Re: [ccp4bb] APBS
Dear Boaz (and others) it immensly improves readability of your emails if you can ask your email client to also include a plain text version of your email on top of the html-version ;-) Cheers, Tim On Tue, Jul 05, 2011 at 05:55:28PM +, Boaz Shaanan wrote: html dir=ltr head meta http-equiv=Content-Type content=text/html; charset=iso-8859-8-i style type=text/css id=owaParaStyle/style /head body style=word-wrap:break-word fpstyle=1 ocsi=0 div style=direction: ltr;font-family: Arial;color: #FF;font-size: 10pt;Hi, divbr /div divThe best place to pose this question would be the APBS bb which you can nbsp;join from this site:/div divbr /div diva href=http://www.poissonboltzmann.org/apbs/;http://www.poissonboltzmann.org/apbs//abr divbr div style=font-family:Tahoma; font-size:13px divYou may also check the FAQ there, maybe your question (#43; an answer) would be there already./div divbr /div divfont face=Times New Roman size=3/fontnbsp; Cheers,/div divbr /div divnbsp; nbsp; nbsp; nbsp; nbsp; nbsp;Boaz/div divfont face=Times New Roman size=3/fontnbsp;/div divfont color=#80 face=Times New Roman size=3emBoaz Shaanan, Ph.D.nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; br Dept. of Life Sciencesnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; br Ben-Gurion University of the Negevnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; br Beer-Sheva 84105nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; br Israelnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; br nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; br E-mail: bshaa...@bgu.ac.ilbr Phone: 972-8-647-2220nbsp;nbsp;Skype: boaz.shaanannbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; br Fax:nbsp;nbsp; 972-8-647-2992 or 972-8-646-1710nbsp;nbsp;nbsp;nbsp;/em/font/div divfont color=#80 face=Times New Roman size=3em/em/fontnbsp;/div divfont color=#80 face=Times New Roman size=3em/em/fontnbsp;/div divfont face=Times New Roman size=3emfont color=#80nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; br br /font/em/font/div font face=Times New Roman size=3/font/div /div div style=font-family: Times New Roman; color: #00; font-size: 16px hr tabindex=-1 div id=divRpF112756 style=direction: ltr; font face=Tahoma size=2 color=#00bFrom:/b CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Reginald McNulty [rmcnu...@uci.edu]br bSent:/b Tuesday, July 05, 2011 8:24 PMbr bTo:/b CCP4BB@JISCMAIL.AC.UKbr bSubject:/b [ccp4bb] APBSbr /fontbr /div div/div div divDear CCP4BB,/div divbr /div divI apologize for the off topic question./div divbr /div divI have determined the 3D structure of a membrane protein transporter and want to make a figure showing the surface charge. So, I ran PDB2PQR and specified pH 5.4. I understand the next step is to run APBS. I know there are different dielectric constants for parts of the protein exposed to membrane and nbsp;cytosolic nbsp;portions. I'm wondering if I need to take this into account when generating a figure for surface charge? If so, I'm wondering how do I tell the program residues that are embedded in the membrane and those that are not?/div divbr /div divIf you could help me answer these questions or point me in the right direction I'd greatly appreciate it./div divbr /div divBest regards,/div divbr /div divReggie McNulty/div divDepartment of Molecular Biology and Biochemistry/div divUC Irvine/div divspan class=Apple-style-span style=color: rgb(0, 0, 255); br /spanspan class=Apple-style-span style=color: rgb(0, 0, 255); /span/div divspan class=Apple-style-span style=color:rgb(0,0,255); font-family:'Times New Roman'; font-size:16pxnbsp;/span/div divspan class=Apple-style-span style=border-collapse:separate; color:rgb(0,0,0); font-family:Helvetica; font-style:normal; font-variant:normal; font-weight:normal;
Re: [ccp4bb] APBS
Leave it to the crystallographers to be the last on the Planet with text-only email readers Just before the ccp4bb will migrate to google+ :) Flip Op 7/6/2011 10:27, Tim Gruene schreef: Dear Boaz (and others) it immensly improves readability of your emails if you can ask your email client to also include a plain text version of your email on top of the html-version ;-) Cheers, Tim On Tue, Jul 05, 2011 at 05:55:28PM +, Boaz Shaanan wrote: html dir=ltr head meta http-equiv=Content-Type content=text/html; charset=iso-8859-8-i style type=text/css id=owaParaStyle/style /head body style=word-wrap:break-word fpstyle=1 ocsi=0 div style=direction: ltr;font-family: Arial;color: #FF;font-size: 10pt;Hi, divbr /div divThe best place to pose this question would be the APBS bb which you cannbsp;join from this site:/div divbr /div diva href=http://www.poissonboltzmann.org/apbs/;http://www.poissonboltzmann.org/apbs//abr divbr div style=font-family:Tahoma; font-size:13px divYou may also check the FAQ there, maybe your question (#43; an answer) would be there already./div divbr /div divfont face=Times New Roman size=3/fontnbsp; Cheers,/div divbr /div divnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;Boaz/div divfont face=Times New Roman size=3/fontnbsp;/div divfont color=#80 face=Times New Roman size=3emBoaz Shaanan, Ph.D.nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; br Dept. of Life Sciencesnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;br Ben-Gurion University of the Negevnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;br Beer-Sheva 84105nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;br Israelnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;br nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;br E-mail: bshaa...