Re: [PyMOL] Retention of ANISO Records was How to merge molecules in Pymol?
Thanks to all who replied, 'create' did the trick of combining multiple objects/molecules into one object quite painless. I was not thinking out of the box, been using create too long to slice and dice my molecules. But it turns out that I have TLS-ANISO records in my original file I'd like to retain, the save command does not carry them over into the combined file, neither are CRYST/SCALE records retained. Any flags I need to set? Cheers, Carsten -Original Message- From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com] Sent: Thursday, June 16, 2011 6:14 PM To: Schubert, Carsten [PRDUS] Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] How to merge molecules in Pymol? Hi Carsten, Is there an (un)documented way of merging multiple molecular objects in Pymol into one molecule, which then can be written in a nicely formatted PDB file? I cobbled something cludgy together with 'multisave' and a couple read-sort-save cycles, but this is ugly and probably quite fragile. An API function might be much more robust. Is there a provision like this in ChemPy? I've already taken care of adjusting each molecule to be unique with respect to chain IDs and IDs, so that would not be an issue. It's documented: * help create * http://www.pymolwiki.org/index.php/Create Create can be used to create a single single-state object or a single multi-state object. The former will just 'do what you say' but may create biologically unrealistic molecules (it just combines the objects). The latter is better as it saves to biologically realistic multi-state pdbs. Try these examples: # method 1 # create a single state (possibly biologically infeasible) molecule # from two objects frag ala frag cys save test.pdb, ala or cys Now load test.pdb. # method 2 # create a single multi-state object from two molecules frag ala frag cys create test, ala, 1, 1 create test, cys, 1, 2 save test.pdb, test, state=0 Cheers, -- Jason On Thu, Jun 16, 2011 at 3:58 PM, Schubert, Carsten [PRDUS] cschu...@its.jnj.com wrote: Hi, Is there an (un)documented way of merging multiple molecular objects in Pymol into one molecule, which then can be written in a nicely formatted PDB file? I cobbled something cludgy together with 'multisave' and a couple read-sort-save cycles, but this is ugly and probably quite fragile. An API function might be much more robust. Is there a provision like this in ChemPy? I've already taken care of adjusting each molecule to be unique with respect to chain IDs and IDs, so that would not be an issue. Any pointers would be appreciated. Cheers, Carsten - - EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol- us...@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Retention of ANISO Records was How to merge molecules in Pymol?
Hi Jason, Good to know. Could we then add this a feature request? I know Pymol is more a 'consumer' and not a 'producer' but in certain instances this would be a nice feature to have. Cheers, Carsten -Original Message- From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com] Sent: Friday, June 17, 2011 11:57 AM To: Schubert, Carsten [PRDUS] Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Retention of ANISO Records was How to merge molecules in Pymol? Hi Carsten, PyMOL doesn't write non-coordinate records to disk. You'll need to write a script to prepend those records. Cheers, -- Jason On Fri, Jun 17, 2011 at 8:15 AM, Schubert, Carsten [PRDUS] cschu...@its.jnj.com wrote: Thanks to all who replied, 'create' did the trick of combining multiple objects/molecules into one object quite painless. I was not thinking out of the box, been using create too long to slice and dice my molecules. But it turns out that I have TLS-ANISO records in my original file I'd like to retain, the save command does not carry them over into the combined file, neither are CRYST/SCALE records retained. Any flags I need to set? Cheers, Carsten -Original Message- From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com] Sent: Thursday, June 16, 2011 6:14 PM To: Schubert, Carsten [PRDUS] Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] How to merge molecules in Pymol? Hi Carsten, Is there an (un)documented way of merging multiple molecular objects in Pymol into one molecule, which then can be written in a nicely formatted PDB file? I cobbled something cludgy together with 'multisave' and a couple read-sort-save cycles, but this is ugly and probably quite fragile. An API function might be much more robust. Is there a provision like this in ChemPy? I've already taken care of adjusting each molecule to be unique with respect to chain IDs and IDs, so that would not be an issue. It's documented: * help create * http://www.pymolwiki.org/index.php/Create Create can be used to create a single single-state object or a single multi-state object. The former will just 'do what you say' but may create biologically unrealistic molecules (it just combines the objects). The latter is better as it saves to biologically realistic multi-state pdbs. Try these examples: # method 1 # create a single state (possibly biologically infeasible) molecule # from two objects frag ala frag cys save test.pdb, ala or cys Now load test.pdb. # method 2 # create a single multi-state object from two molecules frag ala frag cys create test, ala, 1, 1 create test, cys, 1, 2 save test.pdb, test, state=0 Cheers, -- Jason On Thu, Jun 16, 2011 at 3:58 PM, Schubert, Carsten [PRDUS] cschu...@its.jnj.com wrote: Hi, Is there an (un)documented way of merging multiple molecular objects in Pymol into one molecule, which then can be written in a nicely formatted PDB file? I cobbled something cludgy together with 'multisave' and a couple read-sort-save cycles, but this is ugly and probably quite fragile. An API function might be much more robust. Is there a provision like this in ChemPy? I've already taken care of adjusting each molecule to be unique with respect to chain IDs and IDs, so that would not be an issue. Any pointers would be appreciated. Cheers, Carsten -- --- - EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol- users Archives: http://www.mail-archive.com/pymol- us...@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users
[PyMOL] How to merge molecules in Pymol?
Hi, Is there an (un)documented way of merging multiple molecular objects in Pymol into one molecule, which then can be written in a nicely formatted PDB file? I cobbled something cludgy together with 'multisave' and a couple read-sort-save cycles, but this is ugly and probably quite fragile. An API function might be much more robust. Is there a provision like this in ChemPy? I've already taken care of adjusting each molecule to be unique with respect to chain IDs and IDs, so that would not be an issue. Any pointers would be appreciated. Cheers, Carsten -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] New 16 char length restriction of object names in menu?
Has the length of the object name entry in the right hand menu been restricted to 16 characters in v1.4.x? Prior to 1.4.x there seemed to have been no limit on the length of the entry. For instance cmd.load(reallylongmapnamehere, format=ccp4,object=reallylongmapnamehere) would truncate the display of the object to reallylongmapna. I suppose that would be fine for some applications, but in my case I am distributing sessions, which contain fairly long object names to be self-explanatory, so I am dependent on this feature to work. Could this be reverted back to unlimited or at least implement a setting controlling the length of the entry? Thanks Carsten -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New 16 char length restriction of object names in menu?
Hi Jason, thanks for the follow-up. Let us know when the issue is fixed. Cheers, Carsten -Original Message- From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com] Sent: Thursday, May 19, 2011 12:11 PM To: Schubert, Carsten [PRDUS] Cc: pymol-users@lists.sourceforge.net; h...@schrodinger.com Subject: Re: [PyMOL] New 16 char length restriction of object names in menu? Hi Carsten, I'd like to follow up on this. There is no character limit, but there is a bug. PyMOL is inappropriately clipping names in groups if the internal GUI cuts off the end of the name. The current workaround for your sessions is to expand the internal_gui to show the names, and then save your session. I'll look into fixing this ASAP. Cheers, -- Jason On Thu, May 19, 2011 at 11:33 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Carsten, Has the length of the object name entry in the right hand menu been restricted to 16 characters in v1.4.x? Prior to 1.4.x there seemed to have been no limit on the length of the entry. There is no such limit on the length of names. For instance cmd.load(reallylongmapnamehere, format=ccp4,object=reallylongmapnamehere) would truncate the display of the object to reallylongmapna. I suppose that would be fine for some applications, but in my case I am distributing sessions, which contain fairly long object names to be self-explanatory, so I am dependent on this feature to work. Could this be reverted back to unlimited or at least implement a setting controlling the length of the entry? You have a few options. If you want to hide the state-counter to get a few more characters on the line just set state_counter_mode, 0. Alternatively, you could just increase the internal_gui_width--eg set internal_gui_width, 300 Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Pymol 1.4.1 does not load PDBs from command line anymore -- fixed
Sorry Guys, my bad. I had a Homer Simpson moment while writing a wrapper to integrate 32bit and 64bit environments and forgot to pass along arguments to the actual pymol startup script. Apologies... Carsten -Original Message- From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com] Sent: Wednesday, May 11, 2011 6:37 PM To: Schubert, Carsten [PRDUS] Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Pymol 1.4.1 does not load PDBs from command line anymore Hi Carsten, That's pretty odd. Can you please show us exactly what you're typing? Also, please provide the PyMOL and OS versions. Cheers, -- Jason On Wed, May 11, 2011 at 1:33 PM, Schubert, Carsten [PRDUS] cschu...@its.jnj.com wrote: Hi, The latest PyMol (1.4.1, 32bit Linux version) does not load PDB files from the command line anymore. Does anybody have the same problem? What am I missing? Cheers, Carsten - - Achieve unprecedented app performance and reliability What every C/C++ and Fortran developer should know. Learn how Intel has extended the reach of its next-generation tools to help boost performance applications - inlcuding clusters. http://p.sf.net/sfu/intel-dev2devmay ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol- us...@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Achieve unprecedented app performance and reliability What every C/C++ and Fortran developer should know. Learn how Intel has extended the reach of its next-generation tools to help boost performance applications - inlcuding clusters. http://p.sf.net/sfu/intel-dev2devmay ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Pymol 1.4.1 does not load PDBs from command line anymore
Hi, The latest PyMol (1.4.1, 32bit Linux version) does not load PDB files from the command line anymore. Does anybody have the same problem? What am I missing? Cheers, Carsten -- Achieve unprecedented app performance and reliability What every C/C++ and Fortran developer should know. Learn how Intel has extended the reach of its next-generation tools to help boost performance applications - inlcuding clusters. http://p.sf.net/sfu/intel-dev2devmay___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Pymol 1.4.1 does not load PDBs from command line anymore
Hi Alvin, thanks for the reply. Sorry, but I was not clear in describing the problem. What I meant was that loading pdb files as arguments to pymol does not seem to work anymore, i.e. 'shell_prompt # pymol x.pdb y.pdb' does not load x.pdb and y.pdb on startup. At least in 1.3 that mechanism worked. Cheers, Carsten -Original Message- From: Alvin Oga [mailto:pymol.l...@mail.linux-1u.net] Sent: Wednesday, May 11, 2011 5:49 PM To: Schubert, Carsten [PRDUS] Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Pymol 1.4.1 does not load PDBs from command line anymore hi carsten on freebsd, command line works for me ( pymol load pept.pdb ), works as in the molecule changes to the new loaded one i downloaded pymol-1.4.1 from svn and compiled the sources on freebsd- 7.4, 8.2, 6.4 --- downloading/compiling pymol-1.4.1 on debian-sid has problems tho and it doesn't execute properly ( probably because i tend to change pesky/unreasonable system default files ) i can try to download/compile/test on other linux's .. i have centos-5.4, 5.5, 5.6, fedora-core14, opensuse-11.3, 11.4, slackware-12.3 ) centos/fedora supposed to be identical to redhat which linux versions do you have ?? have fun alvin http://Linux-1U.net/BioChem The latest PyMol (1.4.1, 32bit Linux version) does not load PDB files from the command line anymore. Does anybody have the same problem? What am I missing? -- Achieve unprecedented app performance and reliability What every C/C++ and Fortran developer should know. Learn how Intel has extended the reach of its next-generation tools to help boost performance applications - inlcuding clusters. http://p.sf.net/sfu/intel-dev2devmay ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] openGL/GLEW problems when embedding a PyMOL instance in aPyQt4 widget
Kasper, not sure if this will help you, but I think the GLEW stuff was
added recently in V1.4.x and it seems to be still somewhat experimental.
