Re: [ccp4bb] MrBUMP

Hi Riya, You'll need to install at least one of these programs for it to work. What kind of operating system have you got? Clustalw/2 is about the easiest to install and is available from here: ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.0.11/ Let me know if you need any further help with i

[ccp4bb] anisotropic temp for H2O

Dear all, I run refmac5 on TLS & restrained refinement mode. my pdb input file contain anisotropic temp for the amino acid and isotropic temp for the cofactors and water. The refinement parameters is set on mixed isotropic/ anisotropic temp and in TLS parameters the check box add TLS contributio

[ccp4bb] packing diagrammes

Dear all, thanks to everybody who offered their experience and hints. The most convenient way of preparing a packing diagramme, at least for me, was via PyMol as suggested by Michael Klein (see below). One can do something similar with the CCP4 graphics package, but for some reason the pro

[ccp4bb] curved cylindrical helices in PyMOL?

Dear ccp4bb-people, I would like to depict my protein with curved cylindrical helices using PyMOL. (I know and use bobscript "rod fitted" for this purpose and like it.) Anyway, I wonder if anybody has a script or knows how to tell PyMOL to follow the curvature of helices in the cylindrical

Re: [ccp4bb] curved cylindrical helices in PyMOL?

Hi Susanne, On the Pymol menu go to Setting --> Cartoon -->  Cylindrical Helices Kianoush --- On Thu, 8/27/09, Susanne Ressl wrote: From: Susanne Ressl Subject: [ccp4bb] curved cylindrical helices in PyMOL? To: CCP4BB@JISCMAIL.AC.UK Date: Thursday, August 27, 2009, 7:34 AM Dear ccp4bb-peop

Re: [ccp4bb] curved cylindrical helices in PyMOL?

Actually, PyMOL cannot bend cylindrical helices. The workaround is to break them manually: load $PYMOL_PATH/test/dat/1tii.pdb as cartoon set cartoon_cylindrical_helices # Insert a break into the longest helix (only slightly bent) cartoon skip, C/216/CA Cheers, Warren PS. This is the CCP4

Re: [ccp4bb] anisotropic temp for H2O

On Thursday 27 August 2009, Elad Binshtien wrote: > Dear all, > I run refmac5 on TLS & restrained refinement mode. my pdb input file contain > anisotropic temp for the amino acid and isotropic temp for the cofactors and > water. The refinement parameters is set on mixed isotropic/ anisotropic tem

Re: [ccp4bb] anisotropic temp for H2O

In the latest versions of refmac, it has a default selection of TLS groups so that you don't need to create a TLSIN file. I believe this default selection includes waters in the first hydration shell. You should be able to override this with an explicit selection in TLSIN. Cheers Martyn On Thu, 2

[ccp4bb]

Dear All Is there any easy to way write topology and parameter file for a cofactor with specific conformation. Thanks a lot Sajid Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com

Re: [ccp4bb] anisotropic temp for H2O

Hi, I'll take the liberty of replying instead of Elad (my student) who probably won't be back on the net till next week. The feature/problem he reported seems most likely as a difference between the linux and Windows version, unless there is also a difference between v 6.1.1  and 6.1.2 on that

[ccp4bb]

I suspect that your question is CNS-related. Easy is relative, but what you need to do is to uncomment the appropriate DIHEDRAL statements (assuming that used xplo2d, they will be there but mostly commented out). Just figure out what values you need for particular angles. If it is wise to fix li

[ccp4bb] Is there Windows version of O ?

maybe a little offtopic, but I really need anotehr model buiding software that can run on windows system ( I already have coot) I am not a linux guy, I prefer running everything on my PC---I can run ccp4 and coot on PC without any problem. I found Alwyn Jones 's website, which has versio

[ccp4bb] Lipid Removal from Proteins

Hello All, I dug around on the net and found this method to remove lipids from proteins: "Wessel & Fluegge (1984), Anal. Biochem. 138:141-143. It´s a methanol/ chloroform precipitation and gives you a pellet that is easily redissolved. The method was especially devised for removing lipids

[ccp4bb] weak magnet of goniometer of MAR345dtb

Hi, We have recently installed a new home source diffraction system using MAR 345 dtb. It works much better than the rigaku because this new device has automatic motor control system. However, we have a lot of trouble to mount crystals. The magnet of MAR goniometer is significantly weak

Re: [ccp4bb] Lipid Removal from Proteins

I dug around on the net and found this method to remove lipids from proteins: More precisely, from denatured proteins. That's what methanol/chloroform phase does for most proteins. "Wessel & Fluegge (1984), Anal. Biochem. 138:141-143. Itґs a methanol/ chloroform precipitation and gives you a

Re: [ccp4bb] weak magnet of goniometer of MAR345dtb

Dear Aidong, there are some permanent magnet adapters, which you can get from MAR or which you can make yourself. These help, especially with your old pins. Cheers, Manfred. Quoting aidong : Hi, We have recently installed a new home source diffraction system using MAR 345 dtb. It works mu