@bgu.ac.ilbr Phone: 972-8-647-2220nbsp;nbsp;Skype: boaz.shaanannbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;br Fax:nbsp;nbsp; 972-8-647-2992 or 972-8-646-1710nbsp;nbsp;nbsp;nbsp;/em/font/div divfont color=#80 face=Times New Roman size=3em/em/fontnbsp;/div divfont color=#80 face=Times New Roman size=3em/em/fontnbsp;/div divfont face=Times New Roman size=3emfont color=#80nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; br br /font/em/font/div font face=Times New Roman size=3/font/div /div div style=font-family: Times New Roman; color: #00; font-size: 16px hr tabindex=-1 div id=divRpF112756 style=direction: ltr; font face=Tahoma size=2 color=#00bFrom:/b CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Reginald McNulty [rmcnu...@uci.edu]br bSent:/b Tuesday, July 05, 2011 8:24 PMbr bTo:/b CCP4BB@JISCMAIL.AC.UKbr bSubject:/b [ccp4bb] APBSbr /fontbr /div div/div div divDear CCP4BB,/div divbr /div divI apologize for the off topic question./div divbr /div divI have determined the 3D structure of a membrane protein transporter and want to make a figure showing the surface charge. So, I ran PDB2PQR and specified pH 5.4. I understand the next step is to run APBS. I know there are different dielectric constants for parts of the protein exposed to membrane andnbsp;cytosolicnbsp;portions. I'm wondering if I need to take this into account when generating a figure for surface charge? If so, I'm wondering how do I tell the program residues that are embedded in the membrane and those that are not?/div divbr /div divIf you could help me answer these questions or point me in the right direction I'd greatly appreciate it./div divbr /div divBest regards,/div divbr /div divReggie McNulty/div divDepartment of Molecular Biology and Biochemistry/div divUC Irvine/div divspan class=Apple-style-span style=color: rgb(0, 0, 255); br /spanspan class=Apple-style-span style=color: rgb(0, 0, 255); /span/div divspan class=Apple-style-span style=color:rgb(0,0,255); font-family:'Times New Roman'; font-size:16pxnbsp;/span/div divspan class=Apple-style-span style=border-collapse:separate; color:rgb(0,0,0); font-family:Helvetica;
Re: [ccp4bb] APBS
Hi Tim, Sure, does this look better? Actually, the choice is mine (although the default which I prefer, honestly, is HTML). 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 Tim Gruene [t...@shelx.uni-ac.gwdg.de] Sent: Wednesday, July 06, 2011 11:27 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] APBS Dear Boaz (and others) it immensly improves readability of your emails if you can ask your email client to also include a plain text version of your email on top of the html-version ;-) Cheers, Tim On Tue, Jul 05, 2011 at 05:55:28PM +, Boaz Shaanan wrote: html dir=ltr head meta http-equiv=Content-Type content=text/html; charset=iso-8859-8-i style type=text/css id=owaParaStyle/style /head body style=word-wrap:break-word fpstyle=1 ocsi=0 div style=direction: ltr;font-family: Arial;color: #FF;font-size: 10pt;Hi, divbr /div divThe best place to pose this question would be the APBS bb which you can nbsp;join from this site:/div divbr /div diva href=http://www.poissonboltzmann.org/apbs/;http://www.poissonboltzmann.org/apbs//abr divbr div style=font-family:Tahoma; font-size:13px divYou may also check the FAQ there, maybe your question (#43; an answer) would be there already./div divbr /div divfont face=Times New Roman size=3/fontnbsp; Cheers,/div divbr /div divnbsp; nbsp; nbsp; nbsp; nbsp; nbsp;Boaz/div divfont face=Times New Roman size=3/fontnbsp;/div divfont color=#80 face=Times New Roman size=3emBoaz Shaanan, Ph.D.nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; br Dept. of Life Sciencesnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; br Ben-Gurion University of the Negevnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; br Beer-Sheva 84105nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; br Israelnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; br nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; br E-mail: bshaa...@bgu.ac.ilbr Phone: 972-8-647-2220nbsp;nbsp;Skype: boaz.shaanannbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; br Fax:nbsp;nbsp; 972-8-647-2992 or 972-8-646-1710nbsp;nbsp;nbsp;nbsp;/em/font/div divfont color=#80 face=Times New Roman size=3em/em/fontnbsp;/div divfont color=#80 face=Times New Roman size=3em/em/fontnbsp;/div divfont face=Times New Roman size=3emfont color=#80nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; br br /font/em/font/div font face=Times New Roman size=3/font/div /div div style=font-family: Times New Roman; color: #00; font-size: 16px hr tabindex=-1 div id=divRpF112756 style=direction: ltr; font face=Tahoma size=2 color=#00bFrom:/b CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Reginald McNulty [rmcnu...@uci.edu]br bSent:/b Tuesday, July 05, 2011 8:24 PMbr bTo:/b CCP4BB@JISCMAIL.AC.UKbr bSubject:/b [ccp4bb] APBSbr /fontbr /div div/div div divDear CCP4BB,/div divbr /div divI apologize for the off topic question./div divbr /div divI have determined the 3D structure of a membrane protein transporter and want to make a figure showing the surface charge. So, I ran PDB2PQR and specified pH 5.4. I understand the next step is to run APBS. I know there are different dielectric constants for parts of the protein exposed to membrane and nbsp;cytosolic nbsp;portions. I'm wondering if I need to take this into account when generating a figure for surface charge? If so, I'm wondering how do I tell the program residues that are embedded in the membrane and those that are not?/div divbr /div divIf you could help me answer these questions or point me in the right