May be to get you started you could switch to v1.3r1 from the repository
and try to embedd that version. V1.3.x should not contain the new GL
stuff.
Good luck
Carsten
From: Kasper Thofte [mailto:kasper.tho...@gmail.com]
Sent: Tuesday, April 26, 2011 10:34 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] openGL/GLEW problems when embedding a PyMOL instance in
aPyQt4 widget
Dear pymol user and developer community
I am trying to embed a pymol2.PyMOL instance in a PyQt4 widget.
I am using the latest beta v1.4.1 (although it still says v1.4.0 in
layer0/Version.h, I assume you just forgot to update?). I use ubuntu on
a macbook.
I got it to display a black window inside a PyQt4 app, and I was even
able to produce som ugly little white square H atoms one time, plus som
menus only half visible. Yes, kind of strange.
The problem is openGL related. When typing pymol -v at the command line,
it tells me that my openGL version is pre 2.0, which is not true.
(Well, actually I wasn't entirely sure what precisely to look for in the
synaptic package manager, but libqt4-opengl is v4:4.7.0, python-opengl
is v3.0.1, python-qt4-gl is v4.7.4, freeglut3-dev is v2.6.0,
libglew1.5-dev is, well v1.5.2 glutg3-dev is 3.7-25)
Anyway, when I runt the following code (which may also contain the
source of the problem, I don't know):
class PymolQWidget(QGLWidget):
def __init__(self, parent=None):
QGLWidget.__init__(self, parent=parent)
self.pymolInstance = pymol2.PyMOL()
self.pymolInstance.start()
self.pymolInstance.cmd.load('home-directory/GUI/H2.pdb')'
self.pymolInstance.cmd.draw()
self.pymolInstance.cmd.show_as(sticks)
app = QtGui.QApplication(sys.argv)
pymolWidget = PymolQWidget()
pymolWidget.show()
sys.exit(app.exec_())
I get the following error message:
ShaderMgrInit-Error: Could not initialize GLEW:Missing GL version
which means that GLEW_OK!=err at line 145 in layer0/ShaderMgr.c, which
means the glew hasn't been initialized, which is as far as I was able to
get.
Needless to say, help would be greatly appreaciated.
Best,
Kasper Thofte
University of Copenhagent
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Re: [PyMOL] Pymol 1.4 OpenGL issue with openSuSE 11.3 / 11.4
Joachim, I'm running into the same issue on a SuSe SLED10 box. The 32bit binary (on the 64bit OS) displays the same behavior, i.e. only the MESA libs were used. The 64bit version actually core dumps during startup. I opened up a bug report with Schrodinger and they were already working on it (I suppose the crash), but wouldn't hurt to reinforce the fact that the 32bit version only uses the MESA libs (under SuSe?). Good that your tried the more recent drivers, I was planning to do that but haven't got around to do this yet. Cheers, Carsten -Original Message- From: greipel.joac...@mh-hannover.de [mailto:Greipel.Joachim@mh- hannover.de] Sent: Tuesday, March 29, 2011 7:16 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Pymol 1.4 OpenGL issue with openSuSE 11.3 / 11.4 Dear pymol users, pymol 1.4 on openSuSE with NVIDIA Quadro FX 3700/3800 and new NVIDIA drivers (260.xxx and 270.xxx) does not recognize the OpenGL Version correctly. As a result there is a kind of software OpenGL used. The NVIDIA drivers provide OpenGL 3.3.0 but pymol 1.4 complains: Detected OpenGL version prior to 2.0. Shaders unavailable. OpenGL graphics engine: GL_VENDOR: Brian Paul GL_RENDERER: Mesa X11 GL_VERSION: 1.5 Mesa 6.4.2 This leads to a malfunctioning hardware stereo and renders pymol 1.4 unusable for us. Earlier pymol versions do not show that strange behavior. Other programs use the NVIDIA drivers perfectly well and allow displaying structures in hardware stereo. I tried this thing on several machines with the same result. Does anyone have a hint? Regards, -- Dr. rer. nat. Joachim Greipel Med. Hochschule Hannover Biophys. Chem. OE 4350 Carl-Neuberg-Str. 1 30625 Hannover Germany Fon: +49-511-532-3718 Fax: +49-511-532-8924 -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] slab mode fine-tuning
Nadine, Probably the command line is your best friend here. Look into the 'clip near,x' and 'clip far,x' command, which allows to move the front and back clipping planes in x increments. Positive values move towards you, negative values of x away from you. If that does not provide enough fine grained control you may want to think about making a composite picture to 'fake' clipping planes per object. Cheers, Carsten -Original Message- From: Nadine Utz [mailto:nad...@mmb.pcb.ub.es] Sent: Tuesday, March 29, 2011 6:12 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] slab mode fine-tuning Dear pymol users, I am looking for a way to zoom in a molecule, like the slab mode when you are rolling the scroll wheel. The reason why rolling the scroll wheel does not work in my case is that the resulting change is too coarse grained, i.e. either I cannot see all the atoms I want to or there are some atoms in front of the part I am interested in. I tried as well clip slab, x, but then not just atoms in front of the interesting part are not shown but as well behind it. So, what I need is a cross-sectional view of my system, in which only everything in front of the cut is not shown (but everything behind). Thank's a lot for any help, Nadine Dr. Nadine Utz MMB - IRB Barcelona --- --- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] write a script from pse file
Maia, as far as I know a .pse is just a dump of the internal data structure of Pymol. You can save the molecules contained in the session, but the graphical representation and any modifications would need to be recreated. Hopefully Jason proves me wrong ... Cheers, Carsten -Original Message- From: Maia Cherney [mailto:ch...@ualberta.ca] Sent: Sunday, March 13, 2011 7:07 AM To: Jason Vertrees Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] write a script from pse file Hello, I have an old saved session as a pse file. How can I save a script that produced that pse file. It may be easier just to get information about each object in that pse file. Maia --- --- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Different color on each side of strand
Not sure if this is possible but it would be a nice feature to have. Since it mimics the way helices are drawn, when cartoon_highlight_color is set. Cheers, Carsten -Original Message- From: Keitaro Yamashita [mailto:yamash...@castor.sci.hokudai.ac.jp] Sent: Sunday, March 06, 2011 7:32 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Different color on each side of strand Dear all, Sorry for my unclear explanation. I made a picture explaining what I'd like to do. I want to color the front and back of sheets separately. Jason said it should be possible, could anyone tell me how to do it? Cheers, Keitaro 2011/3/7 Jason Vertrees jason.vertr...@schrodinger.com: Hi Keitaro, Use the cartoon_highlight_color setting. For example: set cartoon_highlight_color, red Cheers, -- Jason On Sun, Mar 6, 2011 at 10:01 AM, Keitaro Yamashita yamash...@castor.sci.hokudai.ac.jp wrote: Dear all, Can PyMOL set different colors on each side of cartoon strand? I tried cartoon_discrete_colors but it was not for this purpose. (I mean the sides from which sidechains are protruded.) Thanks in advance, Keitaro - - What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] labeling by a pseudoatom
Roberto,
partial answer to point 3. Adding a _ before an object name hides it
from the panel.
For points 1 or 2. Could you please expand on your question? Is this for
interactive
or scripted mode?
