From: Jonathan G. <jon...@st...> - 2012-12-13 16:10:02
|
Hi All, I have 2 different states of the same molecule......different conformations generated from MD, so the same number of Calpha atoms, with a direct 1:1 mapping between Calphas with the same residue numbering. I would like to draw a "bond" between equivalent C-alpha atoms, and I will then ramp colour along the bond, say blue-white-red. Could I get advice how to draw a bond between 2 Calpha atoms (same resi) from different states Many thanks for the help. Jon Dr. Jonathan M. Grimes, NDM Senior Reseach Fellow University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: Jon...@st..., Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 |
From: Robert C. <rob...@qu...> - 2012-12-13 21:18:16
|
Hi Jon, On Thu, 2012-12-13 16:09 EST, Jonathan Grimes <jon...@st...> wrote: > Hi All, > > I have 2 different states of the same molecule......different > conformations generated from MD, so the same number of Calpha atoms, with > a direct 1:1 mapping between Calphas with the same residue numbering. > > I would like to draw a "bond" between equivalent C-alpha atoms, and I > will then ramp colour along the bond, say blue-white-red. > > Could I get advice how to draw a bond between 2 Calpha atoms (same > resi) from different states I have a script for drawing a cylinder (you can specify the radius and the beginning and ending colors) between two atoms. The script is at: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/draw_cylinder_cgo.py First "run" the script via the "File" menu or via the command line: run draw_cylinder_cgo.py You will then have two new functions defined "draw_cylinder" and "draw_cylinder_cgo". The former allows you to pick two atoms to draw the cylinder between: draw_cylinder name, atom1, atom2, radius, start_color, end_color where each atom is a standard PyMOL selection (defaults to pk1 and pk2) and color is a 3-element RGB tuple defining the color of the cylinder (where each value of R, G and B is between 0 and 1 inclusive). The colors default to (1,1,0). Alternatively, draw_cylinder_cgo takes as arguments the start and end coordinates of the vector in place of atom1 and atom2. Hope that helps. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 <rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc |
From: Robert C. <rob...@qu...> - 2012-12-13 21:54:52
|
Hi, (replying to my own message) On Thu, 2012-12-13 15:52 EST, Robert Campbell <rob...@qu...> wrote: > Hi Jon, > > On Thu, 2012-12-13 16:09 EST, Jonathan Grimes <jon...@st...> > wrote: > > > Hi All, > > > > I have 2 different states of the same molecule......different > > conformations generated from MD, so the same number of Calpha atoms, > > with a direct 1:1 mapping between Calphas with the same residue > > numbering. > > > > I would like to draw a "bond" between equivalent C-alpha atoms, and I > > will then ramp colour along the bond, say blue-white-red. > > > > Could I get advice how to draw a bond between 2 Calpha atoms (same > > resi) from different states > > I have a script for drawing a cylinder (you can specify the radius and the > beginning and ending colors) between two atoms. The script is at: > > http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/draw_cylinder_cgo.py > > First "run" the script via the "File" menu or via the command line: > > run draw_cylinder_cgo.py > > You will then have two new functions defined "draw_cylinder" and > "draw_cylinder_cgo". The former allows you to pick two atoms to draw the > cylinder between: > > draw_cylinder name, atom1, atom2, radius, start_color, end_color > > where each atom is a standard PyMOL selection (defaults to pk1 and > pk2) and color is a 3-element RGB tuple defining the color > of the cylinder (where each value of R, G and B is between 0 and 1 > inclusive). The colors default to (1,1,0). > > > Alternatively, draw_cylinder_cgo takes as arguments the start and end > coordinates of the vector in place of atom1 and atom2. I could add more instructions here. You can specify the colours by name and if you have picked the atoms with the mouse you can easily do something like: draw_cylinder dist1, start_color=red, end_color=yellow and it will default to using atom selections "pk1" and "pk2" and a radius of 0.1 A. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 <rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc |
From: Tsjerk W. <ts...@gm...> - 2012-12-14 09:14:01
|
