From: gilleain t. <gil...@gm...> - 2006-03-06 14:58:00
|
Hi, I found out how to do ... something ... like this the other day. From the "action" (A) menu for an object select Generate->Symmetry Mates. This gives you the option of within 4-100 angstrom. I don't know what it means to select different distances, all I know is that any one of these options gives you lots more copies of that object, presumably where they are in the crystal structure. This came in useful when looking at the results from msdmotif at the ebi, which was giving some ligands as binding twice to the same motif; turns out that one of them was from a neighbour interaction. gilleain On 3/4/06, Blanton Tolbert <bla...@ur...> wrote: > Hi pymol community > > I would like to recapitulate the crystal packing arrangement of a > protein structure to look for neighbor interactions. Is it possible > to do this in pymol? If so, please provide me some insight. > > Thanks, > > > Blanton Tolbert > Graduate Student > University of Rochester > Biophysics and Structural Biology > 585-275-5189 > bla...@ur... > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking scripting langua= ge > that extends applications into web and mobile media. Attend the live webc= ast > and join the prime developer group breaking into this new coding territor= y! > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat= =3D121642 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: <Sri...@ju...> - 2006-03-27 04:19:13
|
<FONT face=3D"Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size= =3D2><DIV>dear sir </DIV><DIV> &nb= sp; iam a pymol user, do we can find area & volu= me of active site in pymol </DIV><DIV>if we can, just tell me how to do it = </DIV><DIV>thanking you </DIV><DIV>srilatha<BR></DIV><DIV>Thanks &= Regards<BR>srilatha potlapelly<BR>MSc Biotechnology<BR></DI= V></FONT>= |
From: Andrea S. <and...@gm...> - 2006-03-27 07:43:48
|
Hi, for this purpose I have used caver program. You can download it free of charge from here http://loschmidt.chemi.muni.cz/caver/download.php I hope this help Regards andrea 2006/3/27, Sri...@ju... <Sri...@ju...>: > dear sir > iam a pymol user, do we can find area & volume of active site= in > pymol > if we can, just tell me how to do it > thanking you > srilatha > Thanks & Regards > srilatha potlapelly > MSc Biotechnology > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking scripting langua= ge > that extends applications into web and mobile media. Attend the live webc= ast > and join the prime developer group breaking into this new coding territor= y! > http://sel.as-us.falkag.net/sel?cmdlnk&kid=110944&bid$1720&dat=121642 > _______________________________________________ PyMOL-users > mailing list PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users -- "La conoscenza libera il genere umano dalla superstizione" J. Watson |
From: Orla O'S. <Orl...@te...> - 2006-04-20 10:56:24
|
=20 Hi all This probably a very stupid question but its driving me mad. I have produced two Raster 3D scences using molscript and have loaded them into pymol.=20 What I want to do is to be able to move them on screen independent of each other. Is this possible? =20 Regards Orla =20 Dr.Orla O'Sullivan Research Officer Biotechnology =20 =20 Moorepark Food Research Centre Teagasc Moorepark Fermoy, Co. Cork Ireland =20 Tel: +353 - (0)25 - 42344 =20 |
From: Noinaj <no...@uk...> - 2006-04-20 16:55:52
|
orla, If in fact you actually have to move molecules independently using the = 'dirty' method that I have suggested, you will probably need the rotate = command too, for more flexibility in setting things up. =20 -------------------------------------------- rotate DESCRIPTION "rotate" can be used to rotate the atomic coordinates of a molecular object. Behavior differs depending on whether or not the "object" parameter is specified. If object is None, then rotate rotates the atomic coordinates according to the axes and angle for the selection and state provided. All representation geometries will need to be regenerated to reflect the new atomic coordinates. If object is set to an object name, then selection and state are ignored and instead of translating the atomic coordinates, the object's representation display matrix is modified. This option is for use in animations only. USAGE rotate axis, angle [,selection [,state [,camera [,object = [,origin]]]]] PYMOL API cmd.rotate(list-or-string axis, string selection =3D "all", int state = =3D 0, int camera =3D 1, string object =3D None) EXAMPLES rotate x, 45, pept NOTES if state =3D 0, then only visible state(s) are affected. if state =3D -1, then all states are affected. ---------------------------------Cheers,Nickreference:http://pymol.source= forge.net/newman/ref/S1000comref.html ----- Original Message -----=20 From: Orla O'Sullivan=20 To: pym...@li...=20 Sent: Thursday, April 20, 2006 6:56 AM Subject: [PyMOL] (no subject) =20 Hi all This probably a very stupid question but its driving me mad. I have = produced two Raster 3D scences using molscript and have loaded them into = pymol.=20 What I want to do is to be able to move them on screen independent of = each other. Is this possible? =20 Regards Orla =20 Dr.Orla O'Sullivan Research Officer Biotechnology =20 =20 Moorepark Food Research Centre Teagasc Moorepark Fermoy, Co. Cork Ireland =20 Tel: +353 - (0)25 - 42344 =20 |
From: O. J. G. <ojg...@mb...> - 2006-05-29 17:05:10
|
=20 =20 Hey again PyMOL gurus, >* O. J. Ganesh <ojg...@mb...> [2006-05-18 16:09] wrote: >>=20 >> Hey PyMOL gurus: >>=20 >> I have a 'perfect' helix. Is there some way to 'loosen' all of the >> angles in the helix so instead of 3.6 residues per turn, I could >> have, say, 8 residues per turn. My goal is to make the helix more >> 'coil-like'. Is this possible? > >Well, if you know the phi/psi angles you like, then you could just = build >it and specify those angles with my build_seq.py script: > >http://adelie.biochem.queensu.ca/~rlc/work/pymol/build_seq.py > >You can specify the phi, psi angles on the command line. Alternatively, >you can create a file of resname, phi, psi and build it with: > >http://adelie.biochem.queensu.ca/~rlc/work/pymol/build_seq_phi_psi.py > >if you don't want the phi/psi angles to be the same for every residue. > >Cheers, >Rob =20 Thanks Robert Campbell, I've actually used the build_seq_phi_psi.py script before, and it is = WONDERFUL! I can (and probably will) use it in this case also. I was = just checking to see if there wasn't an easier way to do this within = PyMOL... Something that would take a selection of a pdb structure and = generally 'loosen' or 'relax' it. (I know it sounds vague.) =20 Thanks again! |
From: Gabrielle M. <Gab...@as...> - 2006-07-07 22:23:06
|
Hello all,=20 I am a new PyMOL user trying to prepare figures for publication. I'm confu= sed about the difference between the isomesh level of the 'mesh' in PyMOL a= nd the contour level of the electron density map that I read in from CCP4. = For example, for one of my figures I created a 3sigma Fo-Fc omit map and r= ead it in to PyMOL. In order to make the density lovely I used the 'map_do= uble' command and created a second 'mesh'. I then adjusted each of these = 'mesh' to a 'level' of 4. Does this mean that my omit map is actually now = contoured to 4sigma, or are the two not related? =20 Thanks for any help, Gabrielle |
From: Donglu X. <do...@ca...> - 2006-07-13 23:51:49
|
Hi Dear Pymol-users, Sorry about this long message. I am struggling to configure X Windwo to enable stereo. Two monitors are connected with the NVIDIA GPU Quadro FX 3400 card. One monitor is ViewSonic VP2030b LCD, another is ViewSonic G225fb CRT. Try to configure X widnow to enable stereo with Xinerama on so that application can cross the screen boundaries. There is no any error or warning message in Xorg.0.log (xorg.conf is below). However, when tried to run stereo application, such as PyMol or Coot, it doesn't work. It came out with different error messages. In PyMol, error is following: X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 78 (X_CreateColormap) Value in failed request: 0x0 Serial number of failed request: 14 Current serial number in output stream: 16 PyMOL: abrupt program termination. In Coot, the error is Gdk-ERROR **: BadValue (integer parameter out of range for operation) serial 390 error_code 2 request_code 78 minor_code 0 Googling doesn't get much useful information. I also tried to use Twinview. The stereo works well. However, the application interface cannot move cross the screen boundaries. The Xinerama enabled setting works perfect with systems connected with a CRT and a LCD monitors (2.4.20-6smp #1 SMP Thu Feb 27 09:36:38 EST 2003 i686 athlon i386 GNU/Linux) (NVIDIA Quadro4 750 XGL). The system with stereo problem is 2.6.9-34.0.1.ELlargesmp #1 SMP Wed May 17 17:19:07 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux xorg.conf and partial of Xorg.0.log files is below. Any help or suggestion is appreciated. Best, -Donglu Xie xorg.conf is following ========================= Section "ServerLayout" Identifier "Dual Layout" Option "Xinerama" "true" Screen 0 "Screen0" Screen 1 "Screen1" RightOf "Screen0" InputDevice "Mouse0" "CorePointer" InputDevice "Keyboard0" "CoreKeyboard" EndSection Section "Files" RgbPath "/usr/X11R6/lib/X11/rgb" FontPath "unix/:7100" EndSection Section "Module" Load "dbe" Load "extmod" Load "fbdevhw" Load "glx" Load "glx" Load "record" Load "freetype" Load "type1" # Load "dri" EndSection Section "InputDevice" Identifier "Keyboard0" Driver "kbd" Option "XkbModel" "pc105" Option "XkbLayout" "us" EndSection Section "InputDevice" Identifier "Mouse0" Driver "mouse" Option "Protocol" "IMPS/2" Option "Device" "/dev/input/mice" Option "ZAxisMapping" "4 5" Option "Emulate3Buttons" "yes" EndSection Section "Monitor" Identifier "LCD" VendorName "Viewsonic" ModelName "VP2030b" HorizSync 24.0 - 92.0 VertRefresh 50.0 - 85.0 Option "dpms" EndSection Section "Monitor" Identifier "CRT" VendorName "Viewsonic" ModelName "G225fb" HorizSync 30.0 - 130.0 VertRefresh 50.0 - 160.0 Option "dpms" Modeline "1600x1200_99.00" 277.61 1600 1728 1904 2208 1200 1201 1204 1270 -HSync +Vsync EndSection Section "Device" Identifier "Videocard0" Driver "nvidia" VendorName "Videocard vendor" BoardName "NVIDIA Quadro FX3400" #VideoRam 262144 BusID "PCI:5:0:0" Option "Stereo" "3" Screen 0 Option "NoPowerConnectorCheck" EndSection Section "Device" Identifier "Videocard1" Driver "nvidia" VendorName "Videocard vendor" BoardName "NVIDIA Quadro FX3400" #VideoRam 262144 BusID "PCI:5:0:0" Screen 1 Option "NoPowerConnectorCheck" EndSection Section "Screen" Identifier "Screen1" Device "Videocard1" Monitor "LCD" DefaultDepth 24 SubSection "Display" Viewport 0 0 Depth 24 Modes "1600x1200" "1400x1050" "1280x1024" "1280x960" "1152x864" "1024x768" "800x600" "640x480" EndSubSection EndSection Section "Screen" Identifier "Screen0" Device "Videocard0" Monitor "CRT" DefaultDepth 24 SubSection "Display" Viewport 0 0 Depth 24 Modes "1600x1200_99.00" "1600x1200" "1400x1050" "1280x1024" "1024x768" "800x600" "640x480" EndSubSection EndSection ==== end of xorg.conf ========== Partial of Xorg.0.log ============================ (II) Module glx: vendor="NVIDIA Corporation" (II) Module nvidia: vendor="NVIDIA Corporation" (II) NVIDIA dlloader X Driver 1.0-8756 Wed Mar 29 15:14:16 PST 2006 (II) NVIDIA Unified Driver for all Supported NVIDIA GPUs (--) Chipset NVIDIA GPU found (--) Chipset NVIDIA GPU found (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 (==) NVIDIA(0): RGB weight 888 (==) NVIDIA(0): Default visual is TrueColor (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) (**) NVIDIA(0): Option "Stereo" "3" (**) NVIDIA(0): Option "NoPowerConnectorCheck" (**) NVIDIA(0): Onboard stereo requested (DIN connector) (**) NVIDIA(0): Enabling RENDER acceleration (II) NVIDIA(0): Skipping Power Connector Check. (II) NVIDIA(0): NVIDIA GPU Quadro FX 3400 at PCI:5:0:0 (--) NVIDIA(0): VideoRAM: 262144 kBytes (--) NVIDIA(0): VideoBIOS: 05.40.02.41.04 (II) NVIDIA(0): Detected PCI Express Link width: 8X (--) NVIDIA(0): Interlaced video modes are supported on this GPU (--) NVIDIA(0): Connected display device(s) on Quadro FX 3400 at PCI:5:0:0: (--) NVIDIA(0): ViewSonic G225f (CRT-0) (--) NVIDIA(0): ViewSonic VP2030 SERIES (CRT-1) (--) NVIDIA(0): ViewSonic G225f (CRT-0): 400 MHz maximum pixel clock (--) NVIDIA(0): ViewSonic VP2030 SERIES (CRT-1): 400 MHz maximum pixel clock (II) NVIDIA(0): Assigned Display Device: CRT-0 (II) NVIDIA(0): Validated modes: (II) NVIDIA(0): "1600x1200_99.00" (II) NVIDIA(0): "1600x1200" (II) NVIDIA(0): "1400x1050" (II) NVIDIA(0): "1280x1024" (II) NVIDIA(0): "1024x768" (II) NVIDIA(0): "800x600" (II) NVIDIA(0): "640x480" (II) NVIDIA(0): Virtual screen size determined to be 1600 x 1200 (--) NVIDIA(0): DPI set to (99, 101); computed from "UseEdidDpi" X config option (**) NVIDIA(1): Depth 24, (--) framebuffer bpp 32 (==) NVIDIA(1): RGB weight 888 (==) NVIDIA(1): Default visual is TrueColor (==) NVIDIA(1): Using gamma correction (1.0, 1.0, 1.0) (**) NVIDIA(1): Option "NoPowerConnectorCheck" (**) NVIDIA(1): Enabling RENDER acceleration (II) NVIDIA(1): NVIDIA GPU Quadro FX 3400 at PCI:5:0:0 (--) NVIDIA(1): VideoRAM: 262144 kBytes (--) NVIDIA(1): VideoBIOS: 05.40.02.41.04 (II) NVIDIA(1): Detected PCI Express Link width: 8X (--) NVIDIA(1): Interlaced video modes are supported on this GPU (--) NVIDIA(1): Connected display device(s) on Quadro FX 3400 at PCI:5:0:0: (--) NVIDIA(1): ViewSonic G225f (CRT-0) (--) NVIDIA(1): ViewSonic VP2030 SERIES (CRT-1) (--) NVIDIA(1): ViewSonic G225f (CRT-0): 400 MHz maximum pixel clock (--) NVIDIA(1): ViewSonic VP2030 SERIES (CRT-1): 400 MHz maximum pixel clock (II) NVIDIA(1): Assigned Display Device: CRT-1 (II) NVIDIA(1): Validated modes: (II) NVIDIA(1): "1600x1200" (II) NVIDIA(1): "1400x1050" (II) NVIDIA(1): "1280x1024" (II) NVIDIA(1): "1280x960" (II) NVIDIA(1): "1152x864" (II) NVIDIA(1): "1024x768" (II) NVIDIA(1): "800x600" (II) NVIDIA(1): "640x480" (II) NVIDIA(1): Virtual screen size determined to be 1600 x 1200 (--) NVIDIA(1): DPI set to (99, 98); computed from "UseEdidDpi" X config option (II) NVIDIA(0): Setting mode "1600x1200_99.00" (II) NVIDIA(0): NVIDIA 3D Acceleration Architecture Initialized (II) NVIDIA(0): Using the NVIDIA 2D acceleration architecture (==) NVIDIA(0): Backing store disabled (==) NVIDIA(0): Silken mouse enabled (**) NVIDIA(0): DPMS enabled (II) NVIDIA(1): Setting mode "1600x1200" (II) NVIDIA(1): NVIDIA 3D Acceleration Architecture Initialized (II) NVIDIA(1): Using the NVIDIA 2D acceleration architecture (==) NVIDIA(1): Backing store disabled (==) NVIDIA(1): Silken mouse enabled (**) NVIDIA(1): DPMS enabled (II) XINPUT: Adding extended input device "NVIDIA Event Handler" (type: Other) (II) XINPUT: Adding extended input device "NVIDIA Event Handler" (type: Other) (II) NVIDIA(0): Setting mode "1600x1200_99.00" (II) NVIDIA(0): NVIDIA 3D Acceleration Architecture Initialized (II) NVIDIA(0): Using the NVIDIA 2D acceleration architecture (**) NVIDIA(0): DPMS enabled (II) NVIDIA(1): Setting mode "1600x1200" (II) NVIDIA(1): NVIDIA 3D Acceleration Architecture Initialized (II) NVIDIA(1): Using the NVIDIA 2D acceleration architecture (**) NVIDIA(1): DPMS enabled (II) NVIDIA(0): Setting mode "1600x1200_99.00" (II) NVIDIA(0): NVIDIA 3D Acceleration Architecture Initialized (II) NVIDIA(0): Using the NVIDIA 2D acceleration architecture (**) NVIDIA(0): DPMS enabled (II) NVIDIA(1): Setting mode "1600x1200" (II) NVIDIA(1): NVIDIA 3D Acceleration Architecture Initialized (II) NVIDIA(1): Using the NVIDIA 2D acceleration architecture (**) NVIDIA(1): DPMS enabled (II) NVIDIA(0): Setting mode "1600x1200_99.00" (II) NVIDIA(0): NVIDIA 3D Acceleration Architecture Initialized (II) NVIDIA(0): Using the NVIDIA 2D acceleration architecture (**) NVIDIA(0): DPMS enabled (II) NVIDIA(1): Setting mode "1600x1200" (II) NVIDIA(1): NVIDIA 3D Acceleration Architecture Initialized (II) NVIDIA(1): Using the NVIDIA 2D acceleration architecture (**) NVIDIA(1): DPMS enabled (II) NVIDIA(0): Setting mode "1600x1200_99.00" (II) NVIDIA(0): NVIDIA 3D Acceleration Architecture Initialized (II) NVIDIA(0): Using the NVIDIA 2D acceleration architecture (**) NVIDIA(0): DPMS enabled (II) NVIDIA(1): Setting mode "1600x1200" (II) NVIDIA(1): NVIDIA 3D Acceleration Architecture Initialized (II) NVIDIA(1): Using the NVIDIA 2D acceleration architecture (**) NVIDIA(1): DPMS enabled |