For scripted mode you could modify the coordinates of the pseudoatom to
be closer to the target atom or not? Otherwise look up the commands in
Edit mode. BTW in Edit mode you can actually mode regular labels with
the mouse as well (Edit Mode: CTRL Middle click)
Hope it helps somewhat
Carsten
-Original Message-
From: rv...@libero.it [mailto:rv...@libero.it]
Sent: Friday, February 25, 2011 5:00 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] labeling by a pseudoatom
Hello everyone,
trying to use a pseudoatom as label I met several problems:
1) How to move the label (pseudoatom) to a target residue?
Is there a simple command to do?
2) How to change the label without messaging the user?
The 'label' command appears not have a 'quiet' option.
3) (less important) How to hide the pseudoatom?
I wish not have the pseudoatom listed among models in the GUI
panel.
4) (less important) I need to execute all these operations by script
(mdo
commands during a movie)
To simplify the movie I wish use only one mdo command
def doAll()
.. all my script here ..
extending the cmd just before the movie start
cmd.extend('doAll', doAll)
and clearing the cmd just at the end of the movie but I don't
know
how.
Is there a way to clear a command?
Thanks,
Roberto
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Re: [PyMOL] Color scale changed in APBS?
Hi Wataru, in addition to what Jason mentioned: Have you tried to look at the potential mapped on the solvent accessible surface and display the molecular surface? If you display the potential like this the colors will be much more muted, on the other hand this is the setting you will find most often displayed in the literature. Another option is to have a look at the charge distribution of your molecule in the actual PQR file. The potential distribution is dependent on the charging algorithm used. I would recommend using/looking into PDQ2PQR, which is available from the APBS website and compare this to the homegrown charging algorithm from PyMol or GRASP for that matter. Hope I did not muddle the water too much Carsten -Original Message- From: Wataru Kagawa [mailto:wkag...@aoni.waseda.jp] Sent: Monday, February 21, 2011 10:04 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Color scale changed in APBS? Dear PyMOL users: I recently used the APBS plugin (v1.3) to display the surface potential of a protein. I noticed that the charged surfaces were much more lightly colored, compared with the surface colors I have calculated in the past (maybe a year ago?) on the same protein, using the same softwares. The default settings and the same range (-10 kT to 10 kT) were used in both cases. Has anyone experienced this? I would appreciate any help. Wataru --- --- Index, Search Analyze Logs and other IT data in Real-Time with Splunk Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. Free Software Download: http://p.sf.net/sfu/splunk-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Index, Search Analyze Logs and other IT data in Real-Time with Splunk Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. Free Software Download: http://p.sf.net/sfu/splunk-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] pymol movie scripting for beginners questions
Aiko, I can't directly comment on your problem, but I had good experience with the eMovie plugin. May be give that a try. http://www.weizmann.ac.il/ISPC/eMovie.html HTH Carsten -Original Message- From: Aiko Matsumoto [mailto:aikomatsumoto1...@googlemail.com] Sent: Friday, February 11, 2011 5:52 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] pymol movie scripting for beginners questions Dear Mailing list! I have just started using pymol to make a molecular movie of a protein ligand system. What I came up with is: ### reinitialize set matrix_mode, 1 set movie_panel, 1 set scene_buttons, 1 set cache_frames, 1 set static_singletons, off set movie_auto_interpolate, off set movie_loop, off config_mouse three_button_motions, 1 set movie_fps, 30 bg_color white load 2fpt-complex-aligned.pdb hide everything, all create ligand, resn ILB and resi 405 create cofactor, resn FMN and resi 398 create substrate, resn ORO and resi 399 create site2, (cofactor substrate) create Nterm, (not resn HOH and resi 30-77) create Cterm, (not resn HOH and resi 78-396) create water1, byres resn HOH within 8 of ligand create water2, byres resn HOH within 8 of site2 create pocket1, byres all within 7 of ligand and not resn HOH create pocket2, byres all within 7 of site2 and not resn HOH create TOP, Cterm site2 create BOTTOM, Nterm create BOTH, TOP BOTTOM show cartoon, TOP BOTTOM show sticks, ligand show sticks, (TOP and (resn FMN or resn ORO)) #show nb_spheres, water1 #show nb_spheres, water2 color meitnerium, ss h color titanium, ss l color thorium, ss s util.cbay ligand util.cbay (TOP and (resn FMN or resn ORO)) #spectrum b, blue_white_red, water1 #spectrum b, blue_white_red, water2 set_view (\ 0.296377361,0.815219104,0.497568905,\ -0.806614339, -0.065306552,0.587461531,\ 0.511405945, -0.575454950,0.638211489,\ 0.0,0.0, -235.838287354,\ 48.424118042, 41.582153320, 30.356651306,\ 185.936691284, 285.739868164, -20.0 ) mset 1 x433 frame 1 mview store, object=TOP mview store, object=BOTTOM mview store frame 180 translate [0,10,0], object=TOP translate [0,-10,0], object=BOTTOM mview store, object=TOP mview store, object=BOTTOM mview store mview interpolate, object=TOP mview interpolate, object=BOTTOM frame 282 util.mroll(180,282,360) mview store, object=TOP mview store, object=BOTTOM mview store frame 382 translate [0,-10,0], object=TOP translate [0,10,0], object=BOTTOM util.mroll(282,382,360) mview store, object=TOP mview store, object=BOTTOM mview store mview interpolate, object=TOP mview interpolate, object=BOTTOM frame 432 set_view (\ 0.264227241,0.815219104,0.515365601,\ -0.842250228, -0.065306552,0.535127521,\ 0.469904959, -0.575454950,0.669362724,\ 0.0,0.0, -152.198883057,\ 47.851242065, 41.281734467, 31.806066513,\ 112.558006287, 191.839767456, -20.0 ) mview store, object=TOP mview store, object=BOTTOM mview store mview interpolate, object=TOP mview interpolate, object=BOTTOM frame 433 mplay ### ### I am just beginning to gain familiarity with this but probably someone can point me into the right direction? My problem is that if I use the script in exactly the way I posted above then I don't get the change view (frame 382 to 432). At the end the 'set view' just shows up without any interpolation. However, when I use a mview reinterpolate statement at the end of the script, then frame 382 to 432 essentially zoom into the binding pocket, which is what I want BUT suddenly all attempts to rotate the system (frames 180 to 280 and 280 to 380) have somehow been disabled, apart from 2 little rocking motions at exactly 2 frames, though I do get the translation right. After day one in using pymol I might not be the expert but even following several examples online (pymol-wiki and such) don't really give me any indication as to what is going on as there doesn't seem to be a really complex movie that allows the study on frames/states plus scenes plus proper complex use of mdo in one and the same example movie. Please please help, I am getting desperate here! Thanks Aiko PhD student Uni Bristol --- --- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb
Re: [PyMOL] Independent Zooming in Grid Mode
Sean,
Just a thought, but the translate command looks like as if it should be
possible to selectively modify the viewmatrix on a per object basis:
translate translates the atomic coordinates of atoms in a
selection. Alternatively, is modifies the matrix associated with
a particular object or object-state.
May be if you create two objects of interest, split states by object and then
play around with the translate command you could achieve that effect.
-Original Message-
From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com]
Sent: Thursday, January 27, 2011 11:03 PM
To: Sean Law
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Independent Zooming in Grid Mode
Hi Sean,
PyMOL is currently not capable of providing and inset-like image or
grid-mode with independent motions. Programming this at the Python
level wouldn't be very easy.
Cheers,
-- Jason
On Wed, Jan 26, 2011 at 9:39 AM, Sean Law magic...@hotmail.com wrote:
Hi PyMOLers,
I was wondering if anybody had a solution for independent when using
grid_mode=on. I want to be able to show, side-by-side, the same
structure
where one structure is zoomed in on a specific part on the
biomolecule and
the other object is zoomed out (viewing the entire molecule). And
as I
turn one of the two structures, the other one turns accordingly. I
think
this would be useful when trying to keep track of the orientation of
the
biomolecule or for docking.
Any suggestions would be greatly appreciated.
Sean
From: pymol-users-requ...@lists.sourceforge.net
Subject: PyMOL-users Digest, Vol 56, Issue 9
To: pymol-users@lists.sourceforge.net
Date: Mon, 24 Jan 2011 22:11:17 +
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Today's Topics:
1. Re: Faster way to find polymer chains? (Tsjerk Wassenaar)
2. Re: Faster way to find polymer chains? (Thomas Holder)
3. unable to open the file (wang_qi)
4. Re: unable to open the file (Christoph Gohlke)
5. Re: Faster way to find polymer chains? (Seth Harris)
6. dialogs in pyMOL (rv...@libero.it)
--
Message: 1
Date: Sun, 23 Jan 2011 10:48:20 +0100
From: Tsjerk Wassenaar tsje...@gmail.com
Subject: Re: [PyMOL] Faster way to find polymer chains?
To: Seth Harris set...@gmail.com
Cc: pymol-users@lists.sourceforge.net
Message-ID:
AANLkTi=jdcwaci5n2jav_vqjybffatyb8cw5q0egq...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1
Oops... That should've been:
polychains = set([i.chain for i in cmd.get_model('polymer').atom])
Sorry for that. :p
Tsjerk
On Sun, Jan 23, 2011 at 10:32 AM, Tsjerk Wassenaar
tsje...@gmail.com
wrote:
Hi Seth,
So you just want to have all unique chain identifiers for the
'polymer' selection? Does the following give what you want?:
polychains = set([i.chain for i in cmd.get_model('polymer')])
Hope it helps,
Tsjerk
On Sun, Jan 23, 2011 at 10:04 AM, Seth Harris set...@gmail.com
wrote:
Hi All,
I am script-plowing through PDB files and extracting unique chain
identifiers only for polymers using PyMOL's polymer selection.