Re: [ccp4bb] APBS
[summer break flame] I'm sure there are a lot more computer admins than crystallographers who prefer high-tech over fancyness - aka outlook usually marking my signed(!) emails as spam ;-) And, yes, I know that both thunderbird/enigmail and kmail combine both very elegantly, but with mutt I can simply use an ssh-client to read my email from anywhere in the world without having to worry too much about security whereas I shall not configure some internet-cafe's email client with my credentials to read my mail in the absence of a private internet connection.. [/summer break flame] Cheers, Tim On Wed, Jul 06, 2011 at 11:09:46AM +0200, Flip Hoedemaeker wrote: Leave it to the crystallographers to be the last on the Planet with text-only email readers Just before the ccp4bb will migrate to google+ :) Flip Op 7/6/2011 10:27, Tim Gruene schreef: Dear Boaz (and others) it immensly improves readability of your emails if you can ask your email client to also include a plain text version of your email on top of the html-version ;-) Cheers, Tim On Tue, Jul 05, 2011 at 05:55:28PM +, Boaz Shaanan wrote: html dir=ltr head meta http-equiv=Content-Type content=text/html; charset=iso-8859-8-i style type=text/css id=owaParaStyle/style /head body style=word-wrap:break-word fpstyle=1 ocsi=0 div style=direction: ltr;font-family: Arial;color: #FF;font-size: 10pt;Hi, divbr /div divThe best place to pose this question would be the APBS bb which you cannbsp;join from this site:/div divbr /div diva href=http://www.poissonboltzmann.org/apbs/;http://www.poissonboltzmann.org/apbs//abr divbr div style=font-family:Tahoma; font-size:13px divYou may also check the FAQ there, maybe your question (#43; an answer) would be there already./div divbr /div divfont face=Times New Roman size=3/fontnbsp; Cheers,/div divbr /div divnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;Boaz/div divfont face=Times New Roman size=3/fontnbsp;/div divfont color=#80 face=Times New Roman size=3emBoaz Shaanan, Ph.D.nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; br Dept. of Life Sciencesnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;br Ben-Gurion University of the Negevnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;br Beer-Sheva 84105nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;br Israelnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;br nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;br E-mail: bshaa...@bgu.ac.ilbr Phone: 972-8-647-2220nbsp;nbsp;Skype: boaz.shaanannbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;br Fax:nbsp;nbsp; 972-8-647-2992 or 972-8-646-1710nbsp;nbsp;nbsp;nbsp;/em/font/div divfont color=#80 face=Times New Roman size=3em/em/fontnbsp;/div divfont color=#80 face=Times New Roman size=3em/em/fontnbsp;/div divfont face=Times New Roman size=3emfont color=#80nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; br br /font/em/font/div font face=Times New Roman size=3/font/div /div div style=font-family: Times New Roman; color: #00; font-size: 16px hr tabindex=-1 div id=divRpF112756 style=direction: ltr; font face=Tahoma size=2 color=#00bFrom:/b CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Reginald McNulty [rmcnu...@uci.edu]br bSent:/b Tuesday, July 05, 2011 8:24 PMbr bTo:/b CCP4BB@JISCMAIL.AC.UKbr bSubject:/b [ccp4bb] APBSbr /fontbr /div div/div div divDear CCP4BB,/div divbr /div divI apologize for the off topic question./div divbr /div divI have determined the 3D structure of a membrane protein transporter and want to make a figure showing the surface charge. So, I ran PDB2PQR and specified pH 5.4. I understand the next step is to run APBS. I know there are different dielectric constants for parts of the protein exposed to membrane andnbsp;cytosolicnbsp;portions. I'm wondering if I need to take this into account when generating a figure for
[ccp4bb] How to evaluate Fourier transform ripples
Dear All, Hi. I was asked in a manuscript revision to discuss about the possible effects of Fourier transformation ripples on the crystallographic results. Specifically, the reviewers question whether ripples may affect on the electron density around heavy metal center which has a Mo-S-As connection. From which angle or in which way this problem should be addressed most convincingly ? Thank you for any suggestion.Best,Conan
[ccp4bb] Plain‐text posting (was: Re: [ccp4bb] APBS)
