> Intel Xeon (32-bit Linux, REFMAC 5.2.0019, compiled with Intel compilers
> 9.1)
> Intel Itanium2 (64-bit Linux, REFMAC 5.2.0019, compiled with Intel
> compilers
> 9.1)
> AMD Opteron (64-bit Linux, REFMAC 5.2.0019, compiled with GNU compilers
> 3.3.3)
> SGI MIPS (IRIX 6.5, REFMAC 5.2.0003, pre-compiled binaries)
>
> I am not doing any refining of the structures.  I just wanted to see what
> the R
> values are when calculated with REFMAC5 (the structures I was looking at
> were
> refined in CNS or X-PLOR) and was confused by the different results with
> the same setting.  Also, should changing the SHANnon_factor affect the R
> values much?  Thanks in advance for your help!
>
> -Billy
>
> And the script I use is pasted below:
>
> #
> # Refmac
> #
> refmac:
> refmac5 \
> HKLIN ./fo.mtz \
> XYZIN ./2oau.pdb \
> XYZOUT ./test.pdb \
> << eor
> #
> # Do not add hydrogens
> #
> MAKE HYDR N
> MAKE LINK N
> MAKE CHECK NONE
> #
> # Input mtz labels
> #
> LABIN FP=FP SIGFP=SIGFP FREE=FREE
> #
> # Set resolution
> #
> REFI RESOlution 3.7 50.00
> #
> # Define NCS
> #
> NCSR NCHAI 7 CHAI A B C D E F G NSPANS 1 1 254 4
> #
> # Refine overall B factor
> #
> REFI BREF OVERall
> #
> # Set Free flag
> #
> FREE 0
> #
> # Number of refinement cycles
> #
> NCYC 0
> #
> # Monitoring level
> #
> MONI MEDI
> #
> # Change Shannon sampling (commented out if testing default behavior)
> #
> SHANNON_FACTOR 1.5
> #
> # end
> #
> end
> eor
>
>

Re: [ccp4bb] electron density maps in Coot vs O / Pymol

[mac minista]

Hi, 

thank you for your suggestions, the difference I am
seeing in the maps is mainly with the Fo-Fc maps i.e.
what appears in coot does not always appear in
O/Pymol. Here are the scripts for FFT and MAPMASK:

FFT

#!/bin/sh

set -e

fft hklin  model.mtz  mapout fofc_f.map 

Re: [ccp4bb] Bio-rad DuoFlow

[Tamir Gonen]

I beg to differ.

I have been an AKTA explorer user for about 5 years and switched to  
DuoFlow about 4 yrs ago and now have one in my own lab. The BioRad  
DuoFlow is awesome. It never ever breaks. I never had any problems  
with this machine at all, it takes any column (pharmacia or  
otherwise) given the right adapters. The AKTA are really cumbersome  
and complicated to use and teach on - its all inside a big black box  
that looks (and feels) like a tank, while the DuoFlow has a really  
simple design, and is basically "plug and play".


The AKTA is really good for analytical applications when you have  
very small amounts of your protein and of course you can detect  
multiple wave lengths at a time (you can add special unit for multi  
wavelengths on the biorad). The DuoFlow struggles  with very small  
protein concentrations (<0.05mg/ml) and the void volume on its tubing  
further dilutes the sample. If you know what you are doing, it is  
easy to optimize the setup in such a way that you minimize the void  
volume on the DuoFlow.


Finally, the AKTA has an in line filter which always gets clogged up  
when you have buffer with detergent. The DuoFlow does not have a  
filter at all which means if your students and postdocs are not  
careful, the filters in the column will get clogged. But all you need  
to do is filter your sample prior to injection.


BioRad service is not so great but if you take care of your machine  
you really dont need to worry. It is really robust. Plus, for the  
price of an explorer you could buy two top-of-the-line DuoFlow  
systems together with columns.


Tamir.


__
Dr Tamir Gonen

Department of Biochemistry
Box 357350
University of Washington
Seattle, WA 98195

Tel: (206) 616 7565 (Office)
(206) 616 8529 (Lab)
Fax: (206) 685 1792
[EMAIL PROTECTED]

http://faculty.washington.edu/tgonen/




On Feb 14, 2007, at 8:19 AM, Frank Lee wrote:



Dear all,

Thanks a lot for all the feedbacks on AKTA prime. They are so  
helpful that I have abandoned the idea of buying one. Now it is a  
choice between AKTA FPLC and Bio-rad DuoFlow. I heard that DuoFlow  
is not as robust as AKTA and that its parts break down often. The  
question is whether quality difference is worth price difference (~ 
$10K). Any feebacks on DuoFlow would be highly appreciated!


