Re: [ccp4bb] a new version of XDS

Hi Folmer, it's just a matter of time, you know, given the short-living license of XDS. ;-) Anyway, I second the request, ciao, s On May 30, 2013, at 8:50 AM, Folmer Fredslund wrote: > Hi all, > > Nice with a new version (I guess that means improvements :-) > > Before I upgrade, I just have

Re: [ccp4bb] a new version of XDS

Hi all, Nice with a new version (I guess that means improvements :-) Before I upgrade, I just have one question: Does the change in the XPARM.XDS format mean that software such as xia2 will be broken? Thanks, Folmer 2013/5/29 Kay Diederichs > ... is available for academic users at http://ho

Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol

Hi Donghui, I don't think that is a problem in PyMOL. The cartoon representation is an idealized form of the secondary structure and does not strictly follow the atomic coordinates of the protein backbone. The strands are flattened and that's why you see the gaps between the strand and the side

Re: [ccp4bb] Screening a protein surface for interaction sites

On 05/29/2013 04:30 PM, Gang Dong wrote: Try FTsite: http://ftsite.bu.edu/. I have seen people using metapocket: http://projects.biotec.tu-dresden.de/metapocket/ Gang On Wed, May 29, 2013 09:17, Karsten Niefind wrote: Dear colleagues, please allow me to ask crystallography experts for adv

Re: [ccp4bb] a new version of XDS

I use Cygwin normally, which seems to work fine for most things... Jacob On Wed, May 29, 2013 at 5:08 PM, Jim Fairman wrote: > You can always use VMWare player to run a virtual machine of a Linux > distribution inside Windows. It's free and it works fairly well. > > > On Wed, May 29, 2013 at

Re: [ccp4bb] "Formageddon" is upon us... Important news from wwPDB! (help-4246)

Hi Rachel, Thanks for clarifying this. Things will be much easier when SPLIT entries are consolidated. That is, when all the software is updated as well. > Entries are split only for reasons of size. 1apg was, sort of, an example of the contrary (see the, now obsolete, reflection file). I th

Re: [ccp4bb] a new version of XDS

You can always use VMWare player to run a virtual machine of a Linux distribution inside Windows. It's free and it works fairly well. On Wed, May 29, 2013 at 1:29 PM, Jacob Keller < j-kell...@fsm.northwestern.edu> wrote: > Any thoughts of making a Windows executable? Might help a lot of users..

[ccp4bb] re big structure

I have been reprimanded by the PDB as: "In this instance we could not recommend matrix formulation because of the substantial conformational differences between individual subunits. Only with the full set of coordinates released can other groups perform independent analyses/evaluation." both

Re: [ccp4bb] a new version of XDS

Sorry, Wolfgang Kabsch has decided against it. Kay Jacob Keller schrieb: >Any thoughts of making a Windows executable? Might help a lot of >users > >JPK > > >On Wed, May 29, 2013 at 4:20 PM, Kay Diederichs < >kay.diederi...@uni-konstanz.de> wrote: > >> ... is available for academic users a

Re: [ccp4bb] a new version of XDS

Any thoughts of making a Windows executable? Might help a lot of users JPK On Wed, May 29, 2013 at 4:20 PM, Kay Diederichs < kay.diederi...@uni-konstanz.de> wrote: > ... is available for academic users at http://homes.mpimf-heidelberg.** > mpg.de/~kabsch/xds/

[ccp4bb] a new version of XDS

... is available for academic users at http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/ Please note that there are some incompatibilities; most notably, the new format of XPARM.XDS is different so that the new INTEGRATE does not work with an old XPARM.XDS. best, Kay smime.p7s Description:

Re: [ccp4bb] "Formageddon" is upon us... Important news from wwPDB! (help-4246)

Dear Robbie, We will continue the practice that any structure deposited as a single PDBx/mmCIF file will be divided into SPLIT files and added to the ftp archive as usual, in all supported formats (PDB, PDBx/mmCIF, PDBML/XML). Entries are split only for reasons of size. SPLIT entries current