Tim Gruene t...@shelx.uni-ac.gwdg.de writes: [summer break flame] I'm sure there are a lot more computer admins than crystallographers who prefer high-tech over fancyness - aka outlook usually marking my signed(!) emails as spam ;-) And, yes, I know that both thunderbird/enigmail and kmail combine both very elegantly, but with mutt I can simply use an ssh-client to read my email from anywhere in the world without having to worry too much about security whereas I shall not configure some internet-cafe's email client with my credentials to read my mail in the absence of a private internet connection.. [/summer break flame] Cheers, Tim On Wed, Jul 06, 2011 at 11:09:46AM +0200, Flip Hoedemaeker wrote: Leave it to the crystallographers to be the last on the Planet with text-only email readers Just before the ccp4bb will migrate to google+ :) Flip [...] Well, I’d like to plonk my support behind good old plain text. I think there are valid reasons for it which are nothing to do with Luddism. The more formatting you put into your emails (unnecessarily, I would say), the more you’re constraining how your emails should be read. Some people might want or need to read your email in a much larger font than you would use. There is a legitimate use for HTML email, in science you might well want to illustrate your thoughts with graphs and chemical diagrams, but HTML for everything as a default, I don’t like! Remember Homer Simpson’s web page? Of course purists would say the most universal email format is US-ASCII, format=flowed… -- Ian Clifton ⚗ Phone: +44 1865 275677 Chemistry Research Laboratory Fax: +44 1865 285002 Oxford University ian.clif...@chem.ox.ac.uk Mansfield Road Oxford OX1 3TA UK
Re: [ccp4bb] Strange density in Arg
On 07/04/2011 04:24 PM, ruheng wrote: Dear all, Recently we are working on an archaebacteria protein which was expressed and purified from E.coli by conventional procedures. After we solved the structure, we found that there is an extra density in one of the argninine as shown in the attached picture. It seems that the density is larger than a methyl group and the atoms in the density are not on one plane. So we are curious about whether the density is a kind of posttranslational modification of arginine residues in the protein, if it is, what kind of modification could it be? And most important, what is the biological significance of this kind modification? Any suggestions and dicussions are appreciated! Best, Heng We saw something like this and modelled it as glycerol. But I dont know how one knows if one is correct!! Eleanor
Re: [ccp4bb] How to evaluate Fourier transform ripples
I note that all three of those atoms should have anomalous scattering and should show up as peaks in anomalous Fourier maps if you collected data carefully enough at multiple wavelengths. The As K edge is 1.04 A, which is easily within reach of most MAD synchrotron beamlines. The Mo peaks are out of range, but you should still see a peak, and could differentiate it from other metals by other methods, such as AAS. On 07/06/11 05:15, conan仙人指路 wrote: Dear All, Hi. I was asked in a manuscript revision to discuss about the possible effects of Fourier transformation ripples on the crystallographic results. Specifically, the reviewers question whether ripples may affect on the electron density around heavy metal center which has a Mo-S-As connection. From which angle or in which way this problem should be addressed most convincingly ? Thank you for any suggestion. Best, Conan -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] How to evaluate Fourier transform ripples
I would be very careful about any bond to As. I would imagine such bonds would be very susceptible to radiolysis with typical radiation used in the diffraction data collection. Have you performed some diffraction experiments of various time lengths (or flux) and seen what happens around this region of the electron density map? Jim On Wed, 6 Jul 2011, conan wrote: Dear All, Hi. I was asked in a manuscript revision to discuss about the possible effects of Fourier transformation ripples on the crystallographic results. Specifically, the reviewers question whether ripples may affect on the electron density around heavy metal center which has a Mo-S-As connection. From which angle or in which way this problem should be addressed most convincingly ? Thank you for any suggestion. Best, Conan
[ccp4bb] FW: Three Nobel Laureates and other famous scientists in a Symposium in Florence (Sept. 23rd 2011) devoted to the chemistry for Life and Health