Best,
Frank

Food fight? Enjoy some healthy debate
in the Yahoo! Answers Food & Drink Q&A.

Re: [ccp4bb] electron density maps in Coot vs O / Pymol

[Paul Emsley]

On Wed, 2007-02-14 at 07:59 -0800, mac minista wrote:
> Dear all,
>  
> I have noticed that going from refmac 5 (script) to generate fo-fc and
> 2fo-fc maps in O / Pymol once and Coot in the other, the outcome is
> not exactly the same electron density maps-I mean some differences are
> seen.  I have used the following columns in Coot (latest version):
> FOFCWT, PHFOFCWT and 2FOFCWT, PH2FOFCWT.  The .o map file was
> generated using FFT, MAPMASK and MAPMAN.
> I want to know why I am not getting identical maps, and if there is a
> solution to avoid this problem then I would really appreciate your
> help.

Well, the devil is in the detail.
a MAPMAN map in O vs a REFMAC MTZ in Coot.  Somewhat apples and oranges.
Stating the obvious: the griding and contour level may well be
different.  The contouring algorithms certainly are.

How about a Coot/Refmac + Mapman map in O 
or a 
MAPMAN map in Coot?  
Then the differences will be more clear?

What do you get if you overlapmap
ADD 1 -1 
and look at differences there?

[ccp4bb] REFMAC5 and Shannon factor

[Billy Poon]

Dear all,

I have been using REFMAC5 to calculate the R values of several structures from
the PDB and was confused by the behavior of the SHANnon_factor keyword.  When I
leave it at the default (set at 1.5 in the source code), I get one set of R
values.  But when I manually set the value to 1.5 (SHANnon_factor 1.5) in the
script, I get a different set of values.  Usually, it's off at the third or
fourth decimal place, but for one case (PDB code 2OAU), I get a difference of
about 0.0116 (0.28416 for default, 0.27258 for manual setting) for the R value
and 0.0184 (0.31653 for default, 0.29818 for manual setting) in the Free R.

I have tested this on the following architectures and they all behave the same
way:

Intel Xeon (32-bit Linux, REFMAC 5.2.0019, compiled with Intel compilers 9.1)
Intel Itanium2 (64-bit Linux, REFMAC 5.2.0019, compiled with Intel compilers
9.1)
AMD Opteron (64-bit Linux, REFMAC 5.2.0019, compiled with GNU compilers 3.3.3)
SGI MIPS (IRIX 6.5, REFMAC 5.2.0003, pre-compiled binaries)

I am not doing any refining of the structures.  I just wanted to see what the R
values are when calculated with REFMAC5 (the structures I was looking at were
refined in CNS or X-PLOR) and was confused by the different results with the 
same setting.  Also, should changing the SHANnon_factor affect the R values 
much?  Thanks in advance for your help!

-Billy

And the script I use is pasted below:

#
# Refmac
#
refmac:
refmac5 \
HKLIN ./fo.mtz \
XYZIN ./2oau.pdb \
XYZOUT ./test.pdb \
<< eor
#
# Do not add hydrogens
#
MAKE HYDR N
MAKE LINK N
MAKE CHECK NONE
#
# Input mtz labels
#
LABIN FP=FP SIGFP=SIGFP FREE=FREE
#
# Set resolution
#
REFI RESOlution 3.7 50.00
#
# Define NCS
#
NCSR NCHAI 7 CHAI A B C D E F G NSPANS 1 1 254 4
#
# Refine overall B factor
#
REFI BREF OVERall
#
# Set Free flag
#
FREE 0
#
# Number of refinement cycles
#
NCYC 0
#
# Monitoring level
#
MONI MEDI
#
# Change Shannon sampling (commented out if testing default behavior)
#
SHANNON_FACTOR 1.5
#
# end
#
end
eor

Re: [ccp4bb] electron density maps in Coot vs O / Pymol

[William Scott]

I use this to get the same maps:

http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/mapcover
http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/mapcoverdiff

I used zsh but I think it should work with current versions of bash.

mac minista wrote:
> Dear all,
>
>   I have noticed that going from refmac 5 (script) to generate fo-fc and
> 2fo-fc maps in O / Pymol once and Coot in the other, the outcome is not
> exactly the same electron density maps-I mean some differences are seen.
>  I have used the following columns in Coot (latest version): FOFCWT,
> PHFOFCWT and 2FOFCWT, PH2FOFCWT.  The .o map file was generated using
> FFT, MAPMASK and MAPMAN.
>   I want to know why I am not getting identical maps, and if there is a
> solution to avoid this problem then I would really appreciate your help.
>
>   With regards
>   Mac
>
>
> -
> Finding fabulous fares is fun.
> Let Yahoo! FareChase search your favorite travel sites to find flight and
> hotel bargains.