From: mati <mat...@we...> - 2006-08-10 07:35:28
|
hello all pymol draw lines between near atom with no real connection between them! I wanted to know if there is a way to prevent pymol of making the bonds (lines) between atom and that pymol will connect atom only by a specific request (like a connect line in the pdb file) CONECT 416 778 (which means connect atoms 416 778) thank you very much mati |
From: Giacomo B. <gba...@pa...> - 2006-11-07 10:21:16
|
Dear Users, =20 I would like with a simple script to export some data regarding distances. Do any of you know how to write an output with all distances that I set up? =20 Thanks in advance =20 Giacomo =20 Giacomo Bastianelli EIMID Ph.D Fellow (www.eimid.org <http://www.eimid.org/> ) Marie Curie EST gba...@pa... Unit=E9 de Bioinformatique Structurale Institut Pasteur 25-28 Rue de Dr.Roux 75015 Paris, France =20 |
From: gilleain t. <gil...@gm...> - 2006-11-07 14:56:45
|
Hi, I don't know how simple you want it, but python lets you print just like: print cmd.distance(a, b) assuming that a and b are strings that are atom selections. See http://www.pymolwiki.org/index.php/Translate_And_Measure for a more complex example! :) gilleain On 11/7/06, Giacomo Bastianelli <gba...@pa...> wrote: > > Dear Users, > > I would like with a simple script to export > some data regarding distances. > Do any of you know how to write an output with > all distances that I set up? > > Thanks in advance > > Giacomo > > > > Giacomo Bastianelli > > EIMID Ph.D Fellow (www.eimid.org) > > Marie Curie EST > > gba...@pa... > > Unit=E9 de Bioinformatique Structurale > > Institut Pasteur > > 25-28 Rue de Dr.Roux > > 75015 Paris, France > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronim= o > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat= =3D121642 > > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > |
From: Bernhard K. <bb...@gm...> - 2007-02-23 10:38:35
|
Hello and good morning, being newly arrived in this list, I am a molecular biologist working recently in endocrinology and epigenetics and living in the black forest in the south west of germany. Since I am not fully content with the picture quality which I can get with Rasmol, I am trying to use PyMOL. However, since I try to adopt my rasmol script for use in PyMOL, I am unable to find how to select individual amino acids, or e.g. polar or basic residues. I am quite convinced that such shortcuts exist. But either the refmanual oder the usermanual lack mentioning any typ of aminoacids, so far as I can say (searching with Acrobat reader). It would be a pleasure if anyone could point me to the proper information. Thanks a lot Bernhard --=20 Bernhard Kleine mail bb...@gm... linux-user Nr. 411598 **************************************** PGP-Key PGP-Fingerprint: 0x6C1D9C2A 3161 A9E2 B661 A242 D9AF 61BF C842 4D18 6C1D 9C2A **************************************** |
From: Tsjerk W. <ts...@gm...> - 2007-02-23 10:50:21
|
Dear Bernhard, The user manual is quite informative where it comes to making selections. There is not a polar/nonpolar grouping made for you, but you can easily select the residues based on their names (resn or r.). select basic, (resn lys,his,arg) As a side note, on this as well as all other user lists, it is preferred that you set a subject line which reflects the question you're asking. Since many of us are dedicating our own time to answering, we usually make a preselection of the mails we could possibly provide an answer to. Mails without subject are likely to be thrown away unread. Cheers, Tsjerk On 2/23/07, Bernhard Kleine <bb...@gm...> wrote: > Hello and good morning, > > being newly arrived in this list, I am a molecular biologist working > recently in endocrinology and epigenetics and living in the black forest > in the south west of germany. > > Since I am not fully content with the picture quality which I can get > with Rasmol, I am trying to use PyMOL. However, since I try to adopt my > rasmol script for use in PyMOL, I am unable to find how to select > individual amino acids, or e.g. polar or basic residues. I am quite > convinced that such shortcuts exist. But either the refmanual oder the > usermanual lack mentioning any typ of aminoacids, so far as I can say > (searching with Acrobat reader). > > It would be a pleasure if anyone could point me to the proper > information. > > Thanks a lot > > Bernhard > -- > Bernhard Kleine > mail bb...@gm... > linux-user Nr. 411598 > **************************************** > PGP-Key PGP-Fingerprint: > 0x6C1D9C2A 3161 A9E2 B661 A242 D9AF > 61BF C842 4D18 6C1D 9C2A > **************************************** > > ------------------------------------------------------------------------- > 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.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > 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 |
From: <Szt...@se...> - 2007-04-16 10:51:17
|
Hello, I would like to ask about building phosphate group at Tyr residue. Is there any posibility to do it at PyMOL programe? Thank you for answer Martin Sztacho |
From: DeLano S. <de...@de...> - 2007-04-19 00:37:30
|
Martin, No, sorry, you will need an external tool to do this. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:de...@de... "Not yet a PyMOL Subscriber, but want to support the project? Email sa...@de... to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor!" -WLD > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf > Of Martin Sztacho > Sent: Monday, April 16, 2007 3:51 AM > To: pym...@li... > Subject: [PyMOL] (no subject) > > Hello, > I would like to ask about building phosphate group at Tyr > residue. Is there any posibility to do it at PyMOL programe? > Thank you for answer > Martin Sztacho > > -------------------------------------------------------------- > ----------- > 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 > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Grigoryan H. <ha...@ya...> - 2008-02-26 15:45:11
|
ha...@ya... --------------------------------- Looking for last minute shopping deals? Find them fast with Yahoo! Search. |
From: Justin L. <j.l...@fz...> - 2009-02-19 13:37:49
Attachments:
signature.asc
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Hello all especially Warren, What does "Sorry, time-sequential stereo 3D not available" mean. It is printed out when I start pymol. I am using current HEAD. Thanks justin -- Justin Lecher Institute for Neuroscience and Biophysics INB 2 - Molecular Biophysics II Research centre Juelich GmbH, 52425 Juelich,Germany phone: +49 2461 61 5385 |
From: Rotem S. <rot...@we...> - 2009-03-24 07:06:47
|
Hi, I'm looking for a way to calculate set of torsion angels from selected residues (for example Chi1 dihedral of all His residues). Is it possible to write PyMOL script for such task ? Any hints to write such script will be appreciated! Thank you Rotem ---------------------------------------------------------- Rotem Sertchook, Ph.D. Bioinformatics Unit, Biological Services Weizmann Institute of Science, Rehovot 76100, Israel. ---------------------------------------------------------- |
From: gilleain t. <gil...@gm...> - 2009-03-24 07:47:51
|