Right
now
my code is a kind of brute force thing like this:
code
??cmd.create (justpolys,polymer)
??polymer_chains=[]
??for a in cmd.index(justpolys):
?? ?q_sel = %s`%d%a
?? ?#print q_sel+:,
?? ?cmd.iterate(q_sel, stored.qry_info =
(chain,resn,resi,name))
?? ?#cmd.iterate_state(1,q_sel, stored.qry_xyz = (x,y,z))
?? ?#print
stored.qry_info[0],stored.qry_info[1],stored.qry_info[2],stored.qry_inf
o[3]
?? ?# Track any unique chains by adding to polymer_chains list if
not
already there
?? ?# first reformat to get rid of flanking ' marks
?? ?thischain=`stored.qry_info[0]`
?? ?thischain=thischain.replace(',)
?? ?if thischain not in polymer_chains:
?? ? ?polymer_chains.append(thischain)
/code
This works, but is quite slow as it iterates over every atom in
every
pdb
just to get out the chain so it is quite redundant.
Is there any way to iterate in a 'chain by chain' fashion? This
q_sel
stuff
is recycled from something Warren suggested for a different
purpose
years
ago, and I only have a loose idea of how that is interacting with
the
cmd.index part. Maybe there's a way to get just the chain from
the
get-go
instead of all the individual atoms? Any reminders on that one or
[PyMOL] Wiki down?
I am just getting a blank page when I try to access the Pymol Wiki. Do other people see the same problem? Carsten -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Wiki down?
OK, works here again as well. Main Page was somehow screwy or I had a dirty cache in my browser From: Nat Echols [mailto:nathaniel.ech...@gmail.com] Sent: Thursday, January 27, 2011 1:09 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Wiki down? On Thu, Jan 27, 2011 at 9:54 AM, Schubert, Carsten [PRDUS] cschu...@its.jnj.com wrote: I am just getting a blank page when I try to access the Pymol Wiki. Do other people see the same problem? Working fine for me (using Safari on a Mac). -Nat -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] colors and font size while ray tracing
Hi Madhavi, with regards to your first question: I usually add text after rendering the stereo figures. That gives much better control and has the advantage that label come out cleaner. Look into Canvas, Photoshop or GIMP to do this. As an additional tip you can control the depth of the labels this way as well. Lets say you want to label Leu76 in the back of the figure, create one label, copy it to the other panel and place the same part of the text on the same atom or point of the residue you want to label. Group the labels and move them to an unobstructive position. Repeat for the other labels. Spheres: Tough to tell, may be you inadvertently changed the depth queue settings and the spheres got lighter. Did the the rest of the figure change as well? HTH Carsten -Original Message- From: Nalam, Madhavi [mailto:madhavi.na...@umassmed.edu] Sent: Thursday, January 20, 2011 2:36 PM To: 'pymol-users@lists.sourceforge.net' Subject: [PyMOL] colors and font size while ray tracing Hello: I am trying to generate stereo figures for my manuscript. When I try to ray trace at higher resolution, the font size (I use label_font_id=4) is becoming very small. If I use any fonts from the settings tab, the font size doesn't change with ray tracing. If I am correct, many journals prefer Helvitica/Arial fonts for the publication quality figures. So my question is are the fonts found in the settings preferred by the journals? If not, can anyone please tell me what can be done to keep the font size from decreasing during ray tracing? Also, I have vdW spheres shown as dots in the figure. The color of the dots for the vdW spheres is very light after I ray trace the figure. Last week when I ray traced the figure from the same PyMOL session, the colors are much darker!! As far as I know, I haven't changed anything in the session file. So can anyone please tell me how to increase the darkness of the vdW spheres? I use PyMOL version 1.3.x on Windows. Thanks in advance, Madhavi --- --- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price- free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] 3D TVs experience with PyMOL?
Hello List: Has anyone been able to put together a workable system where they can run PyMOL from a 3D HDTV using a regular workstation (Linux or Windoze) and the NVIDIA 3D Kit for presentation purposes? I did some preliminary research and while there is a wide range of 3D TVs out there I am not sure about compatibility. For instance a quick look at the Samsung 3D LCD TVs revealed that they don't even have a dual DVI interface, only 15 pin analog, doesn't look as if that is going to work... I'll keep looking, but if anyone is willing to share their experience it would be greatly appreciated. Thanks Carsten -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Force of pure white background when ray tracing with fog
Hi Jason, sorry but it looks as if I've sent you on a wild goose chase. I did some more research and recreated the actual images using some of the original scripts and they look fine. Turns out that the culprit is the RGB to CMYK conversion in Canvas, which I am using to make the panels for publication. Unfortunately the publisher only accepts CMYK figures, so it looks as if I need to tackle this from another angle. Thanks for your help, glad Pymol is not at fault... (-: Cheers, Carsten -Original Message- From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com] Sent: Tuesday, January 04, 2011 4:31 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Force of pure white background when ray tracing with fog Hi Carsten, What version of PyMOL are you using? ray_trace_mode, 3 used to burn the background but doesn't any longer. I just set my background to white and tested all ray_trace_mode settings (with fog on) and the background is pure white. Can you please provide a snippet of code that produces the effect? Cheers, -- Jason On Tue, Jan 4, 2011 at 8:22 AM, Schubert, Carsten [PRDUS] cschu...@its.jnj.com wrote: Hi Pymolers, I just noticed that Pymol produces an off-whitish background when ray tracing a figure with fog enabled. The RGB values are (252,253,254) with my standard settings and are devilishly hard to spot on a monitor, but show up on some printers as a grayish background. Is there a setting or a trick to get rid of this effect and force a pure white background during rendering? I suppose rending with transparent background and pasting in pure white box should do as a post-production workaround, but that is not very convenient especially if the figures are already all made. Cheers, Carsten - - Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol- us...@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 --- --- Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Force of pure white background when ray tracing with fog
Hi Pymolers, I just noticed that Pymol produces an off-whitish background when ray tracing a figure with fog enabled. The RGB values are (252,253,254) with my standard settings and are devilishly hard to spot on a monitor, but show up on some printers as a grayish background. Is there a setting or a trick to get rid of this effect and force a pure white background during rendering? I suppose rending with transparent background and pasting in pure white box should do as a post-production workaround, but that is not very convenient especially if the figures are already all made. Cheers, Carsten -- Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Start PyMOL session in web browser
Hi Martin, not directly applicable to your question, but may be it directs your thinking into a different direction. If I remember correctly Warren pointed out a couple of year ago the p1m file format was supposed to support downloading of structural information from the web with some limited scripting options. Hope this helps. Cheers, Carsten -Original Message- From: Martin Hediger [mailto:ma@bluewin.ch] Sent: Sunday, December 19, 2010 7:38 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Start PyMOL session in web browser Dear all Is it possible to start a PyMOL viewer through a web browser? What I mean by this is, is it possible to view a protein over the internet where the viewing features are provided by some limited PyMOL server? The only thing able to do that right now is Jmol, but i think its very inconvenient to use when viewing large structures such as proteins. Thanks for your answers Martin --- --- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net B_spectrum.p1m Description: B_spectrum.p1m -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Charged Surface Calculation at different pHs?
Steve, you need to use PDB2PQR to generate your pqr file, with choice of pH and then run APBS on that file. I pulled reasonable defaults for APBS from the APBS plugin tool. PDB2PQR is accessible through the APBS website. HTH Carsten From: Soisson, Stephen M [mailto:stephen_sois...@merck.com] Sent: Wednesday, April 07, 2010 12:49 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Charged Surface Calculation at different pHs? Hi- Does anyone know if it is possible to calculate the charged surface using apbs at different pHs? I am assuming the default pH is 7. Thanks in advance- Steve 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. -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] stereo rotation lost with draw command
Norbert, Try something like this for a side-by-side stereo image: turn y,3 draw png left_image.png turn y, -6 draw png right_image.png turn y,3 Caveat is that potential shadows may not be rendered correctly in stereo. That's why the angle option was implemented in ray. HTH Carsten -Original Message- From: Norbert Straeter [mailto:stra...@bbz.uni-leipzig.de] Sent: Fri 2/5/2010 4:42 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] stereo rotation lost with draw command I want to render a stereo image using the draw command instead of ray tracing. Unfortunately, the stereo rotation is lost with the command and the image is flat. If this is not a bug, is there a way to change this behaviour? Norbert Straeter -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Whitespacing?
Not much of a help, but WingIDE Professional Edition has a very good indentation manager, which takes care of the mixed/space tab issues. If you are working in python frequently it is a worthwhile investment. Cheers, Carsten -Original Message- From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com] Sent: Tuesday, January 26, 2010 10:10 AM To: David Hall Cc: pymol-users Subject: Re: [PyMOL] Whitespacing? David, Oh, the joys of open-source. Here's my solution for you: (1) load your file in your favorite editor (2) determine user-desired tab stop setting (3) convert all tabs to spaces in your editor (or search replace tabs with X-spaces) (4) save your file One warning though, I have seen some interpreters crash when they encounter spaces over tabs. -- Jason On Tue, Jan 26, 2010 at 9:12 AM, David Hall li...@cowsandmilk.net wrote: During my editing of dynoplot.py, I noticed that there were some whitespace issues. Normally I consider whitespace a bikeshedding topic, but in python, it is significant, so it matters. When tabs and spaces are mixed, our own personal settings for how tabs are displayed in an editor makes a huge difference in whether the script is understandable. I checked out the git repo of pymol scripts ( http://github.com/jlec/Pymol-script-repo/ ) and did some analysis First, these files switch between some lines where all indenting is tabs to lines where all indenting is spaces: Objects_and_Selections/color_objects.py has 8 tab lines and 34 space lines ThirdParty_Scripts/WFMesh.py has 52 tab lines and 21 space lines biochemical_scripts/pucker.py has 167 tab lines and 5 space lines math_geo_cgo/modevectors.py has 160 tab lines and 2 space lines structural_biology_scripts/DynoPlot.py has 82 tab lines and 27 space lines structural_biology_scripts/Rotamers.py has 86 tab lines and 22 space lines structural_biology_scripts/kabsch.py has 51 tab lines and 4 space lines Second, there are files where the indenting inside a line switches back and forth (numbers are the counts of lines that have both tabs and spaces in indenting): Objects_and_Selections/color_objects.py: 19 ThirdParty_Scripts/WFMesh.py: 29 ThirdParty_Scripts/transform_odb.py: 6 math_geo_cgo/modevectors.py: 12 structural_biology_scripts/DynoPlot.py: 83 structural_biology_scripts/Rotamers.py: 86 structural_biology_scripts/kabsch.py: 1 I've tried using pindent.py ( http://svn.python.org/projects/python/trunk/Tools/scripts/pindent.py ) and PythonTidy ( http://pypi.python.org/pypi/PythonTidy/ ) to generally fix these, but they both run into problems. Is there a general solution out in the python world to automatically fix this? I don't care whether it produces tabs or spaces. I just want one or the other. If someone points me to something, I'm more than willing to run it on these scripts, push them back to github and copy them back onto the wiki. -David - - The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol- us...@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 --- --- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com ___ PyMOL-users
[PyMOL] New Feature Ideas
Jason, here are my feature requests, only slightly biased by the fact that some of them would be useful for my paper now (-: 1) arbitrary clipping planes bound to an object with an intelligent gui to place them. Something akin to be found in Maestro or semi-transparent CGO objects which can be manipulated freely in space and then used to define clipping planes 2) Implementation of bounding planes in raytracing to avoid showing the inside of clipped surfaces, raster3D has this option. I know one can fumble around in Povray to get the same effect, but I'd rather spend my time on something more productive. 3) If 2) is not an easy option, how about raster3D output in addition to povray? Pymol can read raster3d, why not have the output as well. 4) A better density wizard, let's just copy coot and be done with it. Ability to dynamically bind density levels or some other properties to the scroll-wheel for that matter. 5) Updated documentation. One thing that always irritated me as a paying subscriber was the fact that the documentation never kept up with development and the search capabilities were not that great. Don't get me wrong the Wiki and BB are great resources, but I'd expect a bit more of the docs. Also having the internal help functionality for functions and the API up to date would be great. Some functions don't seem to have a doc-string. 6) Integration/bundling of wxPython as an alternative to TCL/Tk?? 7) Internal FFT routines to be able to read map-coefficients 8) A CGO library for commonly used objects like arrows and such Cheers, Carsten -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Preserving sec. structure in states for animation
Hi, I am trying to make a movie form a set of morphed pdb files. Currently the individual files are loaded into the same object with increasing states, all pdb files contain the SHEET and HELIX record created by dssp. The object is then displayed as a cartoon. When I loop over the states I noticed that Pymol only seems to take secondary structure information from the first pdb file into account. For instance I have a helix which is split into 2 during the morph, but only displayed as one helix during the animation, albeit a bit stretched. Loading the individual files produces the right sec. structure. Any idea how I can convince Pymol to update the cartoon representation with each frame? Cheers, Carsten -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Viewport dimensions query
Hi, Does anyone know how to get a hold of the viewport dimensions from within a script? I vaguely remember some posts about this subject, but could not find anything in my archive. Thanks Carsten -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Viewport dimensions query
Yep, thanks Folmer -Original Message- From: Folmer Fredslund [mailto:folm...@gmail.com] Sent: Thursday, September 24, 2009 9:33 AM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Viewport dimensions query Hi Carsten, Is this what you are looking for? http://www.mail-archive.com/pymol- us...@lists.sourceforge.net/msg05888.html Best regards, Folmer Fredslund 2009/9/24 Schubert, Carsten [PRDUS] cschu...@its.jnj.com: Hi, Does anyone know how to get a hold of the viewport dimensions from within a script? I vaguely remember some posts about this subject, but could not find anything in my archive. Thanks Carsten - - Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol- us...@lists.sourceforge.net --- --- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] label a stereo .png image in pymol
Peter, here are some general considerations for stereo images A. The images should be ~63mm apart with respect to a point which you consider to be neutral, i.e. neither lies in front or in the back of the zero-plane B. The distance of the images also put restrictions on their size, which is something you need to consider. Usually it is 1 ½ columns in a journal, if I am not mistaken. C. For labels I use a program like photoshop or canvas, just because one has a wider selection of fonts and they produce antialiased renderings. I usually attach labels to landmarks, with which they share the same depth. For example if you want to label residue 234 and have the residue drawn in stick, you could place both upper left corners of the labels on the CA position, group them and move them out of the way so as they do not interfere with the rest of the graphic. Using this trick ensures that the labels appear in the correct depth. HTH Carsten From: peter hudson [mailto:peter.hudson.pe...@gmail.com] Sent: Monday, September 07, 2009 12:30 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] label a stereo .png image in pymol Hello all I have made a stereo image in pymol and photoadobeshop. But, i would like to label the image file which should like a stereo image label. how that can be done in the pymol. I can do it in photoadobeshop .problem lies her that i am not sure is the labels are really stereo or not? can anyone suggest solutions. I would appreciate that. Thanks in advance peter -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Smooth fading of surface in movie?
Dirk, you could try playing around with different transparency settings in subsequent scenes to emulate the effect. HTH Carsten From: Dirk Kostrewa [mailto:kostr...@genzentrum.lmu.de] Sent: Tuesday, September 01, 2009 8:57 AM To: PyMOLBB Subject: [PyMOL] Smooth fading of surface in movie? Dear Warren, using PyMOL without any additional plug-ins, like slerpy or eMovie, is it possible to fade in or out a surface of, say, a ligand, between scenes? Best regards, Dirk. *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail:kostr...@genzentrum.lmu.de mailto:kostr...@lmb.uni-muenchen.de WWW:www.genzentrum.lmu.de mailto:kostr...@lmb.uni-muenchen.de *** -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] object-specific Z-clipping
Warren, Can PyMol actually write raster3D objects? That's news to me. I did a couple of the clipped, bounded surfaces in raster3d since it supports it supports the option and was easier to implement than in PovRay. Again the biggest drag is always to find the right orientation of the clipping planes. If we can achieve this in PyMol then the rest is fairly easy. Cheers, Carsten -Original Message- From: Warren DeLano [mailto:war...@delsci.com] Sent: Friday, May 01, 2009 8:53 PM To: Schubert, Carsten [PRDUS]; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] object-specific Z-clipping Carsten, I think you're on to something. So long as this rendering problem remains too hard for us to solve with PyMOL alone, probably the next best thing would be for us to figure out at least an interim PovRay or Raster3D-based process for creating such figures. Having an object-selective but non-renderable OpenGL-based clipping plane available could certainly help with that! Cheers, Warren -Original Message- From: Schubert, Carsten [PRDUS] [mailto:cschu...@its.jnj.com] Sent: Thursday, April 30, 2009 1:40 PM To: Warren DeLano; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] object-specific Z-clipping Hi Warren, I would be interested to see the OpenGL version implemented, despite the lack of raytracing support. In a pinch the draw command could just be sufficient to produce a good picture. As for the implementation in a raytracer context I second Tsjerk's and Harry's thoughts on the subject. Probably some sort of PovRay based implementation would help in the interim. What I find most challenging with that approach is the fact that the placement of the clipping objects is difficult to achieve in PovRay since it lacks the interactivity of a graphics program. I.e. finding the right cut through a protein surface when depicting a ligand in a cut-away surface is tough. Although there are other ways to achieve this they require some cheating or creative use of Photoshop/PowerPoint to phrase it differently. I am thinking that if it would be possible to write out the orientation of the clipping planes/slabs as PovRay objects, they could be used as bounding objects in PovRay. Since the placement of the clipping planes is easily achieved in Pymol this could be done interactively. All the user has to do is to associate clipping plane(s) with a graphics object, place the planes and write out the corresponding PovRay code of the object and the planes. Of course the code of the clipping objects needs to be separate from the other stuff, so expanding the PovRay tuple into (matrix,clipping,data) parts would help. Getting it all together requires some knowledge of PovRay but examples in the Wiki should help to get over the initial pain. Any thoughts on this approach? Carsten -Original Message- From: Warren DeLano [mailto:war...@delsci.com] Sent: Wednesday, April 29, 2009 10:36 PM To: Mankin Alexander; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] object-specific Z-clipping Sorry, still not done (I have made two attempts, but both failed). While OpenGL supports arbitrary clipping planes, accomplishing this correctly in the ray tracer is a much harder problem that one might think... Cheers, Warren -Original Message- From: Mankin Alexander [mailto:sh...@uic.edu] Sent: Wednesday, April 29, 2009 6:18 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] object-specific Z-clipping Dear all, Does anyone know whether object-selective z-clipping has been implemented in the newer Pymol version(s)? If not, has anyone found any solution around (since 2002 no new threads on the matter)? Thanks, Shura Mankin -- - --- Register Now Save for Velocity, the Web Performance Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Register Now Save for Velocity, the Web Performance Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf
Re: [PyMOL] object-specific Z-clipping
Hi Warren, I would be interested to see the OpenGL version implemented, despite the lack of raytracing support. In a pinch the draw command could just be sufficient to produce a good picture. As for the implementation in a raytracer context I second Tsjerk's and Harry's thoughts on the subject. Probably some sort of PovRay based implementation would help in the interim. What I find most challenging with that approach is the fact that the placement of the clipping objects is difficult to achieve in PovRay since it lacks the interactivity of a graphics program. I.e. finding the right cut through a protein surface when depicting a ligand in a cut-away surface is tough. Although there are other ways to achieve this they require some cheating or creative use of Photoshop/PowerPoint to phrase it differently. I am thinking that if it would be possible to write out the orientation of the clipping planes/slabs as PovRay objects, they could be used as bounding objects in PovRay. Since the placement of the clipping planes is easily achieved in Pymol this could be done interactively. All the user has to do is to associate clipping plane(s) with a graphics object, place the planes and write out the corresponding PovRay code of the object and the planes. Of course the code of the clipping objects needs to be separate from the other stuff, so expanding the PovRay tuple into (matrix,clipping,data) parts would help. Getting it all together requires some knowledge of PovRay but examples in the Wiki should help to get over the initial pain. Any thoughts on this approach? Carsten -Original Message- From: Warren DeLano [mailto:war...@delsci.com] Sent: Wednesday, April 29, 2009 10:36 PM To: Mankin Alexander; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] object-specific Z-clipping Sorry, still not done (I have made two attempts, but both failed). While OpenGL supports arbitrary clipping planes, accomplishing this correctly in the ray tracer is a much harder problem that one might think... Cheers, Warren -Original Message- From: Mankin Alexander [mailto:sh...@uic.edu] Sent: Wednesday, April 29, 2009 6:18 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] object-specific Z-clipping Dear all, Does anyone know whether object-selective z-clipping has been implemented in the newer Pymol version(s)? If not, has anyone found any solution around (since 2002 no new threads on the matter)? Thanks, Shura Mankin --- --- Register Now Save for Velocity, the Web Performance Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Register Now Save for Velocity, the Web Performance Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] pymol and bonds to symmetry related molecules
Christian, as far as I know, PyMol is only able to draw bonds between atoms within the same object. The easiest way would be to combine the pdb files, probably a good idea to give the symm-mate a different chain or segid and then issue the bond command to draw the bond. HTH Carsten -Original Message- From: Christian Roth [mailto:christian.r...@bbz.uni-leipzig.de] Sent: Monday, April 06, 2009 7:21 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] pymol and bonds to symmetry related molecules Dear all, I have incorporated a bond to a symmetry related molecule in my structure and I want see this bond in my picture. Is it possible to visualize this bond in pymol? Thansk in advance for your help. Christian -- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch-Biomedizinisches Zentrum Fakultät für Chemie und Mineralogie Universität Leipzig Deutscher Platz 5 04103 Leipzig Telefon: +49 (0)341 97 31316 Fax: +49 (0)341 97 31319
Re: [PyMOL] Showing only part of a surface around a ligand
Wulf, suppose you have this scenario: Protein in chain A Ligand in chain I Then create b-site, byres chain A within 5 of chain I show sticks, chain I show surface, b-site should get you close. HTH Carsten BTW If you replace the create command with select your surface will be scribed i.e. with frizzled ends. If this is what you want then you should use select. -Original Message- From: Wulf Blankenfeldt [mailto:wulf.blankenfe...@mpi-dortmund.mpg.de] Sent: Wednesday, March 25, 2009 1:31 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Showing only part of a surface around a ligand Hi all, this question may be resolvable by sufficient RTFMing, but maybe there is someone out there to help me... I am trying to generate a figure in which I want to show only a part of the protein surface around a ligand - pretty much like preset -- ligand sites -- solid surface I have already tried some amateur solutions like splitting the ligand into parts, placing waters to generate pseudo-ligand atoms and the like. Somewhat unsatisfying. I have also realized that I can click on every atom of the protein and do a show surface, but this will drive me insane sooner than later. I guess it must be doable through some magic selection commands - if I could only see how the preset command works, I could probably work it out from there. Can somebody please point me in the right direction? Thanks in advance, Wulf -- ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Procedure for adding packages to pymol site-packages?
Hi, how would I go about adding a package to the $PYMOL_PATH/ext/.../site-packages w/o screwing up the install? For most packages the mechanism is python setup.py install. Would this work to run this from within pymol? Thanks Carsten
Re: [PyMOL] selenomethionine
Scott, the MSEs are probably HETATM records instead of ATOM records. You can either replace the HETATM records to ATOM records or set surface_mode to 1 which allows rendering of surfaces with HETATM records (I think, am a bit fuzzy on that) HTH Carsten -Original Message- From: Scott Lefurgy [mailto:slefu...@aecom.yu.edu] Sent: Wednesday, January 21, 2009 12:20 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] selenomethionine I am looking at a structure that contains selenomethionine (rendered MSE in the sequence). When I Show Surface, Se-Met is not displayed with a surface, but all the other residues are. Is there any way to make a surface over Se-Met as well? Scott --- Scott Lefurgy, Ph.D Department of Microbiology Immunology Albert Einstein College of Medicine Yeshiva University 111 Ullmann Building 1300 Morris Park Ave. Bronx, NY 10461 718-430-2858 slefu...@aecom.yu.edu --- -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] PyMOL crashes under Vista Home Premium Ubuntu 8.04 LTS
Michael, play around with the hash_max value, which seem to partially control how much memory is used during rendering. You can also reduce the quality of the rendering Display-Quality, that should reduce memory requirements too. I know you don't want that, but do you really need max quality? Finally on Unix or even Windoze you can look at how much memory is consumed during rendering using top (on Unix) and the task manager on windows. That should give you some clue if you are really exceeding the physical memory or not. Finally you could split the rendering into smaller pieces, export to Povray, combine the files under a common header and render there, alternatively try if the Draw command gives you what you want, albeit not quite as fancy as the raytracer. HTH Carsten -Original Message- From: Michael Weber [mailto:web...@staff.uni-marburg.de] Sent: Friday, January 16, 2009 7:24 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] PyMOL crashes under Vista Home Premium Ubuntu 8.04 LTS Hi, I have a problem when trying to ray 750,750 a quite large ribosome file with maximum quality. Size of the relevant PyMOL v1.1 file is 100 MB (or 31 MB after reducing objects I do not need for the figure production). PyMOL simply crashes under Windows Vista Home Premium as well as under Ubuntu Linux v8.04 LTS without error report. My dual OS system is a Samsung Aura Seven Notebook (Core2Duo @2.4 GHz each, 3 GB of RAM, NVIDIA GeForce 9200M GS graphics board with 256 MB of RAM, 12 TFT @1280x800 resolution settings). I first thought the RAM under Vista is still insufficient (Vista alone takes 900 MB of the 3 GB of memory) but then I realized that this crash occurs as well under Linux. However, since both OS are 32 bit and therefore to my (limited) knowledge cannot handle more than 2 GB in a single task, RAM limitation might still be an issue to think about, right? I have experienced (and occasionally reported) this type of serious crashes with PyMOL on a broad variety of machines over some years now - usually occurring when trying to render final files - but, sadly, none of these has ever been diagnosed and fixed properly. Maybe this time I am lucky and someone knows what to do? Best regards, Michael. -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Making Stereo Pair Graphics
Buz your image size will automatically be limited by the separation of two equal points in the respective images, which should be ~62 mm apart. Let me know if you need more details. Carsten -Original Message- From: Buz Barstow [mailto:b...@mac.com] Sent: Monday, November 24, 2008 3:01 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Making Stereo Pair Graphics Dear All, I'd like to make a stereo pair graphic using pymol. I'd like to know what is an appropriate size for each image in the pair, and what their separation should be. Thanks! and all the best, --Buz - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] remove cartesian coordinate from w/in transparent metal ions
Tom, you need to hide the 'nonbonded' representation of your ion, which shows up as a little coordinate system i.e. hide nonbonded, chain I#if your ion is in chain I show spheres, chain I set sphere_transparency=0.5, chain I Cheers, Carsten -Original Message- From: Thomas S. Leyh, Ph. D. [mailto:l...@aecom.yu.edu] Sent: Wednesday, October 29, 2008 2:39 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] remove cartesian coordinate from w/in transparent metal ions Every once in a while, I try to show a metal ion as a tranparent sphere and inevetiably get stuck trying to make the tiny cartesian coordinate system that appears at the center of the sphere disappear so it doesn't show through. Suggestions? Tom Leyh
Re: [PyMOL] Electron density map in pymol
Jhon, all the newer builds of PyMol are able to read ccp4 maps, no need to convert to xplor format. As far as your commands are concerned, you are almost there. Try this: load mymap.ccp4, format=ccp4, mymap isomesh map, mymap, 2.0, site, carve=1.6 were map is the name of the map graphical object you want to create, mymap is the name of the object that holds the actual map as defined by the load command. HTH Carsten -Original Message- From: Jhon Thomas [mailto:jhon1.tho...@gmail.com] Sent: Friday, September 26, 2008 7:15 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Electron density map in pymol Hello all pymol users I am new to pymol and trying to open a .xplor map file in pymol to get the electron density map of publication grade. The command i write for pymol to open the file and show electron density map is - 1) I convert ccp4 .map file into the .xplor file through mapman. # mymap.xplor loaded as mymap loaded as state 0. 2) Then i load the .xplor map file into pymol and write the following commands- isomesh map, mymap.xplor, 2.0, site, carve=1.6 isomesh: map or brick object mymap.xplor not found. What could be the problem? can any one give suggestion to solve it? Thanks in advance Jhon
Re: [PyMOL] hydrogen naming
phenix.reduce is an option -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of David A. Horita Sent: Thursday, August 21, 2008 3:32 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] hydrogen naming Hi, How do I get proper (HN,HA, HE1, etc) hydrogen naming when using h_add (instead of H01, H02, ...)? Worst case I can build them in Xplor/CNS; second worst would be if there is a uniform rule per residue that I could write a script to convert on a residue type basis. Thanks, Dave - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm http://www1.wfubmc.edu/biochem/faculty/Horita.htm/
Re: [PyMOL] How to disable automatic atom connection?