From: Giovanna Scapin [mailto:scaping10...@yahoo.com] Sent: Wednesday, July 06, 2011 11:08 AM To: Scapin, Giovanna Subject: Fw: Three Nobel Laureates and other famous scientists in a Symposium in Florence (Sept. 23rd 2011) devoted to the chemistry for Life and Health FYI --- On Fri, 7/1/11, Carlo Mealli cmea...@iccom.cnr.it wrote: Before the General Assembly of the International Council of Science (ICSU), hosted by the Italian CNR in Rome Sept. 27-30 2011, the Symposium From Elementary Chemical Processes to Complex Biological Structures for the Benefit of Life and Human Health will be held in the Aula Magna of the University of Florence (Sept. 23rd 2011) Promoted by the Italian representatives at IUBMB (International Union of Biochemistry and Molecular Biology), IUCr (International Union of Crystallography) and IUPAC (International Union of Pure and Applied Chemistry), the event will have the following speakers of excellence: Yan Tse Lee (Taiwan, Nobel Laureate in Chemistry in 1986 and elected President of the ICSU) Kurt Wuethrich (Svwitzerland, Nobel Laureate in Chemistry in 2002) Venkatraman Ramakrishan (UK, Nobel Laureate in Chemistry in 2009) Sine Larsen (Denmark, President in charge of the IUCr) Kazuyuki Tatsumi (Japan, elected President of the IUPAC) Andrea Mattevi (Italy) Reiko Kuroda (Japan) Al the details and the program are available at the website: http://icsuday.iccom.cnr.it. No registration fee is required but pre-registration at the website is welcome. Sincerely yours, Carlo Mealli -- Dr. Carlo Mealli Istituto di Chimica dei Composti Organometallici ICCOM - CNR Via Madonna del Piano 10 50019 Sesto Fiorentino (Firenze), Italy Tel. +39 055 5225884 Fax +39 055 5225203 E-mail: carlo.mea...@iccom.cnr.it/mc/compose?to=carlo.mea...@iccom.cnr.it President of the Associazione Italiana di Cristallografia (AIC) Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
[ccp4bb] Map Using Both Bijvoet and Dispersive Differences with Model Phases
Dear Crystallographers, it seems to me that for clearly identifying/characterising anomalous scatterers for a solved structure, one could make a map using two datasets: one at the f peak, one low energy remote. One would then use the signal both from the Bijvoet differences in the peak dataset plus the differences between the peak and low-energy datasets, which I think I have seen called dispersive differences. I guess this would be like a MAD map, but using pre-existing model phases--is there such an animal in the software, or would it even be helpful? Jacob Keller -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Map Using Both Bijvoet and Dispersive Differences with Model Phases
Dear all, The following paper describes 'element specific maps', calculated by collecting data immediately above and below an absorption edge. http://journals.iucr.org/d/issues/2005/05/00/he5321/index.html I have used this technique, and it works very well. If anyone is interested I have a set of scripts to take raw mosflm data, scale it and calculate these maps. best wishes James -- Dr. James W. Murray David Phillips Research Fellow Division of Molecular Biosciences Imperial College, LONDON Tel: +44 (0)20 759 48895 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Jacob Keller [j-kell...@fsm.northwestern.edu] Sent: Wednesday, July 06, 2011 5:46 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Map Using Both Bijvoet and Dispersive Differences with Model Phases Dear Crystallographers, it seems to me that for clearly identifying/characterising anomalous scatterers for a solved structure, one could make a map using two datasets: one at the f peak, one low energy remote. One would then use the signal both from the Bijvoet differences in the peak dataset plus the differences between the peak and low-energy datasets, which I think I have seen called dispersive differences. I guess this would be like a MAD map, but using pre-existing model phases--is there such an animal in the software, or would it even be helpful? Jacob Keller -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] How to evaluate Fourier transform ripples
The question about Fourier transformation ripples has a straightforward answer in a fairly typical situation: A) data are collected to the resolution limit of diffraction, B) phases are uniform in quality across the resolution range, which is equivalent to R-free being uniform with respect to resolution within a factor of 2 or so, C) maps are not sharpened. The ripples originate from not including unobserved structure factors. The intensity of diffraction decreases rapidly past the measurability limit, so, in the above situation, the unobserved diffraction contributes very little. Consequently, the answer is that typically one should not see ripples. Ripples should not be confused with the effect of electron density maps being smoothed by vibrations and other forms of disorder. Zbyszek Otwinowski Dear All, Hi. I was asked in a manuscript revision to discuss about the possible effects of Fourier transformation ripples on the crystallographic results. Specifically, the reviewers question whether ripples may affect on the electron density around heavy metal center which has a Mo-S-As connection. From which angle or in which way this problem should be addressed most convincingly ? Thank you for any suggestion.Best,Conan Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353
Re: [ccp4bb] Map Using Both Bijvoet and Dispersive Differences with Model Phases
