[Chimera-users] castp .poc file is not opened in restored session (plain text version)

[Boaz Shaanan]

Hi Eric,


OK, thanks for letting me know. I read on the castp site that they can't cope with multiple models (a-la NMR) in the pdb so thought that I managed to circumvent the problem by giving different chain ID's to the two chains that I extracted from the pdb1 files and by deleting the model cards. I didn't realize that there is program that looks into the atom serial numbers in the pdb (none of the crystallographic programs that I use does).


I'll fix the problem and submit again to the castp site. 


Thanks a lot for your help.


                            Boaz 







 

 

Boaz Shaanan, Ph.D.                                        


Dept. of Life Sciences                                      

Ben-Gurion University of the Negev                          

Beer-Sheva 84105                                            

Israel                                                      

                                                            

E-mail: bshaanan at bgu.ac.il

Phone: 972-8-647-2220  Skype: boaz.shaanan                  

Fax:   972-8-647-2992 or 972-8-646-1710    

 

 

                












From: Eric Pettersen [pett at cgl.ucsf.edu]

Sent: Tuesday, July 26, 2011 4:23 AM

To: בעז שאנן

Cc: chimera-users at cgl.ucsf.edu

Subject: Re: [Chimera-users] castp .poc file is not opened in restored session (plain text version)











On Jul 24, 2011, at 3:54 PM, Boaz Shaanan wrote:






Hi Eric,





Indeed with the daily built of 1.6 the castp file opens up too when restoring the session. However, I noted a strange feature in that a hole from castp is split between two monomers. I used the bug report mechanism  to report this and attached the session
 file (bug #9775). I'd appreciate your input on the issue.







Hi Boaz,

The most reliable way to match the pocket atoms listed in the .poc file to the PDB is by serial number (due to the vagaries of how CASTp formats the .poc file).  Your input PDB (and therefore
 output PDB) has duplicate serial numbers for corresponding atoms in the two chains.  If you open your input PDB in Chimera and write out a new PDB, the new one will have unique serial numbers.  You can use that with the CASTp server and get results that Chimera
 can handle.  Sorry for the hassle.





--Eric








                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu