[PyMOL] spectral coloring
Hi there, i am trying to map b factors on a surface representation. I am using spectrum b,blue_white_red,mymol and the colors are fine. Is there a way to fine tune the color spectrum, such as with the Midpoint and Offset sliders in vmd? Best Martin
[PyMOL] Sticks and distances with individual transparencies
Dear All, I'm trying to write a Pymol script with which produces a mixture of both solid and transparent sticks I'm using the current 1.0 incentive release of MacPymol. After drawing all my sticks I issue following commands, but nothing changes although the log output suggests the change is being set. PyMOLset stick_transparency=0.2, /sca//A/228 and !mc Setting: stick_transparency set for 5 atoms in object mol1. I'd also like to draw selected H-bonds with control of transparency with the rest solid, but have no idea how to do this. -- Mark Mayer Ph.D. LCMN NICHD NIH DHHS Bldg 35, Room 3B 1002 MSC 3712 35 Lincoln Drive Bethesda MD 20892 3712 Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396 Lab web site: http://mayerlab.nichd.nih.gov Send packages, Fedex and anything requiring a signature to: Bldg 35, Room 3B 1004 35 Lincoln Drive Bethesda MD 20892
[PyMOL] coloring based on sequence identity
Hi, I'd like to color a molecule based on its sequence similarity to another molecule. Can this be done in Pymol? Thanks in advance. - Eva
Re: [PyMOL] coloring based on sequence identity
Am Dienstag, 26. Juni 2007 schrieb Eva Vanamee: Hi, I'd like to color a molecule based on its sequence similarity to another molecule. Can this be done in Pymol? If you can quantify similarity in a number you can write it into the b-factors of the atoms and then color it by them. Best Martin -- Wenn Theorie und Realität nicht übereinstimmen, muß entweder die Theorie oder die Realität geändert werden. Das erste nennt man Wissenschaft, das zweite Religion. [Achim Stoesser, 12.8.1999]
Re: [PyMOL] rotate about an abitrary axis
Minh, This type of use is now covered under the rotate command in the official documentation for PyMOL 1.0 ( http://delsci.info/dsc ) as well as in the current open-source code. Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor! -WLD _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Minh Nhat Sent: Friday, June 22, 2007 11:56 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] rotate about an abitrary axis Hi everyone, Is it possible to make a selection rotate about an arbitrary axis (which we can actively define ourself (not x,y, z) ?) Thanks, Send instant messages to your online friends http://uk.messenger.yahoo.com
Re: [PyMOL] Sticks and distances with individual transparencies - repost
Mark, Your confusion arises from the new set_bond command, which must be used when setting bond-specific properties. Please see the official docs on set_bond. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor! -WLD _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Dr. Mark Mayer Sent: Tuesday, June 26, 2007 10:18 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Sticks and distances with individual transparencies - repost Apologies for prior post message font was nearly unreadable Dear All, I'm trying to write a Pymol script with which produces a mixture of both solid and transparent sticks I'm using the current 1.0 incentive release of MacPymol. After drawing all my sticks I issue following commands, but nothing changes although the log output suggests the change is being set. PyMOLset stick_transparency=0.2, /sca//A/228 and !mc Setting: stick_transparency set for 5 atoms in object mol1. I'd also like to draw selected H-bonds with control of transparency with the rest solid, but have no idea how to do this. -- Mark Mayer Ph.D. LCMN NICHD NIH DHHS Bldg 35, Room 3B 1002 MSC 3712 35 Lincoln Drive Bethesda MD 20892 3712 Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396 Lab web site: http://mayerlab.nichd.nih.gov Send packages, Fedex and anything requiring a signature to: Bldg 35, Room 3B 1004 35 Lincoln Drive Bethesda MD 20892
[PyMOL] PyMOL 1.0 and Official Docs
Greetings! As some of you have noticed, PyMOL 1.0 is out (at last!). Though it lacks many of the features and enhancements I had hoped to deliver in the big 1.0, we were long overdue for a major release and so the line was drawn. For those of you new to PyMOL within the past year or so, our software releases are a relatively low-key event: The last thing we want is for everyone to race out and download the latest version, suddenly to discover some horrendous bug right in the middle of orals or a critical corporate presentation. No, no, not that! Instead, we ask people to gradually ease into new versions at a safe time place, while reporting any problems that come up so that we can quickly fix the source and builds before too many other folks encounter them. In terms of features, PyMOL 1.0 is not a huge leap beyond the latest 1.0 beta builds, but there were some last minute tweaks, so please do use caution. So far, so good: the 1.0r0 builds appear stable, and current sponsors can download builds from http://delsci.com/ip. Non-sponsors are welcome to pull compile the open-source code from the Subversion repository hosted at SourceForge http://pymol.sf.net. Free educational-use-only builds of PyMOL 1.0 will be released in early August, before the start of the fall semester. The other big announcement is the opening of our official documentation site, which has also been in the works for over a year. As opposed to the PyMOL Community Wiki, this read-only resource at http://delsci.info/dsc is something you need a paid subscription to access, and it also involves a somewhat tedious email-based registration login process. I apologize in advance for that inconvenience. However, if your company or institution maintains an entity-wide PyMOL subscription, then we can simply reverse-DNS through your whole domain so that you and all your colleagues can access documentation without logging in, much the same way transparent entity-wide access is granted for scientific journals. By the way, if you are thinking of sponsoring the effort or of renewing an existing subscription, please do look into whether we might all save time effort by going entity-wide. Processing of individual and/or laboratory subscriptions takes precious time resources away from development and documentation relative to broader subscriptions. Plus, in addition to saving paperwork, entity-wide subscriptions can potentially benefit a much larger base of users at a much lower per-user cost. So a hearty thank you to everyone who has made PyMOL possible over the past 7 years, whether at the individual, laboratory, departmental, corporate, or institutional level. Although I do not have permission to name most PyMOL sponsors, they include many top universities, research institutes, pharmaceutical companies, and biotech giants, as well as a wide assortment of startup companies, laboratories, and individuals. Thanks also to the contributors of various open-source components and capabilities! Together we are all working together to ensure that PyMOL continues to thrive under terms that remain compatible with the open-source code. Enjoy! Cheers, Warren L. DeLano, Ph.D. DeLano Scientific LLC Sponsorship info at http://pymol.org/funding.html
Re: [PyMOL] Sticks and distances with individual transparencies
Hi Mark, You could've found this one in the archives of this list. Settings work on objects, not on selections. The solution is to make an object for the solid sticks and one for the transparent sticks, using create. Cheers, Tsjerk On 6/26/07, Dr. Mark Mayer may...@mail.nih.gov wrote: Dear All, I'm trying to write a Pymol script with which produces a mixture of both solid and transparent sticks I'm using the current 1.0 incentive release of MacPymol. After drawing all my sticks I issue following commands, but nothing changes although the log output suggests the change is being set. PyMOLset stick_transparency=0.2, /sca//A/228 and !mc Setting: stick_transparency set for 5 atoms in object mol1. I'd also like to draw selected H-bonds with control of transparency with the rest solid, but have no idea how to do this. -- Mark Mayer Ph.D. LCMN NICHD NIH DHHS Bldg 35, Room 3B 1002 MSC 3712 35 Lincoln Drive Bethesda MD 20892 3712 Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396 Lab web site: http://mayerlab.nichd.nih.gov Send packages, Fedex and anything requiring a signature to: Bldg 35, Room 3B 1004 35 Lincoln Drive Bethesda MD 20892 - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