On Wednesday, July 06, 2011 09:46:14 am Jacob Keller wrote: Dear Crystallographers, it seems to me that for clearly identifying/characterising anomalous scatterers for a solved structure, one could make a map using two datasets: one at the f peak, one low energy remote. That would be an approximation of the map it seems you actually want, which would use the F_A amplitude terms from MAD analysis together with your current model phases rather than the MAD phase estimates. You could, for example, use CAD to merge the FA column output by hkl2map with the phases from your current model. Ethan One would then use the signal both from the Bijvoet differences in the peak dataset plus the differences between the peak and low-energy datasets, which I think I have seen called dispersive differences. I guess this would be like a MAD map, but using pre-existing model phases--is there such an animal in the software, or would it even be helpful? Jacob Keller -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Map Using Both Bijvoet and Dispersive Differences with Model Phases
That would be an approximation of the map it seems you actually want, which would use the F_A amplitude terms from MAD analysis together with your current model phases rather than the MAD phase estimates. You could, for example, use CAD to merge the FA column output by hkl2map with the phases from your current model. So I take it that the F_A term from MAD incorporates both anomalous (I guess including both f' and f) and dispersive differences? JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Map Using Both Bijvoet and Dispersive Differences with Model Phases
On Wednesday, July 06, 2011 10:36:20 am Jacob Keller wrote: That would be an approximation of the map it seems you actually want, which would use the F_A amplitude terms from MAD analysis together with your current model phases rather than the MAD phase estimates. You could, for example, use CAD to merge the FA column output by hkl2map with the phases from your current model. So I take it that the F_A term from MAD incorporates both anomalous (I guess including both f' and f) and dispersive differences? TC Terwilliger (1994). MAD Phasing: Bayesian Estimates of FA Acta Cryst. D50, 11-16. -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Map Using Both Bijvoet and Dispersive Differences with Model Phases
There are tools out there that calculate such a map. REVISE is one - I guess i is in the list of CCP4 programs. i often do both maps independently and look at them for common peaks The trouble is that dispersive differences are often less reliable than the anomalous ones.. Eleanor 07/06/2011 06:36 PM, Jacob Keller wrote: That would be an approximation of the map it seo both maps indeprndently and look at them for common peaks. ems you actually want, which would use the F_A amplitude terms from MAD analysis together with your current model phases rather than the MAD phase estimates. You could, for example, use CAD to merge the FA column output by hkl2map with the phases from your current model. So I take it that the F_A term from MAD incorporates both anomalous (I guess including both f' and f) and dispersive differences? JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] How to evaluate Fourier transform ripples
Dear Zbyszek Wouldn't ripples be the results of calculating maps with truncated Fourier summations (unavoidably), and, consequently, be more obvious around a sharp feature such as an heavy atom metal center? The mathematic basis can be found here: http://en.wikipedia.org/wiki/Gibbs_phenomenon With best regards, Thierry Note: sent a 2nd time as it seems that it did not reach the BB the first time. Apologies if the message reaches you twice. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Zbyszek Otwinowski Sent: Wednesday, July 06, 2011 1:19 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How to evaluate Fourier transform ripples The question about Fourier transformation ripples has a straightforward answer in a fairly typical situation: A) data are collected to the resolution limit of diffraction, B) phases are uniform in quality across the resolution range, which is equivalent to R-free being uniform with respect to resolution within a factor of 2 or so, C) maps are not sharpened. The ripples originate from not including unobserved structure factors. The intensity of diffraction decreases rapidly past the measurability limit, so, in the above situation, the unobserved diffraction contributes very little. Consequently, the answer is that typically one should not see ripples. Ripples should not be confused with the effect of electron density maps being smoothed by vibrations and other forms of disorder. Zbyszek Otwinowski Dear All, Hi. I was asked in a manuscript revision to discuss about the possible effects of Fourier transformation ripples on the crystallographic results. Specifically, the reviewers question whether ripples may affect on the electron density around heavy metal center which has a Mo-S-As connection. From which angle or in which way this problem should be addressed most convincingly ? Thank you for any suggestion.Best,Conan Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353 Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] Map Using Both Bijvoet and Dispersive Differences with Model Phases
