Re: [ccp4bb] stuck with COOT installation in openSUSE 11.3

Hello Hena, maybe the libpng12.so.0 libraries on your system happen to be all 32-bit versions. You installed the 64-bit version (because of the "x86_64" in the name of the tar-archive), therefore you also require a 64-bit version of the libpng12.so.0. Do you have such a file in /usr/lib, and if so

[ccp4bb] stuck with COOT installation in openSUSE 11.3

Hello, I could not open the COOT GUI after installing either from 'coot-0.6.1-binary-Linux-x86_64-centos-5-gtk2.tar.gz' or from 'coot-0.6.2-pre-1-revision-3205-binary-Linux-x86_64-centos-5-gtk2.tar.gz' I used the following commands: 1. from /usr/loca/src sudo tar xvzf *.gz as suggested in http:

Re: [ccp4bb] Calculating Difference Maps Between an RCSB data set and an mtz (Different Ligand)

> 2) Scale F-holo and F-apo.  Use "Experimental Phasing", "Data > Preparation",    "Scale and Analyse Data Sets", "Scale refinement using > Scaleit".  Don't    include anomalous differences unless your interest is in > changing    anomalous scatterers.  My notes indicate that Fhscal works > better

Re: [ccp4bb] Calculating Difference Maps Between an RCSB data set and an mtz (Different Ligand)

Yes - you are. - There are some extra steps. Download pdbs and mtz files csymmmatch -pdbin-ref 1.pdb -pdbin 2.pdb -origin-hand -pdbout 2-to-1.pdb That checks they are on same origin and symmetry equivalent. refmac for 1.pdb refmac for 2-to-1.pdb cad to merge two refmac outputs. You will hav

Re: [ccp4bb] Calculating Difference Maps Between an RCSB data set and an mtz (Different Ligand)

Replacing the Coot step by FFT works too. An additional benefit of the Coot approach is that you can use LSQ-matched maps and maps on different grids and space groups. (I was under the impression that that was not quite so easy with FFT.) Also worth noting, Coot does not (yet) do auto-scal

Re: [ccp4bb] crystallizing a complex that's sensitive to ionic strength

Have you tried adding water to your reservoir and allowing it to vapor diffuse into the drop? Kris  Kris F. Tesh, Ph. D. Department of Biology and Biochemistry University of Houston - Original Message From: Tim Gruene To: CCP4BB@JISCMAIL.AC.UK Sent: Mon, February 28, 2011 3:48:25 AM

Re: [ccp4bb] Calculating Difference Maps Between an RCSB data set and an mtz (Different Ligand)

I just looked at a previous thread by Dale Tronrud that explains this. here it is: Re: [ccp4bb] Fo-Fo Difference Map Dale Tronrud Mon, 03 May 2010 16:19:46 -0700 I've struggled with getting CCP4 to calculate Fo-Fo maps, since I usually use other software. The tricks are that the data sets h

[ccp4bb] Calculating Difference Maps Between an RCSB data set and an mtz (Different Ligand)

Trying to calculate a difference map from a dataset downloaded from the RCSB and one I have. The following applies: Object find the difference between two bound ligands of the same structure in the same space group. My following work path has been: 1) Convert mmCIF to mtz (RCSB data set) 2) Use

Re: [ccp4bb] CCP4 for iphones

On 2/25/11 5:41 PM, Nat Echols wrote: On Fri, Feb 25, 2011 at 2:10 PM, Sean Seaver wrote: I've been curious if there has been discussion about moving data processing and refinement to a software as a service

Re: [ccp4bb] CCP4 for iphones

In a sentence, primarily due to cost and power constraints mobile devices don't (currently) have the horsepower to do any serious *generic* number crunching, as would be required for anything of interest to this community. On the topic of using otherwise-idle compute time, our group has a publicly

Re: [ccp4bb] Teaching powerpoints

I have brought my collection of teaching powerpoints etc. up to date. They are available free for educational purposes. Please send me an email if you wish to receive the password for accessing them. If you previously obtained this password from me it should still be valid. George Prof. George

[ccp4bb] AW: [ccp4bb] coot

Hi Zheng I think, it's much easier to go this way: Coot -> Extensions -> NCS -> Copy NCS Chain or Copy NCS Residue Range Cheers Stefan -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Zheng Zhou Gesendet: Montag, 28. Februar 2011 12:13 An:

[ccp4bb] Postdoc position available, University of Bristol, UK

Dear all, I have a 3 yr postdoc position available in my lab (Biochemistry, Bristol), starting early/mid April. Please see below for further particulars. Informal enquires welcome, though full applications MUST be made via the University of Bristol website (http://www.bris.ac.uk/boris/

Re: [ccp4bb] Density sharpening with Truncate?

Dear Randy, thanks for your comment - a good point with the likelihood target estimated from E-values! So, in principle, there shouldn't be any difference in maximum-likelihood refinement using sharpened data or not. However, for curiosity, in one case at 4.3 A resolution and a sharpening B-f

Re: [ccp4bb] coot

Hi, Stefanie Are those 6 molecules related by NCS? If so, you can model one first, and use transform_coords_molecule (imol, rtop) to generate others. I used to do this five times for a pentamer: output_pdb='template' for i in range (2,6): transform_coords_molecule (1, [[x1, y1, z1, x2, y

Re: [ccp4bb] Density sharpening with Truncate?

Hi, I'm on Garib's side here. The way the maximum likelihood targets work, the variances are defined relative to the average intensity in a resolution shell, so if you change the falloff the variances will change in the same way. In fact, one way to implement maximum likelihood refinement is

[ccp4bb] coot

Hello everybody, Currently I am refining my 6 x 220 amino acid structure and I was wondering if COOT is automatically writing a kind of protocol what I am changing in my pdb file when I am fitting-in new residues or mutate amino acids. If so where can I find it? Thanks a lot, Stefanie Dr. Ste

Re: [ccp4bb] crystallizing a complex that's sensitive to ionic strength

Dear Hua, adding water as suggested by Jan Kern could also be accomplished in a more sophisticated way by using dialysis buttons. They require large volumes, though, 5mul is the minimum as far as I know. At the fancy end of this you could try the TOPAZ system by fluidigm. At the ECM in Darmsta

Re: [ccp4bb] Density sharpening with Truncate?

Dear CCP4ers, I really would sharpen the structure factors, not only the electron density maps. The simple reason is: if sharpening emphasizes enough information at higher resolution to help interpreting the electron density maps, refinement will also benefit from this information. Of course,

Re: [ccp4bb] Off Topic: Web or e-tools for booking instrument time

Hi All, I have used MRBS http://mrbs.sourceforge.net/ to manage booking of a large number of instruments for a few years. Free, open source, simple, local installation, works very well. regards, Dmitry -- Dr. Dmitry Veprintsev Biomolecular Research Laboratory, OFLC/103 Paul Scherrer Institut