Hi, I think that it probably is possible to do this from within pymol, and probably quite convenient for single molecules. However, there are two other possible approaches, which would be helpful for multiple molecules. Firstly, there is a program called 'dang' made by the Richardson group: http://kinemage.biochem.duke.edu/software/dang.php and secondly, might I humbly submit that I have a program I call 'Tailor' that is intended for measuring and analysing (to a limited extent) selected parts of proteins: http://tailor.sourceforge.net/docs/index.html gilleain On Tue, Mar 24, 2009 at 7:06 AM, Rotem Sertchook <rot...@we...> wrote: > Hi, > I'm looking for a way to calculate set of torsion angels from selected > residues (for example Chi1 dihedral of all His residues). Is it possible to > write PyMOL script for such task ? Any hints to write such script will be > appreciated! > > Thank you > Rotem > > > > > > > ---------------------------------------------------------- > Rotem Sertchook, Ph.D. > Bioinformatics Unit, Biological Services > Weizmann Institute of Science, > Rehovot 76100, Israel. > ---------------------------------------------------------- > > ------------------------------------------------------------------------------ > Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are > powering Web 2.0 with engaging, cross-platform capabilities. Quickly and > easily build your RIAs with Flex Builder, the Eclipse(TM)based development > software that enables intelligent coding and step-through debugging. > Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > |
From: Joel T. <joe...@ot...> - 2009-09-01 22:56:54
|
PS is it possible to run two versions at once on a PC (a quick test failed) _________________________________ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 |
From: Raluca M. A. <r.a...@sn...> - 2009-11-06 13:51:43
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It is with great sadness that myself and the Scientific Visualization Unit learned of the sudden death of Warren Delano. We have made great use and have profited heavily of the instruments and kind help offered by DeLano not just to us, but to the entire community. Our deepest condolences to the family and colleagues surrounding the generous soul of Warren, a person that we counted as a friend, even if we never met directly. Raluca and the SciVis group |
From: Christian De F. <cde...@gm...> - 2010-05-28 17:42:26
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Please stop sending me daily emails.... its very annoying, i would appreciate if you erase me from the list Thank you! |
From: Thomas J. <jue...@gm...> - 2010-05-28 17:49:27
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Hi Chris, the emails are only sent to you because you subscribed to the pymol-users list. If you don't want them anymore you need to unsubscribe. Click on "Show details" at the top of this email. Click then on: unsubscribe Unsubscribe from this mailing-list That will do the magic. On Fri, May 28, 2010 at 10:42, Christian De Ford <cde...@gm...> wrote: > Please stop sending me daily emails.... its very annoying, i would > appreciate if you erase me from the list > Thank you! > ------------------------------------------------------------------------------ > > > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
From: Nat E. <nat...@gm...> - 2010-05-28 17:53:25
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On Fri, May 28, 2010 at 10:49 AM, Thomas Juettemann <jue...@gm...>wrote: > Hi Chris, > > the emails are only sent to you because you subscribed to the pymol-users > list. > If you don't want them anymore you need to unsubscribe. > > Click on "Show details" at the top of this email. Click then on: > unsubscribe Unsubscribe from this mailing-list > > That will do the magic. Or click on the link at the bottom of *every email sent to the list*: > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: niloofar n. <nil...@ya...> - 2011-09-04 12:37:19
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Deal list, I would like to calculate partial charges of my pdb. Is it possible to do it by Pymol? If not, Is anyone know any server or software to do it? I have another question too, when aligning two structure in Pymol, there is a RMSD for the total structure, is there any command to calculate the RMSD for a specific region of the alignment. Any offer would be appreciated. kind regards. Niloofar |