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Hao, thanks for the link http://www.igs.cnrs-mrs.fr/Caspr2/RMSDcalc.cgi It helped me a lot! I also found what I did wrong with LSQKAB in ccp4i. In my case, the two superposed molecules have different chain IDs and one is not continous. A tried several variations: * I defined no matching residue range: this didn't work maybe because of the gap in one molecule * I defined a shorter residue range (without the gap) and entered chain A or B: this didn't work, too * I defined a short residue range and left the "chain" blank: this worked. Perhaps you, Fang Sheng, also had two molecules that had either a gap or differend chains? Many thanks, Petra ----- Original Message ----- From: "Stein, ND (Norman)" <[EMAIL PROTECTED]> To: "Petra Wollmann" <[EMAIL PROTECTED]>; "fang sheng" <[EMAIL PROTECTED]>; <[email protected]> Cc: <[EMAIL PROTECTED]> Sent: Friday, August 25, 2006 11:59 AM Subject: RE: [ccp4bb]: TOP : "garbage on line" ? > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > The "garbage on line" error message originates from the LSQKAB program rather than TOPP. (The superpose molecules task in ccp4i calls LSQKAB as well as TOPP.) If you can send me your log file and input files, I will investigate. > > The basic TOPP program used by ccp4i should work on both Windows and Unix based systems. The top3d and topsearch scripts mentioned in the TOPP documentation only work on unix based systems. > > Norman Stein > CCP4 > > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of > Petra Wollmann > Sent: 24 August 2006 17:44 > To: fang sheng; [email protected] > Subject: Re: [ccp4bb]: TOP : "garbage on line" ? > > > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > dear all, > > I also wanted to use "superpose molecules" and I had the same failure > message. > As I'm working on Windows, maybe this problem only exists in a windows > operating system? > > For superposing molecules there are a lot of programs. The reason I'm using > this CCP4 program is that I would like to have an output graph of RMSD for > each residue of the two molecules. Does anyone know another progam to do > this? > > many thanks, > Petra > > ----- Original Message ----- > From: "fang sheng" <[EMAIL PROTECTED]> > To: <[email protected]> > Sent: Thursday, August 24, 2006 5:52 PM > Subject: [ccp4bb]: TOP : "garbage on line" ? > > > > *** For details on how to be removed from this list visit the *** > > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > > > Hello, All, > > > > I am trying to use program "TOP"( TOPP in latest version of CCP4) to > compare > > two similar structures and that is what I see in the log file when it > fails. > > " garbage on line". If you have any experience dealing with this kind of > > problem or any idea about how to fix it, please tell me and it is greatly > > appreciated. > > > > another question is does anybody know where to get SHP program? I see from > > paper people use it to do structual comparison. Wondering if it is better > > than TOPP. > > > > best > > > > Fang Sheng > > > > _________________________________________________________________ > > Check the weather nationwide with MSN Search: Try it now! > > http://search.msn.com/results.aspx?q=weather&FORM=WLMTAG > > > > > > >
