Re: [PyMOL] Sequence Viewer Details
pymol-users-boun...@lists.sourceforge.net wrote on 03/03/2007 12:40:13 AM: Hello, Where can I find information about the sequence viewer? I would like to know more about the red zeros, etc. --Kevin Hi Kevin - I'm not sure of the best source of info for the sequence viewer, but the red zeros you're probably referring to are actually the letter O, and represent the oxygen of water molecules in the pdb file. - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
Re: [PyMOL] Electrostatic surface visualization
On 3/3/07, se...@uniroma2.it se...@uniroma2.it wrote: Dear all, I'm new to this list and to the software. I used PyMOL and APBS to calculate an electrostatic surface for a small protein (I'm using the WindowsXP version) and everything seems fine. Now I would like to visualize this surface AND the secondary structure of the protein, in order to understand the positive and negative regions. How I can do? Some software show the surface in trasparency but it seems this is not possible in PyMOL. You can do this with commands like set transparency, 0.5, myproteinname or set transparency, 0.2, iso_pos A related question: it is possible to color the secondary structure according to the electrostatic surface properties? I have an NMR titration of this protein with its partner: I would like to relate the shifts of the NH backbone with the electrostatic surface. Not sure about that one. -Michael I looked at the archive but I haven't found an answer. Thanks in advance, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, Tor Vergata via della Ricerca Scientifica, 00133, Rome, Italy e-mail:se...@uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328 - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net
[PyMOL] problems using selection wildcards?
Dear list, Has anyone else noticed problems with some selection wildcards in 0.99rev8? I can still do things like delete thingy_* to delete the models thingy_001, thingy_002, etc. But when I try things like color nitrogen, name N* nothing happens. I can do color nitrogen, name N+, but that only gets backbone amides. color nitrogen, name NH+ (or NH*) does nothing. This seemed to work reliably in the last release. For the nonce I'm using the symbol selector, but I found atom selection wildcards oh-so-convenient... Am I doing something wrong? Jacob -- Jacob Corn The Berger Lab UC Berkeley - Molecular and Cell Biology jc...@uclink.berkeley.edu phone: 510-643-8893 fax: 510-643-9290
Re: [PyMOL] problems using selection wildcards?
Jacob, Are you looking at a nucleic acid structure perhaps? PyMOL automatically disables the asterisk wildcard for atom names in PDB structures read which contain asterisks in the atom name field (as do many NA structures...). To restore it, unset atom_name_wildcard, object-name But then note that PyMOL will then be unable to distinguish C2 in the base from C2* in the sugar, etc. However, if you issue this first, alter all, name=string.replace(name,*,') Then you will be able to distinguish C2 from C2' and still have your atom name wildcards! Cheers, DeLano Scientific LLC -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Jacob Corn Sent: Monday, March 05, 2007 9:29 AM To: pymol-users Subject: [PyMOL] problems using selection wildcards? Dear list, Has anyone else noticed problems with some selection wildcards in 0.99rev8? I can still do things like delete thingy_* to delete the models thingy_001, thingy_002, etc. But when I try things like color nitrogen, name N* nothing happens. I can do color nitrogen, name N+, but that only gets backbone amides. color nitrogen, name NH+ (or NH*) does nothing. This seemed to work reliably in the last release. For the nonce I'm using the symbol selector, but I found atom selection wildcards oh-so-convenient... Am I doing something wrong? Jacob -- Jacob Corn The Berger Lab UC Berkeley - Molecular and Cell Biology jc...@uclink.berkeley.edu phone: 510-643-8893 fax: 510-643-9290 -- --- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforge CID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] WRL Output
My 2 cents' worth: How about skipping over the ancient and limiting WRL format and adopt a cross-platform solution. For example, Collada is gaining momentum in the 3D community (https://collada.org/public_forum/welcome.php) and provides an open standard digital asset schema for interactive 3D applications. Thanks, JP Cartailler -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Markus Wahl Sent: Friday, March 02, 2007 11:28 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] WRL Output Dear all, I wondered whether there is a possibility in PyMol to export the rendered polygon data in any kind of 3D format such as wrl or inventor? Best, Markus -- PD Markus Wahl, Ph.D. Max-Planck-Institut fuer Biophysikalische Chemie Abteilung Zellulaere Biochemie/Roentgenkristallographie Am Fassberg 11 D-37077 Goettingen Germany Phone: +49 (0)551-201-1046 Fax: +49 (0)551-201-1197 eMail: mw...@gwdg.de Homepage: http://www.mpibpc.mpg.de/groups/wahl - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDE V ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] plug-ins on Mac OSX - X11?
Dear PyMOL users, I am a newcomer to this list and largely to PyMOL. I have a lot of experience with Jmol since my work is oriented toward publishing on the web. I would like to be able to generate surface MEP coloring in PyMOL for proteins. I'm on Mac OSX 10.4, and I've downloaded/installed APBS and the APBS plug-in for PyMOL. Then I realized I had to install X11, so I found my original OSX 10.4 install discs, and have tried installing X11 three times with no luck (twice tried a custom install of X11 only, the third time I bit the bullet and installed the entire Xcode tools package. Still no sign of X11 on my machine.) Has anyone experienced this and found a way to deal with it? I have already changed the name of MacPyMol.app to PyMolX11Hybrid.app, as per the instructions on the web site, but when I open the newly named pymol app, it asks me where X11 is... Thanks in advance, Frieda /// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com ///
Re: [PyMOL] plug-ins on Mac OSX - X11?
Frieda, We too have experienced problems ourselves attempting to install X11 on Macintosh computers that have been patched since the original Mac OS X install. The only sure fix we know of is to do a clean OS install from the original CD, being sure to select the X11 option, which is not enabled by default. Once X11 is installed, then subsequent updates can safely be reinstalled. Perhaps someone else on the mailing list knows of an alternate way of getting X11 onto an existing Mac? -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Frieda Reichsman Sent: Monday, March 05, 2007 5:24 PM To: Users List PyMOL Subject: [PyMOL] plug-ins on Mac OSX - X11? Dear PyMOL users, I am a newcomer to this list and largely to PyMOL. I have a lot of experience with Jmol since my work is oriented toward publishing on the web. I would like to be able to generate surface MEP coloring in PyMOL for proteins. I'm on Mac OSX 10.4, and I've downloaded/installed APBS and the APBS plug-in for PyMOL. Then I realized I had to install X11, so I found my original OSX 10.4 install discs, and have tried installing X11 three times with no luck (twice tried a custom install of X11 only, the third time I bit the bullet and installed the entire Xcode tools package. Still no sign of X11 on my machine.) Has anyone experienced this and found a way to deal with it? I have already changed the name of MacPyMol.app to PyMolX11Hybrid.app, as per the instructions on the web site, but when I open the newly named pymol app, it asks me where X11 is... Thanks in advance, Frieda /// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com ///