It'll depend on your data, but you'd probably be better off using the inflection (rather than peak) and remote datasets for dispersive difference maps. This signal is usually fairly weak to begin with, and not using the infection datasets weakens it further. Pete FWIW - my understanding is that dispersive is often used to distinguish differences in f' from Bijvoet differences (in f'') during MAD, at least when treating MAD as MIRAS. Jacob Keller wrote: Dear Crystallographers, it seems to me that for clearly identifying/characterising anomalous scatterers for a solved structure, one could make a map using two datasets: one at the f peak, one low energy remote. One would then use the signal both from the Bijvoet differences in the peak dataset plus the differences between the peak and low-energy datasets, which I think I have seen called dispersive differences. I guess this would be like a MAD map, but using pre-existing model phases--is there such an animal in the software, or would it even be helpful? Jacob Keller
[ccp4bb] Postdoctoral position available in UCSF to study structural biology of HIV-host interaction
Postdoctoral Position Available Laboratory of Professor Robert M. Stroud, Ph.D. ( http://www.msg.ucsf.edu/stroud/index.htm) Department of Biochemistry and Biophysics University of California San Francisco, USA SUMMARY DESCRIPTION: Structural biology of HIV-host interaction The Stroud Laboratory seeks a postdoctoral fellow to pursue the structural characterization of protein-protein complexes between HIV-1Integrase (IN) and Vpu and their human interacting partners. The HIV initiative in Stroud lab is part of larger effort in UCSF to understand HIV-host interaction ( http://harc.ucsf.edu/). This position offers the opportunity to work in highly collaborative and intellectually stimulating environment. The successful candidate will have the opportunity to: 1. Express and purify HIV-host protein-protein complexes 3. Crystallize and determine the macromolecular structure of these proteins and protein-protein complexes START DATE: Preference will be given to candidates who can start immediately REQUIREMENTS: Ph.D. in biochemistry, biophysics and structural biology. Experience with expression of recombinant proteins in variety of hosts (E.coli, SF9 etc.) and purification of proteins to a high degree of homogeneity are required. Prior experience with protein crystallization and structure determination is strongly desirable. Experience with biochemical assays and analyzing protein-protein interactions is also desirable. APPLICATION: Please send your CV/Resume describing your relevant skills and a list of three references to: stroud...@gmail.com
[ccp4bb] More cool stuff from the Protein Data Bank in Europe (pdbe.org)
Hi all, As you may recall, the Protein Data Bank in Europe (PDBe; http://pdbe.org) carried out a substantial make-over of its website last summer, including the launch of several new features (such as PDBprints - http://pdbe.org/pdbprints - and a biologist-friendly structure browser - http://pdbe.org/browse). Earlier this year, there was a further update which included new features such as Quips (http://pdbe.org/quips), a slideshow widget called PDBportfolio (http://pdbe.org/portfolio), a compound-based PDB browser (http://pdbe.org/compounds), PDB highlights (http://pdbe.org/highlights) and a user-friendly overview of every weekly release (http://pdbe.org/latest) of both PDB (in terms of both entries and chemical compounds) and EMDB (maps and headers). Now it's time for the 2011 summer update. Below is a brief description of the new features and services - in the coming weeks we will post more detailed descriptions of some of these. As always, the URL http://pdbe.org will take you to the PDBe website. Most of the features can be accessed through the PDBe Tools menu on the left side of the front page, or you can use the shortcut URLs mentioned below. -- If you can't wait to find out what cool new features are now available, here are the highlights: #1 - UniPDB (http://pdbe.org/unipdb), a widget for graphical display of coverage in the PDB of any UniProt entry, e.g. http://pdbe.org/unipdb?uniprot=P03023 #2 - PDBeXpress (http://pdbe.org/express), several easy-to-use yet powerful analyses of the PDB #3 - taxonomy-based browser of the PDB archive (http://pdbe.org/taxonomy) #4 - revamped NMR pages (http://pdbe.org/nmr) #5 - Vivaldi (http:/pdbe.org/vivaldi), interactive visualisation, validation and analysis of NMR models and data, e.g. http://pdbe.org/vivaldi/2keo #6 - revamped EM-related pages (http://pdbe.org/emdb) #7 - graphs and statistics about contents and trends in the contents of EMDB (http://pdbe.org/emstats) #8 - LeView (http://pdbe.org/leview), a Java tool to create 2D diagrams of ligands and the interactions in their binding site #9 - improved atlas pages for PDB entries, e.g. http://pdbe.org/1cbs #10 - many other smaller (or under-the-hood) improvements -- A bit more detail: - UniPDB is a new service that provides instant, graphical, up-to-date information (taken from SIFTS; see http://pdbe.org/sifts) about the coverage in the PDB of any protein sequence in UniProt. It can be used through the PDBe website or be included in your own web pages. For a description, see http://pdbe.org/unipdb - for an example, see http://pdbe.org/unipdb?uniprot=P03023 (this is for the lac repressor - note how the PDBlogos instantly reveal which are X-ray or NMR entries, which entries contain DNA, etc.). - PDBeMotif (http://pdbe.org/motif) is one of the most powerful services available for analysing PDB entries in terms of structure, sequence