Re: [ccp4bb] Current "best" software for computing volumes of active sites
Hi, At the request of Gerard, I have rescued the USF packages into github https://github.com/martynwinn/Uppsala-Software-Factory So far, I have done nothing with this, so no guarantees that the code still compiles or that the old binaries still work. Nevertheless, it does contain a cavity.lib file for voidoo (in fact, 4 variants). Perhaps that helps. cheers Martyn -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Fred Vellieux Sent: 04 April 2019 07:24 To: ccp4bb Subject: [ccp4bb] Current "best" software for computing volumes of active sites Hi CCP4BBers, With software constantly changing, new versions arriving to us and new software reaching the intended audience, I am looking for the most appropriate piece(s) of software to compute the volume of active site "cavities" in related 3D structures. I have tried to use Voidoo however I do not know where to download an initial (and fairly comprehensive) cavity.lib file which I'd modify if need be. The links on the USF web site appear to be broken. I am running Linux. Thanks for the advice, Fred. Vellieux To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Current "best" software for computing volumes of active sites
You can have a look at Caver. I find it quite easy to use and it worked for me on some weirdly shaped cavities. Gianluca Santoni, serial crystallographer ESRF structural biology group 71 avenue des Martyrs 38027 Grenoble cedex (France) On 04/04/2019 08:24, Fred Vellieux wrote: Hi CCP4BBers, With software constantly changing, new versions arriving to us and new software reaching the intended audience, I am looking for the most appropriate piece(s) of software to compute the volume of active site "cavities" in related 3D structures. I have tried to use Voidoo however I do not know where to download an initial (and fairly comprehensive) cavity.lib file which I'd modify if need be. The links on the USF web site appear to be broken. I am running Linux. Thanks for the advice, Fred. Vellieux To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Current "best" software for computing volumes of active sites
Well, I don't know if that is the newest appropriate piece of software, but pdbsum does automatic calculation of clefts using MOLE I think. It does provide jmol and rasmol scripts and volume and surface calculations. Cheers Christian On Thu, Apr 4, 2019 at 8:24 AM Fred Vellieux wrote: > Hi CCP4BBers, > > With software constantly changing, new versions arriving to us and new > software reaching the intended audience, I am looking for the most > appropriate piece(s) of software to compute the volume of active site > "cavities" in related 3D structures. > > I have tried to use Voidoo however I do not know where to download an > initial (and fairly comprehensive) cavity.lib file which I'd modify if > need be. The links on the USF web site appear to be broken. > > I am running Linux. > > Thanks for the advice, > > Fred. Vellieux > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Current "best" software for computing volumes of active sites
Hi CCP4BBers, With software constantly changing, new versions arriving to us and new software reaching the intended audience, I am looking for the most appropriate piece(s) of software to compute the volume of active site "cavities" in related 3D structures. I have tried to use Voidoo however I do not know where to download an initial (and fairly comprehensive) cavity.lib file which I'd modify if need be. The links on the USF web site appear to be broken. I am running Linux. Thanks for the advice, Fred. Vellieux To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