Hey :) Can't resist the challenge... For any given ensemble, you can draw a trace through the C-alphas using the following lines, illustrated here for the NMR ensemble '1NMR': # Get the structure fetch 1nmr # Get the number of states n = cmd.count_states('1nmr') # Collect the C-alpha coordinates # This calls get_model for every state and extracts the coordinates for every model-state # The resulting list is transposed, such that each list entry contains the coordinates for one C-alpha over all states x=zip(*[cmd.get_model('1nmr and n. ca',state=i+1).get_coord_list() for i in range(n)] ) # Now draw the traces by building a CGO model cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(r)) for i in [9.0]+u+v+[0.1,1,1-(1.*f)/r,1-(1.*f)/r,1,1-(1.+f)/r,1-(1.+f)/r]],"trace") The 9.0 is the CGO code for a cylinder (pymol.cgo.CYLINDER). The 0.1 is the radius, and the following six values are the start and end RGB values, which are related to the state number, such that they end up from white to red. For more complex colors it would be nice to have a rgb() function that would return a color according to some scheme, given a fraction, which would make that last command cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(r)) for i in [9.0]+u+v+[0.1]+rgb((1.*f)/r,scheme=...)+rgb((1.+f)/r,scheme=...)],"trace") Hope it helps, Tsjerk On Thu, Dec 13, 2012 at 10:54 PM, Robert Campbell < rob...@qu...> wrote: > Hi, > > (replying to my own message) > > On Thu, 2012-12-13 15:52 EST, Robert Campbell > <rob...@qu...> wrote: > > > Hi Jon, > > > > On Thu, 2012-12-13 16:09 EST, Jonathan Grimes < > jon...@st...> > > wrote: > > > > > Hi All, > > > > > > I have 2 different states of the same molecule......different > > > conformations generated from MD, so the same number of Calpha atoms, > > > with a direct 1:1 mapping between Calphas with the same residue > > > numbering. > > > > > > I would like to draw a "bond" between equivalent C-alpha atoms, and > I > > > will then ramp colour along the bond, say blue-white-red. > > > > > > Could I get advice how to draw a bond between 2 Calpha atoms (same > > > resi) from different states > > > > I have a script for drawing a cylinder (you can specify the radius and > the > > beginning and ending colors) between two atoms. The script is at: > > > > > http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/draw_cylinder_cgo.py > > > > First "run" the script via the "File" menu or via the command line: > > > > run draw_cylinder_cgo.py > > > > You will then have two new functions defined "draw_cylinder" and > > "draw_cylinder_cgo". The former allows you to pick two atoms to draw the > > cylinder between: > > > > draw_cylinder name, atom1, atom2, radius, start_color, end_color > > > > where each atom is a standard PyMOL selection (defaults to pk1 and > > pk2) and color is a 3-element RGB tuple defining the color > > of the cylinder (where each value of R, G and B is between 0 and 1 > > inclusive). The colors default to (1,1,0). > > > > > > Alternatively, draw_cylinder_cgo takes as arguments the start and end > > coordinates of the vector in place of atom1 and atom2. > > I could add more instructions here. You can specify the colours by > name and if you have picked the atoms with the mouse you can easily do > something like: > > draw_cylinder dist1, start_color=red, end_color=yellow > > and it will default to using atom selections "pk1" and "pk2" and a radius > of 0.1 A. > > Cheers, > Rob > -- > Robert L. Campbell, Ph.D. > Senior Research Associate/Adjunct Assistant Professor > Dept. of Biomedical & Molecular Sciences > Botterell Hall Rm 644 > Queen's University, > Kingston, ON K7L 3N6 Canada > Tel: 613-533-6821 > <rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc > > > ------------------------------------------------------------------------------ > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial > Remotely access PCs and mobile devices and provide instant support > Improve your efficiency, and focus on delivering more value-add services > Discover what IT Professionals Know. Rescue delivers > http://p.sf.net/sfu/logmein_12329d2d > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada |
From: Tsjerk W. <ts...@gm...> - 2012-12-14 11:53:25
|