[ccp4bb] Bio-rad DuoFlow

[Frank Lee]

Dear all,

Thanks a lot for all the feedbacks on AKTA prime. They are so helpful that I 
have abandoned the idea of buying one. Now it is a choice between AKTA FPLC and 
Bio-rad DuoFlow. I heard that DuoFlow is not as robust as AKTA and that its 
parts break down often. The question is whether quality difference is worth 
price difference (~$10K). Any feebacks on DuoFlow would be highly appreciated!

Best,
Frank

 
-
Food fight? Enjoy some healthy debate
in the Yahoo! Answers Food & Drink Q&A.

[ccp4bb] electron density maps in Coot vs O / Pymol

[mac minista]

Dear all,
   
  I have noticed that going from refmac 5 (script) to generate fo-fc and 2fo-fc 
maps in O / Pymol once and Coot in the other, the outcome is not exactly the 
same electron density maps-I mean some differences are seen.  I have used the 
following columns in Coot (latest version): FOFCWT, PHFOFCWT and 2FOFCWT, 
PH2FOFCWT.  The .o map file was generated using FFT, MAPMASK and MAPMAN.
  I want to know why I am not getting identical maps, and if there is a 
solution to avoid this problem then I would really appreciate your help.
   
  With regards
  Mac

 
-
Finding fabulous fares is fun.
Let Yahoo! FareChase search your favorite travel sites to find flight and hotel 
bargains.

Re: [ccp4bb] Multi-copies in one assymetric unit

[Petrus H Zwart]

> This isnt any real help but I cant solve a ferritin structure in 
> SG I432 
> - it probably forms a cage like the other feritins around the 
> origin, 
> but every solution I get clashes with others..
> After listening to a lecture by a small molecule crystallographer 
> I 
> wondered whether there isnt some crystal defect but I am not sure 
> how to 
> monitor it..
> Eleanor


Hi Elenaor, 

Your problem reminds me of this paper:

http://journals.iucr.org/a/issues/2004/04/00/lc0065/index.html

Not sure if it is related (probably not), but the phenomenon itself is 
interesting

Cheers

Peter

Re: [ccp4bb] AKTA prime

[Flip Hoedemaeker]

 Talking about akta's and beyond... Im offered a 2nd hand Pharmacia FPLC,
but in order to run it with a PC I'd need a copy of FPLCManager. The
software is not sold anymore by Pharmacia --> Amersham --> GE. Would anybody
have a copy lying around by any chance? 

Thx,

Flip

Re: [ccp4bb] AKTA prime

[artem]

Hi,

Don't forget system losses (friction in the tubing). An empty AKTA prime
typically eats up about 0.25 MPa so your maximum is closer to 0.7MPa loss
on column.

Artem
>
>
>  Dear Frank,
>  AKTA prime delivers a max. pressure of 1 MPa. The 24 ml SEC columns can
> be run at pressures
>  up to 1.5 (S200) or even 3 MPa (superose 12). If your column is in pretty
> good shape, expect to
>  reach 0.9 MPa at 0.4 ml/min for S200. So you can use an AKTA prime, but
> ...
>  Best
>  Clemens
>
>
>  At 11:16 PM 2/13/2007, you wrote:
>
>  Dear all,
>
>  I need to decide between buying an AKTA prime and an AKTA FPLC from GE
> health care. I understand AKTA prime is a low-pressure system, but
> because it is too much cheaper than AKTA FPLC, it is still very
> attractive to me.
>
>  I will mainly use it for Nickel columns and gel filtration columns, and I
> am worried about the latter. Is it true that using AKTA prime, you can
> only run the 24 ml Superdex 200 column at 0.1 or 0.2 ml/min?
>
>  Could anyone who has used AKTA prime give me some feedbacks? I would
> appreciate it.
>
>  Best,
>  Frank
>
>
>  Need Mail bonding?
>  Go to the  Yahoo! Mail Q&A for  great tips from Yahoo! Answers users.
>  Jun.-Prof. Dr. Clemens Steegborn
>  Ruhr-University Bochum
>  Dept. Physiol. Chemistry, MA 2/141
>  Universitaetsstr. 150
>  44801 Bochum, Germany
>
>  phone: 0049 234 32 27041
>  fax: 0049 234 32 14193
>  email: [EMAIL PROTECTED]

[ccp4bb] X-ray crystallography PhD-positions in Hannover Medical School

[Roman Fedorov]

The Institute for Biophysical Chemistry at Hannover Medical School invites
motivated and enthusiastic young scientists to apply for PhD positions.