[ccp4bb] the large structure now in the pdb

I am surprised that the fuss about the structure 3J3Q the pdb documentation states "For all structures deposited as complex assemblies, we will archive symmetry information as appropriate in _pdbx_point_symmetry or _pdbx_helical_symmetry records." For the cone shaped viral capsid discussed in 1

Re: [ccp4bb] To build ssDNA to base pair with the other strand of DNA in coot

> I am wondering whether there is a function I could use to build the > missing bases in one strand of the DNA to base pair with the other > strand of DNA which is complete... Calculate->Other modeling tools-> Base pair... -- Coot verendus est

[ccp4bb] To build ssDNA to base pair with the other strand of DNA in coot

Hi all, I am working on solving the crystal structure of a protein-DNA complex. I could complete one strand of the DNA to fit the electron density using Coot, but for the other strand, the density for several bases at each end of the DNA is not clear and it's missing several bases at each end of th

Re: [ccp4bb] use only companies that you know to purchase chemicals

> Just curious - why registration date indicates unsavory nature of "Jieke"? >From what I have seen people set up fake companies and use them as a front to >scam as many people as possible until they are discovered and someone posts >that it is a scam. Once they are found out they establish the

Re: [ccp4bb] use only companies that you know to purchase chemicals

On Wed, 2013-05-29 at 12:30 -0400, Jeremy Stevenson wrote: > In this particular case you can see the website was registered in > September of 2012, which is a good indication that it was set up just > to scam people. Just curious - why registration date indicates unsavory nature of "Jieke"? -- A

Re: [ccp4bb] use only companies that you know to purchase chemicals

Jackie, My heart goes out to you. I got scammed much worse than you. Someone posing as a distributor said they had several customers in China that wanted to place orders for our equipment. They got me to fly out to China and asked me to buy gifts for the president of their company. It turned ou

[ccp4bb] CSHL X-ray Methods in Structural Biology Course Oct 14-29, 2013: Application deadline June 15th

Hey Everybody, I wanted to draw your attention again to the upcoming application deadline on June 15, 2013 for the CSHL X-ray Methods in Structural Biology Course to be held October 14-29, 2013. Also please also pass this on to any colleagues, friends, professors, research associates, grad stud

Re: [ccp4bb] Dimple on windows?

On Tue, May 28, 2013 at 11:44:55AM +, Björn Kauppi wrote: > Is there any way to install the dimple script on my windows CCP4i > installation? > It will be included in the next version of the ccp4 suite. For now you can try command-line version from: http://devtools.fg.oisin.rc-harwell.ac.uk/

Re: [ccp4bb] how to make the crystal thicker

Dear Yan: I had a similar problem with the crystal(thin, thread diffraction in one direction ). Many try with the crystal optimization failed. However using micro-focus beamline with a small oscillation angel (0.1- 0.2 degree) I could collect a full data set and successfully processed with XDS.

Re: [ccp4bb] how to make the crystal thicker

There are many variables you can adjust, not sure how many you have tried. Here are a few that pop up first for me: Seeding (if growth is not well controlled) Changing drop ratio or vapor diffusion set up (sitting vs hanging vs under oil) to control the kinetic process as well as the final poin

Re: [ccp4bb] Screening a protein surface for interaction sites

Try FTsite: http://ftsite.bu.edu/. Gang On Wed, May 29, 2013 09:17, Karsten Niefind wrote: > Dear colleagues, > > please allow me to ask crystallography experts for advice in a > bioinformatics issue: > > Which methods (programs, servers) would you use and recommend to search > computationally on

[ccp4bb] Screening a protein surface for interaction sites

Dear colleagues, please allow me to ask crystallography experts for advice in a bioinformatics issue: Which methods (programs, servers) would you use and recommend to search computationally on the surface of a protein/protein complex (> 1100 aa) for concave and convex interaction sites with