Hi Jon, You also have to update the three numbers before. So to go from white to blue is cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(n)) for i in [9.0]+u+v+[1.3, 1-(1.*f)/n,1-(1.*f)/n,1, 1-(1.+f)/n,1-(1.+f)/n,1 ]],"trace") If you want to go from blue to white to red, it's probably easiest to split it in two: a=n/2 b=n-n/2 cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(n))[:a] for i in [9.0]+u+v+[1.3, (1.*f)/a,(1.*f)/a,1, (1.+f)/a,(1.+f)/a,1 ]],"trace_a") cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(n))[a:] for i in [9.0]+u+v+[1.3, 1,1-(1.*f-a)/b,1-(1.*f-a)/b, 1,1-(1.+f-a)/b,1-(1.+f-a)/b ]],"trace_b") For the capping, you can use spheres: cmd.load_cgo([i for j in x for u,f in zip(j,range(n))[:a] for i in [6.0, (1.*f)/a,(1.*f)/a,1, 7.0]+u+[1.3]],"spheres_a") cmd.load_cgo([i for j in x for u,f in zip(j,range(n))[a:] for i in [6.0, 1,1-(1.*f-a)/b,1-(1.*f-a)/b, 7.0]+u+[1.3]],"spheres_b") For more complex color schemes, you would definitely want a rgb function. Hope it helps, Tsjerk On Fri, Dec 14, 2012 at 12:25 PM, Jonathan Grimes <jon...@st...>wrote: > > thanks tsjerk > > ive been playing with the values at the end......and i can,t change it > to go from > white to blue....or even red to blue.... > > i tried....white to blue....so 1,1,1 to 0,0, 1 > > cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(n)) for i in > [9.0]+u+v+[1.3,1,1-(1.*f)/n,1-(1.*f)/n, 1-(1.+f)/n,1-(1.+f)/n,1 ]],"trace") > > so 1,1-(1.*f)/n,1-(1.*f)/n, corresponds to 1,1,1....where f/n is the > fraction along the cylinder..... > > and then i changed the last 3 numbers to 1-(1.+f)/n,1-(1.+f)/n,1....which > i thought would go to 0 , 0 ,1 > > but i get a bond but the color doesnt go smoothly from white to blue ?? > > is there also a nice way to cap the cylinder so it had a rounded end ?? > > thanks > jon > > > Dr. Jonathan M. Grimes, > NDM Senior Reseach Fellow > University Research Lecturer > Division of Structural Biology > Wellcome Trust Centre for Human Genetics > University of Oxford > Roosevelt Drive, > Oxford OX3 7BN, UK > > Email: Jon...@st..., Web: www.strubi.ox.ac.uk > Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 > > > > On 14 Dec 2012, at 09:13, Tsjerk Wassenaar wrote: > > Hey :) > > Can't resist the challenge... > For any given ensemble, you can draw a trace through the C-alphas using > the following lines, illustrated here for the NMR ensemble '1NMR': > > # Get the structure > fetch 1nmr > > # Get the number of states > n = cmd.count_states('1nmr') > > # Collect the C-alpha coordinates > # This calls get_model for every state and extracts the coordinates for > every model-state > # The resulting list is transposed, such that each list entry contains the > coordinates for one C-alpha over all states > x=zip(*[cmd.get_model('1nmr and n. ca',state=i+1).get_coord_list() for i > in range(n)] ) > > # Now draw the traces by building a CGO model > cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(r)) for i in > [9.0]+u+v+[0.1,1,1-(1.*f)/r,1-(1.*f)/r,1,1-(1.+f)/r,1-(1.+f)/r]],"trace") > > The 9.0 is the CGO code for a cylinder (pymol.cgo.CYLINDER). The 0.1 is > the radius, and the following six values are the start and end RGB values, > which are related to the state number, such that they end up from white to > red. For more complex colors it would be nice to have a rgb() function that > would return a color according to some scheme, given a fraction, which > would make that last command > > cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(r)) for i in > [9.0]+u+v+[0.1]+rgb((1.*f)/r,scheme=...)+rgb((1.+f)/r,scheme=...)],"trace") > > Hope it helps, > > Tsjerk > > > On Thu, Dec 13, 2012 at 10:54 PM, Robert Campbell < > rob...@qu...> wrote: > >> Hi, >> >> (replying to my own message) >> >> On Thu, 2012-12-13 15:52 EST, Robert Campbell >> <rob...@qu...> wrote: >> >> > Hi Jon, >> > >> > On Thu, 2012-12-13 16:09 EST, Jonathan Grimes < >> jon...@st...> >> > wrote: >> > >> > > Hi All, >> > > >> > > I have 2 different states of the same molecule......different >> > > conformations generated from MD, so the same number of Calpha atoms, >> > > with a direct 1:1 mapping between Calphas with the same residue >> > > numbering. >> > > >> > > I would like to draw a "bond" between equivalent C-alpha atoms, >> and I >> > > will then ramp colour along the bond, say blue-white-red. >> > > >> > > Could I get advice how to draw a bond between 2 Calpha atoms (same >> > > resi) from different states >> > >> > I have a script for drawing a cylinder (you can specify the radius and >> the >> > beginning and ending colors) between two atoms. The script is at: >> > >> > >> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/draw_cylinder_cgo.py >> > >> > First "run" the script via the "File" menu or via the command line: >> > >> > run draw_cylinder_cgo.py >> > >> > You will then have two new functions defined "draw_cylinder" and >> > "draw_cylinder_cgo". The former allows you to pick two atoms to draw >> the >> > cylinder between: >> > >> > draw_cylinder name, atom1, atom2, radius, start_color, end_color >> > >> > where each atom is a standard PyMOL selection (defaults to pk1 and >> > pk2) and color is a 3-element RGB tuple defining the color >> > of the cylinder (where each value of R, G and B is between 0 and 1 >> > inclusive). The colors default to (1,1,0). >> > >> > >> > Alternatively, draw_cylinder_cgo takes as arguments the start and end >> > coordinates of the vector in place of atom1 and atom2. >> >> I could add more instructions here. You can specify the colours by >> name and if you have picked the atoms with the mouse you can easily do >> something like: >> >> draw_cylinder dist1, start_color=red, end_color=yellow >> >> and it will default to using atom selections "pk1" and "pk2" and a radius >> of 0.1 A. >> >> Cheers, >> Rob >> -- >> Robert L. Campbell, Ph.D. >> Senior Research Associate/Adjunct Assistant Professor >> Dept. of Biomedical & Molecular Sciences >> Botterell Hall Rm 644 >> Queen's University, >> Kingston, ON K7L 3N6 Canada >> Tel: 613-533-6821 >> <rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc >> >> >> ------------------------------------------------------------------------------ >> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial >> Remotely access PCs and mobile devices and provide instant support >> Improve your efficiency, and focus on delivering more value-add services >> Discover what IT Professionals Know. Rescue delivers >> http://p.sf.net/sfu/logmein_12329d2d >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Biocomputing Group > Department of Biological Sciences > 2500 University Drive NW > Calgary, AB T2N 1N4 > Canada > > ------------------------------------------------------------------------------ > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial > Remotely access PCs and mobile devices and provide instant support > Improve your efficiency, and focus on delivering more value-add services > Discover what IT Professionals Know. Rescue delivers > > http://p.sf.net/sfu/logmein_12329d2d_______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > > > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada |
From: lloyd r. <llo...@gm...> - 2012-12-16 15:37:56
|
Dear All, I have a wierd bug with pymol after a recent update to Ubuntu 12.10. If I use any auxiliary (not in pymol) software such as notepads, gedit, etc..Pymol then does some sort of switch if it is open at the same time for selections. It changes from residue, to atom, to whole molecule in the selection, depending on how much or how many times you go and type something in gedit. It then does not allow you to rotate the molecule, or change the menu selections anymore. I then have to re-start the computer, or re-install pymol to re-set the normal operations. This is extremely problematic, as pymol is a good program to quickly look at specific residues, etc...when doing massive text based tabulations of specific residues, and a necessary orientation and check visually is needed on the side to keep track of things. Needless to say the uses for anything else, such as making images, etc.. Has anyone experienced this, or more importantly, does anyone have a patch or bug fix. Sincerely, Stephan Watkins |
From: Jason V. <jas...@sc...> - 2012-12-17 19:35:16
|
Hi Stephan, I use Ubuntu 12 and haven't had any problems with PyMOL. I do have problems with my mouse in all apps, but that's not PyMOL's fault. Do you know anyone else with these problems? Have you asked around the Ubuntu community? Cheers, -- Jason On Sun, Dec 16, 2012 at 10:37 AM, lloyd riggs <llo...@gm...> wrote: > > Dear All, > > I have a wierd bug with pymol after a recent update to Ubuntu 12.10. If I use any auxiliary (not in pymol) software such as notepads, gedit, etc..Pymol then does some sort of switch if it is open at the same time for selections. It changes from residue, to atom, to whole molecule in the selection, depending on how much or how many times you go and type something in gedit. It then does not allow you to rotate the molecule, or change the menu selections anymore. I then have to re-start the computer, or re-install pymol to re-set the normal operations. This is extremely problematic, as pymol is a good program to quickly look at specific residues, etc...when doing massive text based tabulations of specific residues, and a necessary orientation and check visually is needed on the side to keep track of things. Needless to say the uses for anything else, such as making images, etc.. > > Has anyone experienced this, or more importantly, does anyone have a patch or bug fix. > > Sincerely, > > Stephan Watkins > > ------------------------------------------------------------------------------ > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial > Remotely access PCs and mobile devices and provide instant support > Improve your efficiency, and focus on delivering more value-add services > Discover what IT Professionals Know. Rescue delivers > http://p.sf.net/sfu/logmein_12329d2d > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Martin H. <ma...@bl...> - 2012-12-20 13:37:45
