Re: [PyMOL] ray_trace_mode, 1 - white outline
Hi Nathan, set ray_trace_gain, 0 set ray_trace_color, black If your background color is something other than black, use that color instead. Cheers, -- Jason On Wed, Mar 16, 2011 at 1:27 PM, NATHAN THOMSEN wrote: > For some reason I am getting white outlines in saved pymol sessions with > ray_trace_mode, 1. Does anyone know what is causing this and/or a quick way > to switch to the black outlines. This does not occur with new sessions, > only when I open a saved session. Thanks! > - Nathan > -- > 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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
[PyMOL] ray_trace_mode, 1 - white outline
For some reason I am getting white outlines in saved pymol sessions with ray_trace_mode, 1. Does anyone know what is causing this and/or a quick way to switch to the black outlines. This does not occur with new sessions, only when I open a saved session. Thanks! - Nathan -- 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] 3D Projector successful cases
Hi David, > Thank you very much. Have you tried to use it with a Mac ? We have not tried it with a Mac. The only stereo I can currently get on the Mac is Zalman. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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] 3D Projector successful cases
> We've had great success with the ViewSonic PJD6531w > (http://www.viewsonic.com/products/pjd6531w.htm). It's bright, clear So are you guys using the DLP link (3d sync) technology of the projector with DLP link capable glasses? -- 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] 3D Projector successful cases
Jason, Thank you very much. Have you tried to use it with a Mac ? We have a Mac Pro with a Quadro FX 5600 Card and would be great to use the projector from there. We already use it with Nuvision glasses 60GX and a CRT display. Best, David On 16/03/2011, at 17:47, Jason Vertrees wrote: > Hi David, > >> I would like to know which 3D Projector setups are you using and can >> certify that work with PyMOL. Which combinations of projector, >> Glasses, Emitters, OS, etc ... Actually work for you. > > We've had great success with the ViewSonic PJD6531w > (http://www.viewsonic.com/products/pjd6531w.htm). It's bright, clear > and looks great in 3D. You need the NVidia 3D Nvision system (we use > the 3-pin connector, but have had success with the USB port too), > glasses (not cheap), and a Quadro card (some start near $99 now). In > our conference room, we run Windows. I've been able to push 3D from > the Quadro 570 and up. The new volumes look fantastic in 3D. > > Cheers, > > -- Jason > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 -- 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] 3D Projector successful cases
Hi David, > I would like to know which 3D Projector setups are you using and can > certify that work with PyMOL. Which combinations of projector, > Glasses, Emitters, OS, etc ... Actually work for you. We've had great success with the ViewSonic PJD6531w (http://www.viewsonic.com/products/pjd6531w.htm). It's bright, clear and looks great in 3D. You need the NVidia 3D Nvision system (we use the 3-pin connector, but have had success with the USB port too), glasses (not cheap), and a Quadro card (some start near $99 now). In our conference room, we run Windows. I've been able to push 3D from the Quadro 570 and up. The new volumes look fantastic in 3D. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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
[PyMOL] 3D Projector successful cases
Dear PyMOL Users, We're looking forward to buy an active 3D Projector for PyMOL Visualization. I would like to know which 3D Projector setups are you using and can certify that work with PyMOL. Which combinations of projector, Glasses, Emitters, OS, etc ... Actually work for you. Any help would be appreciated since the information on the list is very scarce. Also, the wiki mentions 2 projectors (DepthQ, Mirage) but they are expensive and the information is old. Thanks in advance. Best Regards, David -- 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
[PyMOL] Summary: Problem reading multiframe pdb file for animation