The research projects will be performed within the framework of DFG-funded
programs and aims to determine the principles by which particular structural
features relate to the mechanisms that underlie the biological function of motor
proteins. 
The projects require a multi-facetted approach including X-ray crystallography,
molecular modelling and computer-based design, fast kinetics, and
microscopy-based techniques.

The ideal candidate should have a solid background in protein biochemistry and
biophysics. A good experience in recombinant protein expression and purification
is required and experience in protein crystallization, structure determination
and molecular modelling would be advantageous.

Facilities available include a protein crystallization laboratory fully-equipped
for high-throughput protein crystallography, access to synchrotron radiation
sources, graphical workstations and Linux cluster for model building and
computational molecular design, Dictyostelium discoideum and E.coli expression
systems, FPLC purification, state-of-the-art equipment for time-resolved laser
spectroscopy and analytical ultracentrifugation, HiTech Stopped-Flow and Applied
Photophysics p-Star-180 equipment for kinetics measurements, static and dynamic
light-scattering spectrofluorimeter, large selection of high-end microscopes
including a 4-Pi super-resolution confocal microscope.

Contact: Applications should include the following: letter of interest,
curriculum vitae,
academic certificates and the names and contact details of two referees. All
applications should be sent to

Prof. Dietmar J. Manstein
Email: [EMAIL PROTECTED]
Homepage: http://www.mh-hannover.de/institute/bpc/
Postal address:
MHH, Institute for Biophysical Chemistry, OE4350
Carl-Neuberg-Straße 1, D-30623 Hannover




-- 
Dr. Roman Fedorov
Biophysikalische Chemie, OE 4350
Medizinische Hochschule Hannover
Carl-Neuberg-Strasse 1
30625 Hannover
Germany

e-mail: [EMAIL PROTECTED]
Phone: +49 511 532 3705

Re: [ccp4bb] x86-64

[Serge Cohen]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Phil;

If you are using gcc/g++ (and also most likely gfortran) you should  
add the option -m32 to the compiler (this will make sure the code is  
compiled for 32bits, so you can link it with 32bits libraries).


I don't know how you could do the same when using intel's compilers...

Serge.

Le 14 févr. 07 à 11:00, Phil Evans a écrit :

I'm just starting to use a 64-bit Linux machine (running some sort  
of RedHat Enterprise system) as a development machine


Our general CCP4 installation is from the binary download (redHat  
option) (presumably built on a 32-bit machine), which seems to run  
OK on a range of different Linux machines


However if I compile on the 64-bit machine & try to link with these  
libraries, it doesn't work


r/bin/ld: skipping incompatible /public/xtal/ccp4-6.0/ccp4-6.0.2- 
linux/lib/libccp4f.a when searching for -lccp4f

/usr/bin/ld: cannot find -lccp4f
collect2: ld returned 1 exit status
make: *** [scala] Error 1


Is it possible to set compile flags to produce something (.o) which  
will link with th distributed libraries, and produce an executable  
which will run on other (32-bit) Linux machines?


In the mean time, I'm doing a complete source build on the 64-bit  
machine


Phil


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Version: GnuPG v1.4.3 (Darwin)

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D7gopAqky0LXuUtYfegzSPY=
=i3PD
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Re: [ccp4bb] x86-64 found it

[Phil Evans]

found it: compiler switch "-m32", works

sorry for the message (but it might be useful to others, I suppose)

Phil


On 14 Feb 2007, at 10:00, Phil Evans wrote:

I'm just starting to use a 64-bit Linux machine (running some sort  
of RedHat Enterprise system) as a development machine


Our general CCP4 installation is from the binary download (redHat  
option) (presumably built on a 32-bit machine), which seems to run  
OK on a range of different Linux machines


However if I compile on the 64-bit machine & try to link with these  
libraries, it doesn't work


r/bin/ld: skipping incompatible /public/xtal/ccp4-6.0/ccp4-6.0.2- 
linux/lib/libccp4f.a when searching for -lccp4f

/usr/bin/ld: cannot find -lccp4f
collect2: ld returned 1 exit status
make: *** [scala] Error 1


Is it possible to set compile flags to produce something (.o) which  
will link with th distributed libraries, and produce an executable  
which will run on other (32-bit) Linux machines?


