[From nobody Fri Oct 18 16:37:01 2019 From: Sean Connell <sconnell@cicbiogune.es> To: "chimera-users@cgl.ucsf.edu List" <chimera-users@cgl.ucsf.edu> Subject: Question about multi align viewer Mime-Version: 1.0 (Mac OS X Mail 6.6 \(1510\)) Content-Type: multipart/signed; boundary="Apple-Mail=_63236D2D-CD86-4E36-ABEC-C4B295362144"; protocol="application/pgp-signature"; micalg=pgp-sha1 --Apple-Mail=_63236D2D-CD86-4E36-ABEC-C4B295362144 Content-Type: multipart/alternative; boundary="Apple-Mail=_506EA74F-1EEB-407A-A415-9D02C53453C2" --Apple-Mail=_506EA74F-1EEB-407A-A415-9D02C53453C2 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Hello I was wondering if it is possible to calculate conservation = statistics using only subsets of the aligned sequence. The reason I ask = is that in my alignment I have differently families of proteins that = have slightly different functions and I would like to highlight residues = that are conserved in one subset but not in the other? --------------------------------- Sean Connell, PhD CICbioGUNE Parque Tecnol=F3gico de Vizcaya, Ed. 800 48160 Derio Phone: +34 946 572 529 sconnell@cicbiogune.es skype: io2-76 --------------------------------- --Apple-Mail=_506EA74F-1EEB-407A-A415-9D02C53453C2 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1 <html><head><meta http-equiv=3D"Content-Type" content=3D"text/html = charset=3Diso-8859-1"></head><body style=3D"word-wrap: break-word; = -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hello = I was wondering if it is possible to calculate conservation statistics = using only subsets of the aligned sequence.  The reason I ask is = that in my alignment I have differently families of proteins that have = slightly different functions and I would like to highlight residues that = are conserved in one subset but not in the other?<br><br><div = apple-content-edited=3D"true"> <div style=3D"orphans: 2; text-align: -webkit-auto; text-indent: 0px; = widows: 2; word-wrap: break-word; -webkit-nbsp-mode: space; = -webkit-line-break: after-white-space; "><div style=3D"orphans: 2; = text-align: -webkit-auto; text-indent: 0px; widows: 2; word-wrap: = break-word; -webkit-nbsp-mode: space; -webkit-line-break: = after-white-space; "><div><span class=3D"Apple-style-span" = style=3D"border-collapse: separate; border-spacing: 0px; "><div = style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; = -webkit-line-break: after-white-space; "><span class=3D"Apple-style-span" = style=3D"border-collapse: separate; border-spacing: 0px; "><div = style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; = -webkit-line-break: after-white-space; "><div style=3D"color: rgb(0, 0, = 0); font-family: Helvetica; font-size: medium; font-style: normal; = font-variant: normal; font-weight: normal; letter-spacing: normal; = line-height: normal; text-transform: none; white-space: normal; = word-spacing: 0px; -webkit-text-size-adjust: auto; = -webkit-text-stroke-width: 0px; = ">---------------------------------</div><div><div style=3D"color: = rgb(0, 0, 0); font-family: Helvetica; font-size: 11px; font-style: = normal; font-variant: normal; font-weight: normal; letter-spacing: = normal; line-height: normal; text-transform: none; white-space: normal; = word-spacing: 0px; -webkit-text-size-adjust: auto; = -webkit-text-stroke-width: 0px; "><font face=3D"Arial" size=3D"2" = style=3D"font-size: 11px; ">Sean Connell, PhD</font></div><div = style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-size: 11px; = font-style: normal; font-variant: normal; font-weight: normal; = letter-spacing: normal; line-height: normal; text-transform: none; = white-space: normal; word-spacing: 0px; -webkit-text-size-adjust: auto; = -webkit-text-stroke-width: 0px; "><font face=3D"Arial" size=3D"2" = style=3D"font-size: 11px; ">CICbioGUNE</font></div><div style=3D"color: = rgb(0, 0, 0); font-family: Helvetica; font-size: 11px; font-style: = normal; font-variant: normal; font-weight: normal; letter-spacing: = normal; line-height: normal; text-transform: none; white-space: normal; = word-spacing: 0px; -webkit-text-size-adjust: auto; = -webkit-text-stroke-width: 0px; "><font face=3D"Arial" size=3D"2" = style=3D"font-size: 11px; ">Parque Tecnol=F3gico de Vizcaya, Ed. = 800</font></div><div style=3D"color: rgb(0, 0, 0); font-family: = Helvetica; font-size: 11px; font-style: normal; font-variant: normal; = font-weight: normal; letter-spacing: normal; line-height: normal; = text-transform: none; white-space: normal; word-spacing: 0px; = -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><font = face=3D"Arial" size=3D"2" style=3D"font-size: 11px; ">48160 = Derio</font></div><div style=3D"color: rgb(0, 0, 0); font-family: = Helvetica; font-size: 11px; font-style: normal; font-variant: normal; = font-weight: normal; letter-spacing: normal; line-height: normal; = text-transform: none; white-space: normal; word-spacing: 0px; = -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><font = face=3D"Arial" size=3D"2" style=3D"font-size: 11px; ">Phone: = +34 </font> 946 572 529</div><div><font face=3D"Arial"><span = style=3D"font-size: 11px; "><a = href=3D"mailto:sconnell@cicbiogune.es">sconnell@cicbiogune.es</a></span></= font></div></div><div><span style=3D"font-size: 11px; ">skype: = io2-76</span></div></div></span></div></span><span = class=3D"Apple-style-span" style=3D"border-collapse: separate; = border-spacing: 0px; "><div style=3D"word-wrap: break-word; = -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span = class=3D"Apple-style-span" style=3D"border-collapse: separate; = border-spacing: 0px; "><div style=3D"word-wrap: break-word; = -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; = ">---------------------------------</div></span></div></span></div><div = style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; = font-style: normal; font-variant: normal; font-weight: normal; = letter-spacing: normal; line-height: normal; text-transform: none; = white-space: normal; word-spacing: 0px; -webkit-text-size-adjust: auto; = -webkit-text-stroke-width: 0px; "><br></div></div><br = class=3D"Apple-interchange-newline"></div><br = class=3D"Apple-interchange-newline"><br = class=3D"Apple-interchange-newline"> </div> <br></body></html>= --Apple-Mail=_506EA74F-1EEB-407A-A415-9D02C53453C2-- --Apple-Mail=_63236D2D-CD86-4E36-ABEC-C4B295362144 Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename=signature.asc Content-Type: application/pgp-signature; name=signature.asc Content-Description: Message signed with OpenPGP using GPGMail -----BEGIN PGP SIGNATURE----- iQEcBAEBAgAGBQJSPBgBAAoJEDDqb12PygWequQH/RRwoniaMIEIyDOLXsTv4D8a 9NaixPGkkrtr5GW9imP3znWsYQMW7/Ld8vAMS1AvXQdxIJDq2VoxFlA1L9yUmgR/ ecNssEHWfPw+04zF2r1r87AazfyaIhQLCZhSyZ+JkSa1vsnxiWULuijKLcfMX4XW hHd8jmnjZq9CyUigK+MVMMHfnse0P/zOzz47ZgBrRoKg4xBqL3ZDtSlpiI2IO09U nNwuH3Af3/hHjtPgP1FT0APcW8cg4w2yhH4/zzUfXrgcG913Pjv4yA55S0h42pT/ RxfVpZr+DDXkuRYQfdQc5IG7UPDId34MZUoU66ia5JkN9flihU6tzLQFh30ONkA= =NfSm -----END PGP SIGNATURE----- --Apple-Mail=_63236D2D-CD86-4E36-ABEC-C4B295362144-- ]