Hi, Thanks. Several suggestions have been made: 1. UCSF Chimera can plot %ID and %Similarity 2. Consurf can plot conservation scores 3. AL2CO can also plot conservation scores
I have a protein with a fast molecular clock, so I need to think about this a bit more. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 ________________________________________ From: Clarke, Oliver <oc2...@cumc.columbia.edu> Sent: Saturday, March 16, 2019 8:36 PM To: Reza Khayat Subject: [EXTERNAL] Re: CCP4BB Digest - 15 Mar 2019 to 16 Mar 2019 (#2019-81) Hi Reza You can do more or less this using the ConSurf server - or just load up your sequence alignment in Chimera, then you can assign %Id or similarity as a per residue attribute. Cheers Oli > On Mar 16, 2019, at 8:03 PM, CCP4BB automatic digest system > <lists...@jiscmail.ac.uk> wrote: > > There is 1 message totaling 85 lines in this issue. > > Topics of the day: > > 1. Sequence variability mapped on a PDB > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=mHsISDQB0vMNkVfujg2cyrjzMe8aKat1p6zN9FYsEA8&m=ZmMzJkfCzdmPaPhY7cm2zQcfuIrR3KDlZD7qrRixWTQ&s=sQss7RNE76p554TmXg2pwxPP_yDf-o7Q-IojETfs_VY&e= > > ---------------------------------------------------------------------- > > Date: Sat, 16 Mar 2019 23:42:18 +0000 > From: Reza Khayat <rkha...@ccny.cuny.edu> > Subject: Sequence variability mapped on a PDB > > ?Hi, > > > Can someone direct me to a program that can replace the B-factors of a PDB > with sequence variability calculated from a sequence alignment? I'm have > tried the PVS server, but my sequence alignment is too large for its liking. > Thanks. > > > Best wishes, > Reza > > > Reza Khayat, PhD > Assistant Professor > City College of New York > Department of Chemistry > New York, NY 10031 > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=mHsISDQB0vMNkVfujg2cyrjzMe8aKat1p6zN9FYsEA8&m=ZmMzJkfCzdmPaPhY7cm2zQcfuIrR3KDlZD7qrRixWTQ&s=sQss7RNE76p554TmXg2pwxPP_yDf-o7Q-IojETfs_VY&e= > > ------------------------------ > > End of CCP4BB Digest - 15 Mar 2019 to 16 Mar 2019 (#2019-81) > ************************************************************ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