and chemistry (for an example, see http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Structural_motifs_in_the_PDB). However, it is also quite complex to use. For this reason, we have begun to develop small modules of PDBeMotif (and other) functionality that are presented in such a way that they are very easy to use by non-experts and provide answers to common but complex questions (such as: what ligands can bind in a site that contains Arg, Tyr and Asp? [1] or: which residue types are found most often in the binding sites of retinoic acid? [2]). From the results pages you can explore the hits using the advanced options of PDBeMotif. This service is called PDBeXpress and the first modules can be accessed at http://pdbe.org/express - we welcome your suggestions for future modules! - A new PDB browser has been added (see http://pdbe.org/browse for an overview of all available browser modules) - it allows analysis of the archive in terms of taxonomy. So, if you want to know what the predominant fold class [3] or quaternary structure [4] is for all mammalian proteins in the PDB, or who has determined the most structures of proteins from P. falciparum [5], this browser is for you. You can access it at http://pdbe.org/taxonomy - The NMR-related pages at PDBe (http://pdbe.org/nmr) have been reorganised. In addition, a new service (called Vivaldi) for interactive analysis, display and validation of NMR entries in the PDB is now available. It can be used by experts and non-experts alike, has a wizard option to help you customise the display and provides extensive explanations of the quantities that you are displaying (as linear graphs or on the 3D structure). You can can view clustering and domain organisation from OLDERADO, analyse validation data from CING and VASCO, find out which residues have restraint violations, etc. Well worth a try, even (or rather: especially!) if you are not an NMRtist! It can be accessed at
[ccp4bb] Home SAXS systems
Dear CCP4 bulletin board: I am doing some research on home SAXS systems (i.e., the BioSAXS from Rigaku, among others) and was interested in finding out what the community's experience has been with these systems in performing SAXS experiments at home. I'll post a summary of all the responses to the bb. Thanks in advance, Rebecca
[ccp4bb] How to delete loops from Protein for crystallization
Hi all I am thinking to delete flexible loop for crystallization of my protein. But i am not sure how to decide which area i should delete. This protein have around 20% sequence identity with other solved structure. Can anybody suggest me how to proceed for that. Is there any established strategy for that one? Obayed Ullah
Re: [ccp4bb] how to distinguish between phase separation, spherulite, and microcrystalline?
Lucky you that Tassos is not awake yet :-) 3 MB attachment... Anyhow the microcrystalline one is the most interesting of those 4 I'd try to change the protein:precipitant ratio and wold introduce maybe a pH screen. What are those conditions ? Jürgen On Jul 6, 2011, at 6:35 PM, joybeiyang wrote: Dear All, I am having difficulties in distinguishing phase separation, spherulite and microcrystalline in some of my drops. I have attached the photos of these drops, would someone kindly help me with this? (The names of the photos already show my uncertainty, so just skip the description here) Thank you so much in advance. Best, Bei 2011-07-06 joybeiyang PEGRx G7_Phase Seperation or microcrystalline.JPGPhase seperation or Heavy precipitation or microcrystalline.JPGIndex E10_Spherulite or Phase seperation.JPGIndex E8_Phase seperation or Spherulite.JPG .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
[ccp4bb] Natrix screen
Wanted to get an opinion. I set up a screen a while ago and got these very small cubic looking crystals 2-3 days later amidst a lot of precipitant. The condition was Natrix E1 (0.04M LiCl, 0.02M MgCl2, 0.04M Sodium Cacodylate pH5.5, 30% MPD, 0.02M Hexammine Cobalt (III) chloride). This protein's rather difficult to make, and I don't have a lot of it left frozen in the fridge after setting up the screens. Was wondering if anyone's ever observed salt crystals forming from this condition before? My protein's in 20mM HEPES pH7.5, 100mM NaCl, 5mM DTT. Thanks to all for any thoughts.
Re: [ccp4bb] Natrix screen
Hi Peter, If the crystals are brownish, then it may be crystals of Hexamine cobalt (III) chloride. If you have the final dialysis buffer of the protein, setting up a crystallization trial with just the buffer may help you distinguish between salt and protein. Hope this helps, Wataru On 2011/07/07, at 11:24, Peter Hsu wrote: Wanted to get an opinion. I set up a screen a while ago and got these very small cubic looking crystals 2-3 days later amidst a lot of precipitant. The condition was Natrix E1 (0.04M LiCl, 0.02M MgCl2, 0.04M Sodium Cacodylate pH5.5, 30% MPD, 0.02M Hexammine Cobalt (III) chloride). This protein's rather difficult to make, and I don't have a lot of it left frozen in the fridge after setting up the screens. Was wondering if anyone's ever observed salt crystals forming from this condition before? My protein's in 20mM HEPES pH7.5, 100mM NaCl, 5mM DTT. Thanks to all for any thoughts.