I believe show valence=on,your_selection will do the trick. Where your_selection is the ligand or whatever you want to display. Good luck Carsten -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of Piter_ Sent: Monday, July 14, 2008 3:28 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] How to disable automatic atom connection? Hi all. How can I disable automatic atom connection in pymol. I want Pymol to make bonds only using connect field in pdb file. Thanks. Petro.
Re: [PyMOL] different transparency surfaces proteins
Joris, you should be able to apply different transparency settings if your proteins are part of different objects i.e. set transparency=0.8, sel1 set transparency=0.5, sel2 HTH Carsten -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of Beld, Joris Sent: Wednesday, July 09, 2008 1:02 PM To: PyMOL-users@lists.sourceforge.net Subject: [PyMOL] different transparency surfaces proteins Dear all, Two questions which I haven't been able to find on the web: Is there a way to set different surface transparency levels for a couple of different proteins compiled in one pymol session, all displayed as surface?! Is there a nice way to give pymol more priority/RAM to do difficult (big protein particle surfaces) ray tracing? Or would POVray do a better job at that? Thanks a lot. Best, Joris Beld ETH Zürich Switzerland
Re: [PyMOL] drawing axes
Just to add onto what Tsjerk had to say about running python snippets in a .pml script. You can also encapsulate the python code in blocks like this: python your python code here python end This works with all newer version of pymol (1.0) and enhances readability of the code quite a bit. HTH Carsten -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of Tsjerk Wassenaar Sent: Wednesday, June 11, 2008 3:25 AM To: David Goldenberg Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] drawing axes Hi David, Regarding the first part of your question, the way to load a python (not a PyMol) script is: run axes.py .. and not @axes.py. The latter is used for loading PyMol scripts (.pml). You _can_ use python code in a .pml script, but then you better, or in some cases have to, start with a slash (/) to let the command parser know that there's python code coming. Hope it helps, Tsjerk On Wed, Jun 11, 2008 at 12:10 AM, David Goldenberg goldenb...@biology.utah.edu wrote: Hi, I would like to make a figure that shows a set of coordinate axes aligned in a particular way with respect to a molecule. I have found the axes.py script (copied at the bottom of this message) on the PyMol Wiki, but have run into the following problems: 1. I can't get the script to load and run properly in MacPymol. I get a long string of error messages beginning with: PyMOL@axes.py PyMOLfrom pymol.cgo import * PyMOLfrom pymol import cmd PyMOLfrom pymol.vfont import plain PyMOLobj = [ Traceback (most recent call last): File /Applications/Molecular Graphics/MacPyMOL.app/pymol/modules/pymol/parser.py, line 208, in parse exec(layer.com2+\n,self.pymol_names,self.pymol_names) File string, line 1 obj = [ ^ SyntaxError: unexpected EOF while parsing I can get the script to run with an old version (0.98) of the Mac-X11 hybrid. I can live with this, if necessary. 2. Once I have the axes and the molecule loaded, I would like to place a particular atom at the origin and then rotate the molecule into a particular orientation. I thought that I could do the first part by using the translate command, by moving the molecule by amounts that correspond to the negative of the initial coordinates of the atom of interest. That is, if the initial coordinates (from the pdb file) are, 1,-2,2, it seems that if I do translate [-1,2,-2] I should move the molecule so that the atom is at the origin. But, this doesn't happen; The molecule moves, but not along the expected axes. There is clearly something about the coordinate system and the translate command that I don't understand. Any suggestions for how to go about this would be greatly appreciated! David The script: # axes.py from pymol.cgo import * from pymol import cmd from pymol.vfont import plain # create the axes object, draw axes with cylinders coloured red, green, #blue for X, Y and Z obj = [ CYLINDER, 0., 0., 0., 10., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0., CYLINDER, 0., 0., 0., 0., 10., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0., CYLINDER, 0., 0., 0., 0., 0., 10., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0, ] # add labels to axes object (requires pymol version 0.8 or greater, I # believe cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0 ,3,0],[0,0,3]]) cyl_text(obj,plain,[10.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0], [0,0,3]]) cyl_text(obj,plain,[0.,10.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0], [0,0,3]]) cyl_text(obj,plain,[0.,0.,10.],'Z',0.20,axes=[[3,0,0],[0,3,0], [0,0,3]]) # then we load it into PyMOL cmd.load_cgo(obj,'axes') -- Department of Biology University of Utah 257 South 1400 East Salt Lake City, UT 84112-0840 Telephone: (801) 581-3885 Fax: (801) 581-2174 E-mail: goldenb...@biology.utah.edu Lab web page: http://www.biology.utah.edu/goldenberg -- --- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ 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 -- --- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source.
[PyMOL] Embeding commands in PyMol session?
Hi, is it possible to embed commands or scripts into a pymol session? I am routinely creating PyMol sessions for users who for the most part have no clue how to use PyMol. So I'd like to include a dialog or message, which gets displayed after the session has loaded and clues the user in how to start or at least what he is looking at. Cheers, Carsten
Re: [PyMOL] Embeding commands in PyMol session?
Hi Warren, I got all that covered already. I think I have a way of doing what I want. I just define the help on the first scene and predisplay it upon loading. That should do the trick. Cheers, Carsten -Original Message- From: DeLano Scientific [mailto:del...@delsci.info] Sent: Friday, April 25, 2008 3:28 PM To: Schubert, Carsten [PRDUS]; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] Embeding commands in PyMol session? Hi Carsten, The best way to share PyMOL content with novice users is via pre-defined scenes stored in a session file. Users can then simply open the session file and use Page Down to iterate through the scenes. Each scene can be annotated with text, for example: scene 001, store, The target structure (press the Page Down key). ... scene 002, store, Surface of the binding site. ... scene 003, store, Our lead compound ABC-12346. ... NOTE: For multi-line annotations, you need to use the Python form of the command: cmd.scene(003,store,My first line of text\nMy second line of text) Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Schubert, Carsten [PRDUS] Sent: Friday, April 25, 2008 6:38 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Embeding commands in PyMol session? Hi, is it possible to embed commands or scripts into a pymol session? I am routinely creating PyMol sessions for users who for the most part have no clue how to use PyMol. So I'd like to include a dialog or message, which gets displayed after the session has loaded and clues the user in how to start or at least what he is looking at. Cheers, Carsten -- --- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java .sun.com/javaone ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] hardware stereo problem
Joris, this is a well known problem with the NVIDIA cards. It gets better with the newer highend cards but does not go away completely. You may want to invest in such a card and play around with different drivers. Carsten -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of Joris Beld Sent: Wednesday, March 12, 2008 4:44 AM To: PyMOL-users@lists.sourceforge.net Subject: [PyMOL] hardware stereo problem Dear Pymol users, We have a problem with one of our hardware stereo equipped PCs. For some reason, hardware stereo works fine for about 30sec but than switches to an inverted 3D image. And it keeps switching back and forth between the 'normal' 3D image and the inverted one, every 30sec. This is pretty annoying and even after reinstalling winXP, the right nvidia driver and playing around with all possible nvidia settings, we cannot find the problem. The problem is not Pymol specific, having the same problem in DSviewer. Does anybody recognize this problem? The PC (AMD X2, 4GB, Nvidia quadro4 980XGL) is running winXP and one of the latest pymol builds (1.0r2). The monitor is a high-end 21 (EIZO Flexscan T966) and we are using a stereographics emitter. Thanks a lot in advance. Best, Joris Beld ETH Zürich Switzerland -- --- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] How to make the dashed line having more dots?