In the mean time, I'm doing a complete source build on the 64-bit  
machine


Phil

[ccp4bb] x86-64

[Phil Evans]

I'm just starting to use a 64-bit Linux machine (running some sort of  
RedHat Enterprise system) as a development machine


Our general CCP4 installation is from the binary download (redHat  
option) (presumably built on a 32-bit machine), which seems to run OK  
on a range of different Linux machines


However if I compile on the 64-bit machine & try to link with these  
libraries, it doesn't work


r/bin/ld: skipping incompatible /public/xtal/ccp4-6.0/ccp4-6.0.2- 
linux/lib/libccp4f.a when searching for -lccp4f

/usr/bin/ld: cannot find -lccp4f
collect2: ld returned 1 exit status
make: *** [scala] Error 1


Is it possible to set compile flags to produce something (.o) which  
will link with th distributed libraries, and produce an executable  
which will run on other (32-bit) Linux machines?


In the mean time, I'm doing a complete source build on the 64-bit  
machine


Phil

Re: [ccp4bb] AKTA prime

[Clemens Steegborn]

Dear Frank,
AKTA prime delivers a max. pressure of 1 MPa. The 24 ml SEC columns can
be run at pressures
up to 1.5 (S200) or even 3 MPa (superose 12). If your column is in pretty
good shape, expect to
reach 0.9 MPa at 0.4 ml/min for S200. So you can use an AKTA prime, but
...
Best
Clemens

At 11:16 PM 2/13/2007, you wrote:
Dear all,
I need to decide between buying an AKTA prime and an AKTA FPLC from GE
health care. I understand AKTA prime is a low-pressure system, but
because it is too much cheaper than AKTA FPLC, it is still very
attractive to me.
I will mainly use it for Nickel columns and gel filtration columns, and I
am worried about the latter. Is it true that using AKTA prime, you can
only run the 24 ml Superdex 200 column at 0.1 or 0.2 ml/min?
Could anyone who has used AKTA prime give me some feedbacks? I would
appreciate it.
Best,
Frank

Need Mail bonding?
Go to the

Yahoo! Mail Q&A for

great tips from Yahoo! Answers users. 

Jun.-Prof. Dr. Clemens Steegborn
Ruhr-University Bochum
Dept. Physiol. Chemistry, MA 2/141
Universitaetsstr. 150
44801 Bochum, Germany
phone: 0049 234 32 27041
fax: 0049 234 32 14193
email: [EMAIL PROTECTED] 

Re: [ccp4bb] Multi-copies in one assymetric unit

[Eleanor Dodson]

Well - you can hardly get a higher symmetry space group to match some of 
the NC related molecules!

Good luck with the number 6.

This isnt any real help but I cant solve a ferritin structure in SG I432 
- it probably forms a cage like the other feritins around the origin, 
but every solution I get clashes with others..
After listening to a lecture by a small molecule crystallographer I 
wondered whether there isnt some crystal defect but I am not sure how to 
monitor it..

Eleanor

Yanming Zhang wrote:

Sorry I forget to tell ya the details:

The SG of my Data is cubic P4332. Cell is 251.34A in all three 
dimensions.

Resolution is 3.1A. 5,6,7,8 might be the possible copies from Matthew
coeficient. But I just trust 6 because Chinese like the number 6
(happy Chinese new year by the way :)). No pseudo translation judged 
by Native Patterson. Self-rotation at the section kappa=180 shows 
strong peaks at phi=45 and psi=45.At the stage of map generation, the 
Rfree is 42% R is 38%.

Thanks!
Yanming


On Tue, 13 Feb 2007, Eleanor Dodson wrote:

Sometimes this sort of disorder is due to an error , so the first 
thing is to check very carefully that the solution makes sense.


Why are you so sure there are 6 copies in the asymmetric unit?

In situations like this I first worry about SG.

Is there a pseudo-translation vector? This can make it hard to decide 
on the SG..


Is there an alternate spacegroup with fewer molecules in the asymm unit?

What does the self rotation show?



Yanming Zhang wrote:

Dear All,

Maybe this is a trivial question:

My data should have 6 molecules in one assymetric unit.  MR could 
find out 4 molecules. After this, no matter how hard I have tried, 
no more molecules can be found. At this stage, I suppose that all 
other copies are dis-ordered. And go ahead to do refinement with 4 
molecules (ABCD) available.
The density for A is quite good. But for BCD are very dis-ordered. 
Many breaks in chains. I'd like to ask you:

In a situation like this, should I:
A, Use NCS for all copies?
B Do not use NCS at all?
C, Use NCS just for BCD? (even dis-ordered, but similar)?
What is the trick to lower down Rfree as soon as possible, if you 
have experienced the same situation before?



Thanks

Yanming