The solution (thanks to Jason) is to change all instances of: HEADER to: REMARK in the pdb file. Then opening the file results in the correct behavior (as before) of loading one object with 40 frames. Regards, Peter Stern > Dear PyMol experts: > > When using Open-Source PyMOL 0.99rc6 I read in a pdb file which has > 40 coordinate sets (each is one frame in an animation) each beginning > with: > HEADER Output iset= n "_G=r_0_01" > then a list of the pdb coordinates > and ending with: > ENDMDL > "n" ranges from 0 to 39. > This results in the following output: > HEADER Output iset= 0 "_G=r_0_01" > HEADER Output iset= 1 "_G=r_0_01" > ObjectMolReadPDBStr: read MODEL 1 > ObjectMolReadPDBStr: read MODEL 2 > etc. ... > ObjectMolReadPDBStr: read MODEL 39 > ObjectMolReadPDBStr: read MODEL 40 > CmdLoad: "/home/psstern/pymol/_G=r_0_01.pdb" loaded as "_G=r_0_01". > > This then displays one molecule with 40 frames and the animation can be > activated by clicking on the red arrow. > > However, when using Open-Source PyMOL 1.3 the same file results in > different behavior. Instead of reading in one object with 40 frames > it reads in 40 different objects and displays all of them. The output > I get is: > HEADER Output iset= 0 "_G=r_0_01" > HEADER Output iset= 1 "_G=r_0_01" > HEADER Output iset= 2 "_G=r_0_01" > etc. ... > HEADER Output iset=38 "_G=r_0_01" > HEADER Output iset=39 "_G=r_0_01" > CmdLoad: loaded 40 objects from "/home/psstern/pymol/_G=r_0_01.pdb". > > Is this a bug or am I missing some parameter which is set differently > by default for the two versions? I couldn't find a solution in the > on-line documentation. > > Regards, > Peter Stern > > -- 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] Problem reading multiframe pdb file for animation
Hi Peter, > When using Open-Source PyMOL 0.99rc6 I read in a pdb file which has > 40 coordinate sets (each is one frame in an animation) each beginning > with: > HEADER Output iset= n "_G=r_0_01" Please replace your HEADER stamps with REMARK in your PDB file. Then load with multiplex=0. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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] Adding Hydrogens
I've had good results with MolProbity ( http://molprobity.biochem.duke.edu/index.php?MolProbSID=6b810d461879ca495f8d7898629dc18c&eventID=15) in the past. I had a script that would let me cycle through all of the HIS residues, add hydrogens, and cycle between states. It's broken at the moment. The trick was that PyMOL doesn't care about the name of the residue, so you have to manually cycle the valences. On Wed, Mar 16, 2011 at 11:22 AM, Martin Hediger wrote: > Dear All > I would like to ask if the PyMOL function to add hydrogens to an entire > protein also has options, meaning is it possible to set the protonation > state of individual residues specifically? Like in a list or something? > h_add, His202:+1 or so? > And, it can be relevant at what atom a residue gets protonated: His can > be protonated at Nd, or Ne or both. Is there a way to control this? > > On a more general note: what other smart hydrogen adding tools are there > out there anyway? Does anyone know a really smart tool for this? I know > OpenBabel has a pH parameter. But on the other hand OpenBabel just > appends the hydrogens to the PDB file, whereas PyMOL really writes them > within the block of atoms corresponding to one residue. > Also, AutoDock can add hydrogens and it even has an option for the > protonation state of histidine, but it doesn't seem to work in my case. > > Thanks for your answers and input. > martin > > > -- > 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 > -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- 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] APBS values
I am replying since your question did not get addressed in the past, but know that I am not intimately familiar with PyMOL code or python. I do have a thought, though, if using a grid approximation would work. I have done some work with using MRC density map format in pymol, partly in anticipation of the v1.4 improvements that will come (I wanted to link to them, but can't find it...). There is a 3D grid described by these files, usually encoding density information. I have edited (or created) these maps to encode other types of data. You could use them to record the potential value at each point in the grid. Then the comparison of your two (or more) equal volume structures is just comparing grid points with the same [x,y,z] triple. On Tue, Mar 15, 2011 at 3:39 PM, Matteo Pendleton wrote: > I posed this question some while back and thought I'd submit it again as my > question wasn't answered completely. > > Is it possible to have APBS spit out a list of values for points on the > surface? I'd like to be able to quantitatively compare surface > electrostatics of volumetrically identical proteins. I've been able to > export a mesh of points on the solvent accessible surface but would also > like to have electrostatic potential values at those points. > > Thanks! > > Matt Pendleton > > > -- > 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 > -- Michael Zimmermann Ph.D. student in Bioinformatics and Computational Biology Department of Biochemistry, Biophysics and Molecular Biology Iowa State University -- 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
