Re: [ccp4bb] Calculation of volume/size of cavity

[Boaz Shaanan]

Hi, You could try CASTp (http://sts.bioengr.uic.edu/castp/). If your protein is in the pdb it may well be in their database, if not, just upload it.   Cheers,             Boaz     Boaz Shaanan, Ph.D.                                         Dept. of Life Sciences                                      Ben-Gurion University of the Negev                          Beer-Sheva 84105                                            Israel                                                                                                                  E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220  Skype: boaz.shaanan                  Fax:   972-8-647-2992 or 972-8-646-1710                          From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Zhou, Tongqing (NIH/VRC) [E] [tz...@mail.nih.gov] Sent: Thursday, May 31, 2012 8:41 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Calculation of volume/size of cavity Dear All,   I am looking for a way to calculate the size of a protein cavity which is occupied by a loop from a ligand protein. The goal is to see what’s the maximum length of peptide allowed in this cavity.   Thanks,   Tongqing   Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4609B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************