Re: [ccp4bb] Bio-rad DuoFlow

(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 s

Re: [ccp4bb] Bio-rad DuoFlow

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

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

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

Re: [ccp4bb] Bio-rad DuoFlow

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 an

Re: [ccp4bb] REFMAC5 and Shannon factor

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 keywo

Re: [ccp4bb] Bio-rad DuoFlow

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 "DuoFl

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

"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 c

Re: [ccp4bb] x86-64

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

Re: [ccp4bb] mtz to hkl conversion

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

Re: [ccp4bb] mtz to hkl conversion

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 ref

[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

Re: [ccp4bb] Bio-rad DuoFlow

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 bu

Re: [ccp4bb] REFMAC5 and Shannon factor

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/

Re: [ccp4bb] REFMAC5 and Shannon factor

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 value

[ccp4bb] DENSITY MODIFICATION PROGRAM

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

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

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

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 Coo

Re: [ccp4bb] AKTA prime

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,

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

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): FOFCW

Re: [ccp4bb] REFMAC5 and Shannon factor

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

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

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

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)

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

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 ha

[ccp4bb] REFMAC5 and Shannon factor

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 (S

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

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 notice

[ccp4bb] Bio-rad DuoFlow

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 qua

[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): FOF

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

> 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 th

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] AKTA prime

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

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

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

Re: [ccp4bb] x86-64

-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 sam

Re: [ccp4bb] x86-64 found it

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

[ccp4bb] x86-64

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 mach

Re: [ccp4bb] AKTA prime

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:

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

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 ge