[ccp4bb] ccp4 on Mac Intel

Dear all, I have installed ccp4 with the dmg package, and everything is installed nicely in the Application folder, and I can get ccp4i working just by launching from the ccp4 icon. However, I would also like to have the commands working from a X11 terminal, to get it working for, say xia2.

Re: [ccp4bb] reproducibility of protein crystals

sometimes， a little bit change of concentration of your precipitate or pH buffer can affect your crystal. My suggestion is setup a appropriate gradient of your precipitate and additive.

Re: [ccp4bb] ccp4 on Mac Intel

Hi Klaus, that's pretty much the point. With the .dmg install, there are no setup files coming. I know I could use fink and Bill Scott's way to install the package, and have everything running, but was wondering if it would have been possible with the .dmg installation, much faster and

Re: [ccp4bb] ccp4 on Mac Intel

Charles and Guillermo, thanks a zillion. Shame on me, I could't find the scripts! Well, it'll be good to have already v. 6.2 ... ciao, s On May 3, 2011, at 11:26 AM, Charles Ballard wrote: Hi Sebastiano you open an X11 windows, then source /Applications/ccp4-6.2.0/bin/ccp4.setup-sh .

[ccp4bb] problem with cif file for a new ligand in Coot

Hello all: I am trying to generate a cif file for a new ligand using PRODRG server. The server generates cif file without any problem. The problem comes when I try to load the cif file in Coot and try to model the ligand into the electron density. It gives an error message like this..

Re: [ccp4bb] problem with cif file for a new ligand in Coot

On 03/05/11 14:08, Nalam, Madhavi wrote: Hello all: I am trying to generate a cif file for a new ligand using PRODRG server. The server generates cif file without any problem. The problem comes when I try to load the cif file in Coot and try to model the ligand into the electron density. It

[ccp4bb] Postdoctoral position in structural virology

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Dear Friends, I have noticed an issue in a pdb file, the term insertion code. Does anyone know anything about it? what is it used for? Thanks in Advance, Jahan Alikhajeh, Ph.D, Technical Supervisor, MAN Corporation LTD, Keshavarz Boulevard, Ghods Avenue No. 41, 5th Floor, Tehran,

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I suggest that you go to the PDB web site and look through the format documentation for the description of ATOM records. Frances Bernstein = Bernstein + Sons * * Information Systems Consultants

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On Tue, 2011-05-03 at 13:27 +, Jahan Alikhajeh wrote: term insertion code. Does anyone know anything about it? what is it used for? It may be used to follow WuKabat numbering for antibodies. Frankly, it it is something that can be easily avoided (after all, 32A is simply the 33rd

[ccp4bb] difference simulated annealing map

what is the difference simulated annealing map and how can i generate it haytham wahba Ph.D student Biochemistry Dep UdeM

[ccp4bb] Ultrafiltration membrane filters

Hi All, I was wondering if anyone had troubles with PES (Polyethersulfone) ultrafiltration membrane filters (Vivaspin, Amicon,...) using 5 mM DTT containing buffer. It seems whether or not it is possible for DTT to react with sulfone

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Hi James, The concept of insertion code arose when one species was sequenced and studied and then it turned out that there were both insertions and deletions in the sequence of the analogous molecule for some other species. In analyzing and discussing structure, e.g. the catalytic

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James, interesting that you chose residue number 32 for your example, because that is the number of one of the two active-site ASPs in the aspartic proteinase family (the other is ASP 215) that I (with Tom Blundell others) worked on for many years. So Ed, it's not just relevant to the WuKabat

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[ccp4bb] INSERTION CODE

Just giving this thread a title. James On May 3, 2011, at 10:06 AM, Ian Tickle wrote: James, interesting that you chose residue number 32 for your example, because that is the number of one of the two active-site ASPs in the aspartic proteinase family (the other is ASP 215) that I (with Tom

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On Tue, 2011-05-03 at 18:06 +0100, Ian Tickle wrote: So Ed, it's not just relevant to the WuKabat numbering for antibodies. Obviously, it was meant to be an example of use, not the only example. The idea that one would _not_ use consistent numbering (and therefore insertion codes) across

Re: [ccp4bb] Dehydration treatments

Israel, Here is a paper that describes a phenomenon like what you have observed: Structure. 2003 Feb;11(2):139-45. Dehydration converts DsbG crystal diffraction from low to high resolution. Heras B, Edeling MA, Byriel KA, Jones A, Raina S, Martin JL. And another review that touches briefly on

[ccp4bb] Please help with Raster3D (linux version)

Dear All I tried to make a stereo picture using Raster3D installed on a linux box with the following command: stereo3d -tiff xxx.tif xxx.r3d but got an error message: stereo3d: normal3d seems to be OK stereo3d: rendering left eye view stereo3d: rendering right eye view stereo3d: joining left

Re: [ccp4bb] Please help with Raster3D (linux version)

On Tuesday, May 03, 2011 02:00:26 pm jie liu wrote: Dear All I tried to make a stereo picture using Raster3D installed on a linux box with the following command: stereo3d -tiff xxx.tif xxx.r3d but got an error message: stereo3d: normal3d seems to be OK stereo3d: rendering left eye