JunJun there are a couple of settings which relate to dashes. Go to Setting-Edit All... and filter by dash. You need to play around with these settings to get the desired effect. Be aware, some of these changes only become visible after raytracing. Cheers Carsten -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of JunJun Liu Sent: Tuesday, March 04, 2008 1:16 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] How to make the dashed line having more dots? Hello everybody, I want to make a picture on which two close atoms are connected by a dashed line. I use the distance command to make the dashed line. However, there's only one dot to compose the whole dashed line. Is there a way to make the dashed line having more dots? == What I want: Atom_A Atom_B What PyMol gives: Atom_A - Atom_B === One more question on the dashed line. Can I modify the dashed line properties, like making it stronger or more compact? Thanks! Junjun -- --- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Isotropic thermal ellipsoids
Warren, this thread gave me an idea about an enhancement request I had for some time. Would it be possible to extend the molecular object module in a way that 2 or more general properties per atoms would be available in PyMol in addition to b and q. For instance in Grasp 2 properties (Prop1, Prop2) are available, which can be used to visualize user defined properties, like distance of an atom from other atoms, partial charges or any other computed property. Right now if one wants to display these properties they have to be placed into either b and q, which actually may contain values one likes to keep around. This probably requires some serious reworking of the internals, but may be worth the effort. Cheers Carsten -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of DeLano Scientific Sent: Friday, February 22, 2008 2:39 PM To: 'Tsjerk Wassenaar'; 'Thomas Stout' Cc: PyMOL-users@lists.sourceforge.net Subject: Re: [PyMOL] Isotropic thermal ellipsoids Tsjerk, Close, but the relationship isn't linear. RMS displacement is c*sqrt(temperature-factor), where c is a constant. The following equation can be found in crystallography texts: B = U * 8 * pi^2. where U is a mean squared displacement and B is the temperature factor. If I've done the math correctly, then the PyMOL input to show root-mean-squared (RMS) displacement would be: from math import sqrt,pi alter all, vdw = sqrt(b/8)/pi show spheres However, given all the fitting performed in the data reduction and structure refinement, absolute temperature factors many not be a reliable measure of absolute RMS displacement in any sort of modeling or analysis work. It is probably safer to stick with relative, qualitative comparisons within a single structure, keeping in mind that vdw could be scaled by systematic biases. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Tsjerk Wassenaar Sent: Friday, February 22, 2008 1:11 AM To: Thomas Stout Cc: PyMOL-users@lists.sourceforge.net Subject: Re: [PyMOL] Isotropic thermal ellipsoids Hi Tom, Does what you're trying to do come down to: alter all, vdw=b/100 show spheres ? Cheers, Tsjerk On Fri, Feb 22, 2008 at 1:42 AM, Thomas Stout tst...@exelixis.com wrote: Hi All -- Yes, I know I want to do something silly here, but does anyone know of a jiffy that will generate anisotropic thermal parameters for an isotropic atom? My end goal is to create a figure showing a ligand as ball-and-stick where the spheres are scaled by the B-factor. Since I'm not dealing with ultra-high resolution data, I just have normal isotropic atoms. I'd like to use the new ellipsoids functionality in PyMOL, but it requires anisotropic atom lines. Obviously, I could write a python script that would scale the vdW radii by some normalization of the B-factor, but I thought I could be lazy and use what Warren has already built into PyMOL. Thanks! -Tom PS -- I'm thinking of something like the -iso feature of rastep in Ethan Merritt's Raster3D suite.. This email (including any attachments) may contain material that is confidential and privileged and is for the sole use of the intended recipient. Any review, reliance or distribution by others or forwarding without express permission is strictly prohibited. If you are not the intended recipient, please contact the sender and delete all copies. Exelixis, Inc. reserves the right, to the extent and under circumstances permitted by applicable law, to retain, monitor and intercept e-mail messages to and from its systems. -- --- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ 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 -- --- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
[PyMOL] Cartoon mode not stored in scene description?
Hi I am trying to define 2 scenes, in one the protein is represented in cartoon automatic mode in the other with cartoon putty. Pymol (1.0 on Linux or 1.1b on Windows) both only draw the recalled scenes in putty mode. Is that expected behaviour? I would have thought that the cartoon mode is part of a scene description? The colors do get updated between the scenes. Here is a code snipped to make this clearer: cartoon automatic refresh scene F1, store cartoon putty spectrum b, palette=rainbow, minimum=0, maximum=60,selection=prot and name CA scene F2, store Cheers Carsten
Re: [PyMOL] displaying unit cell in PyMol
Satinder, make sure you have the correct CRYST record in your file, then load it and in the graphics GUI under S(how) select the Cell menu item. That should do the trick. Cheers Carsten -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of Satinder K. Singh Sent: Tuesday, May 08, 2007 10:55 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] displaying unit cell in PyMol Hello, I am trying to visualize potential heavy metal sites in PyMol. I can read in the ha.pdb output from SOLVE, but I would also like to see the boundaries of the unit cell. In O, I know you can do that with the command sym_cell, but I haven't been able to figure out how to do it in PyMol nor I have been able to find a command anywhere on the web. Could someone tell me if this in indeed possible in PyMol and what the command is? Thanks. Kind regards, Satinder
Re: [PyMOL] Suse 10 and PyMOL crashes
Joris, just an idea. Check if the /dev entry for your video card has the right permissions. For the nvidia board I observed that sometimes the entries (/dev/nvidia0 and/or /dev/nvidiactl) are crw-- instead of crw-rw-rw. Check if changing the permissions on these entries or changing the owner makes any difference. good luck Carsten -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of Joris Beld Sent: Wednesday, October 04, 2006 2:15 AM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Suse 10 and PyMOL crashes Dear all, Unfortunately having a similar problem with Suse10 and PyMOL. - Freshly installed Suse 10 (KDE3.4) system with binary of 0.99 pymol. - the weird thing is: pymol starts fine if logged in as root - logged in as a user (pymol was 'installed' as a user, not as root!) pymol crashes on start up with a segmentation fault /usr/share/pymol/pymol/pymol: line 14: 20717 Segmentation fault $PYMOL_PATH/pymol.exe $@ - the thing i noticed is that as root the GL_RENDERER is recognized during start up of pymol, as a user the GL_RENDERER says 'unknown board'. So, although my system doesn't freeze, it seems to be a similar problem. Anyone a good idea how to solve this? (I don't want to su to root everytime i want to run pymol) Thanks a lot in advance. Best wishes, Joris Beld -- --- 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
[PyMOL] Newline character in scene annotation message
Hi I am trying to combine a scene with annotations spanning several lines. So far something like scene new, store, message=Line1\nLine2 would produce some nice coloration effects but not a newline character. I was able to use the api function to do the trick mesg=line1\nline2 cmd.scene(new,store,message=mesg) but I was wondering is there a way to use the non API function in the same way? Thanks Carsten
RE: [PyMOL] Stereo 3D News
Hi All: just a quick follow up on Warren mentioning the Sharp 3D LCD display. After a couple of trials with various drivers I got the LCD to work under the following setup: Nvidia Quadro FX1100 with driver V67.22 Windows XP with all the latest SPs and patches installed (may not matter) One head of the graphics card connected to a CRT the other to the Sharp LCD Stereographics Din connector hocked up to the graphics card Primary to installing the driver you need to make sure to get rid of all the proprietary Nvidia stereo stuff, that really messed up another machine we tried to get this to work on. Stereo works only on one of the stereo enabled devices at the same time and this device needs to be assigned to be the primary monitor. To get the Sharp LCD to cooperate find the Additional OpenGl Settings in the Display Properties - settings - Advanced - Quadro FX1100 dialog and switch to Use color interleaved Monitor and enable Enable stereo in OpenGL. close all the open dialogs, reboot was not necessary for me, launch your favorite quad buffer stereo enabled application switch to stereo on both the application and the monitor, et voila. Going back to using shutter glasses just requires to switch the primary monitor back to the CRT and switch back from the color interleaved monitor to the onboard DIN connector. Have not tried this under linux, I need to look into how to set the dual head environment up. I also imagine that the dynamic switch between the monitors may be problematic and require a restart of the X-server. The monitor works nice, but the stereo puts more strain on the eyes than regular shutter glasses. Cheers, Carsten Carsten Schubert, Ph.D. Structural Biology JJ PRD (Exton) 665 Stockton Drive, Exton, PA, 19341, USA eMail: cschu...@prdus.jnj.com Tel:610-458-5264 Ext:6579 Fax:610-458-8249 -Original Message- From: Warren DeLano [mailto:war...@delanoscientific.com] Sent: Monday, February 07, 2005 5:30 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Stereo 3D News Topic (1): If any of you are going to LinuxWorld next week in Boston, be sure to stop by the Emperor Linux booth (# 1821 - http://www.emperorlinux.com). They are slotted to demonstrate a new Linux-based laptop from Sharp Electronics that has their latest 15 autostereoscopic 3D LCD display -- running a PyMOL demo of course :). It is too early to say for sure, but I think that the Sharp 3D LCD technology has a good shot at displacing shutter-glasses as the dominant technology over the next couple of years. You get most of the convenience of stereo 3D in-a-window without needing a bulky CRT display on your desk and without having to deal with those expensive fragile glasses. Glasses-free stereo 3D rocks! It is the future, and it is here for you today. My focus is on Sharp because they are the first company with a workable stereo LCD solution suited to our specific needs. Though the 3D sweet spot is supposed to be tuned for just one person at a time, in my opinion, at least 3 and perhaps even as many as 5 people can realistically gather around one of their displays and benefit from greatly enhanced depth perception. With PyMOL, it works for surfaces, electron density, cartoons, spheres, sticks, and even line representations -- basically everything! In short, I believe that our 3D use case requirements in chemistry and structural biology are fully met by the Sharp technology, and so far, most of those who have seen PyMOL running on such a display have agreed with this assessment. Even seasoned medicinal chemists down on 3D have changed their tune after seeing it in action. User interface content outside the 3D window is certainly affected in appearance but remains quite useable in most cases. Full-time crystallographers will of course need a display larger than 15 (one is hopefully in the works), but casual stereo-graphics users should be quite happy with the standard size. It works just like a normal 1024x768 LCD display when not in stereo mode (easily toggled via button or software). The only other practical limitation I have noticed with Sharp's autostereoscopic LCD technology is that you need to draw using lines that are at least 2 pixels wide in order to insure that both eyes receive complete depth information. So long as that rule is followed, the depth quality is as good as shutter glasses. Unfortunately, these displays aren't yet compatible with off-the-shelf QBS stereo 3D software, but DeLano Scientific is committed to insuring that commercially-supported versions of PyMOL work just fine on these displays. Sorry Mac users -- only Windows and Linux only for now, since OS X still doesn't support stereo-3D in a window (though not for lack of trying on my part!). The displays also require an nVidia-based graphics card. Standalone 15 display: http://www.pcmag.com/article2/0,1759,1647634,00.asp Laptop (prior generation):