[PyMOL] Adding Hydrogens
Dear All I would like to ask if the PyMOL function to add hydrogens to an entire protein also has options, meaning is it possible to set the protonation state of individual residues specifically? Like in a list or something? h_add, His202:+1 or so? And, it can be relevant at what atom a residue gets protonated: His can be protonated at Nd, or Ne or both. Is there a way to control this? On a more general note: what other smart hydrogen adding tools are there out there anyway? Does anyone know a really smart tool for this? I know OpenBabel has a pH parameter. But on the other hand OpenBabel just appends the hydrogens to the PDB file, whereas PyMOL really writes them within the block of atoms corresponding to one residue. Also, AutoDock can add hydrogens and it even has an option for the protonation state of histidine, but it doesn't seem to work in my case. Thanks for your answers and input. martin -- 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] Problem reading multiframe pdb file for animation
Hi Peter, If you could send me the PDB (or one like it) I'd like to see it. The known flags for controlling how PyMOL loads multi-state files are: discrete= 0 or 1 If 0, then all states must have the same number of atoms and similar connectivity If 1, then all states are treated as different molecular structures, so can have differing numbers of atoms and bonds multiplex= 0 or 1 If 0, then load the N-state file as one N-state object If 1, then load the N-state file as N one-state objects So, what happens in v1.3 if you write: load fileName.pdb, multiplex=0 Cheers, -- Jason On Wed, Mar 16, 2011 at 10:23 AM, wrote: > Dear PyMol experts: > > When using Open-Source PyMOL 0.99rc6 I read in a pdb file which has > 40 coordinate sets (each is one frame in an animation) each beginning > with: > HEADER Output iset= n "_G=r_0_01" > then a list of the pdb coordinates > and ending with: > ENDMDL > "n" ranges from 0 to 39. > This results in the following output: > HEADER Output iset= 0 "_G=r_0_01" > HEADER Output iset= 1 "_G=r_0_01" > ObjectMolReadPDBStr: read MODEL 1 > ObjectMolReadPDBStr: read MODEL 2 > etc. ... > ObjectMolReadPDBStr: read MODEL 39 > ObjectMolReadPDBStr: read MODEL 40 > CmdLoad: "/home/psstern/pymol/_G=r_0_01.pdb" loaded as "_G=r_0_01". > > This then displays one molecule with 40 frames and the animation can be > activated by clicking on the red arrow. > > However, when using Open-Source PyMOL 1.3 the same file results in > different behavior. Instead of reading in one object with 40 frames > it reads in 40 different objects and displays all of them. The output > I get is: > HEADER Output iset= 0 "_G=r_0_01" > HEADER Output iset= 1 "_G=r_0_01" > HEADER Output iset= 2 "_G=r_0_01" > etc. ... > HEADER Output iset= 38 "_G=r_0_01" > HEADER Output iset= 39 "_G=r_0_01" > CmdLoad: loaded 40 objects from "/home/psstern/pymol/_G=r_0_01.pdb". > > Is this a bug or am I missing some parameter which is set differently > by default for the two versions? I couldn't find a solution in the > on-line documentation. > > Regards, > Peter Stern > > -- > 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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
[PyMOL] Problem reading multiframe pdb file for animation
Dear PyMol experts: When using Open-Source PyMOL 0.99rc6 I read in a pdb file which has 40 coordinate sets (each is one frame in an animation) each beginning with: HEADER Output iset= n "_G=r_0_01" then a list of the pdb coordinates and ending with: ENDMDL "n" ranges from 0 to 39. This results in the following output: HEADER Output iset= 0 "_G=r_0_01" HEADER Output iset= 1 "_G=r_0_01" ObjectMolReadPDBStr: read MODEL 1 ObjectMolReadPDBStr: read MODEL 2 etc. ... ObjectMolReadPDBStr: read MODEL 39 ObjectMolReadPDBStr: read MODEL 40 CmdLoad: "/home/psstern/pymol/_G=r_0_01.pdb" loaded as "_G=r_0_01". This then displays one molecule with 40 frames and the animation can be activated by clicking on the red arrow. However, when using Open-Source PyMOL 1.3 the same file results in different behavior. Instead of reading in one object with 40 frames it reads in 40 different objects and displays all of them. The output I get is: HEADER Output iset= 0 "_G=r_0_01" HEADER Output iset= 1 "_G=r_0_01" HEADER Output iset= 2 "_G=r_0_01" etc. ... HEADER Output iset=38 "_G=r_0_01" HEADER Output iset=39 "_G=r_0_01" CmdLoad: loaded 40 objects from "/home/psstern/pymol/_G=r_0_01.pdb". Is this a bug or am I missing some parameter which is set differently by default for the two versions? I couldn't find a solution in the on-line documentation. Regards, Peter Stern -- 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