|
Dear PyMOL users In a directory are PDB files of combined size equal to around 3MB. When I load all files into PyMOL, I observe that the required RAM of PyMOL (MacOS X 10.6) increases by roughly this amount. When I delete all objects, the RAM requirement remains the same and when I then reload all structures, the RAM requirement increases even further. I'm currently using PyMOL to batch process a number of files where a structure is loaded, modified and then deleted again from the objects list. This then results in RAM requirements of over 1GB and together with other applications, I run out of memory. Is there a way I can prevent PyMOL from behaving this way? Best regards and thanks for any help Martin |
From: Jason V. <jas...@sc...> - 2012-12-20 14:53:48
|
Hi Martin, Which version of PyMOL are you using? Cheers, -- Jason On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger <ma...@bl...> wrote: > Dear PyMOL users > In a directory are PDB files of combined size equal to around 3MB. When > I load all files into PyMOL, I observe that the required RAM of PyMOL > (MacOS X 10.6) increases by roughly this amount. > When I delete all objects, the RAM requirement remains the same and when > I then reload all structures, the RAM requirement increases even further. > I'm currently using PyMOL to batch process a number of files where a > structure is loaded, modified and then deleted again from the objects > list. This then results in RAM requirements of over 1GB and together > with other applications, I run out of memory. > Is there a way I can prevent PyMOL from behaving this way? > > Best regards and thanks for any help > Martin > > ------------------------------------------------------------------------------ > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial > Remotely access PCs and mobile devices and provide instant support > Improve your efficiency, and focus on delivering more value-add services > Discover what IT Professionals Know. Rescue delivers > http://p.sf.net/sfu/logmein_12329d2d > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Martin H. <ma...@bl...> - 2012-12-20 15:17:52
|
Hi Jason, I'm using PyMOL 1.3. Best regards Martin On 20.12.12 15:53, Jason Vertrees wrote: > Hi Martin, > > Which version of PyMOL are you using? > > Cheers, > > -- Jason > > On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger <ma...@bl...> wrote: >> Dear PyMOL users >> In a directory are PDB files of combined size equal to around 3MB. When >> I load all files into PyMOL, I observe that the required RAM of PyMOL >> (MacOS X 10.6) increases by roughly this amount. >> When I delete all objects, the RAM requirement remains the same and when >> I then reload all structures, the RAM requirement increases even further. >> I'm currently using PyMOL to batch process a number of files where a >> structure is loaded, modified and then deleted again from the objects >> list. This then results in RAM requirements of over 1GB and together >> with other applications, I run out of memory. >> Is there a way I can prevent PyMOL from behaving this way? >> >> Best regards and thanks for any help >> Martin >> >> ------------------------------------------------------------------------------ >> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial >> Remotely access PCs and mobile devices and provide instant support >> Improve your efficiency, and focus on delivering more value-add services >> Discover what IT Professionals Know. Rescue delivers >> http://p.sf.net/sfu/logmein_12329d2d >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... > > |
From: Jason V. <jas...@sc...> - 2012-12-20 16:06:40
|
Martin, That sounds like a memory leak in v1.3. Can you try a newer version of PyMOL and let us know if it still happens? We've fixed lots of bugs since v1.3. Also, is your script simply iterating over structures and deleting them when done? You sure you're not missing a cleanup step somewhere? (Any chance we can see the script or a stub of it?) Cheers, -- Jason On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger <ma...@bl...> wrote: > Hi Jason, > I'm using PyMOL 1.3. > > Best regards > Martin > > > > > > On 20.12.12 15:53, Jason Vertrees wrote: >> >> Hi Martin, >> >> Which version of PyMOL are you using? >> >> Cheers, >> >> -- Jason >> >> On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger <ma...@bl...> wrote: >>> >>> Dear PyMOL users >>> In a directory are PDB files of combined size equal to around 3MB. When >>> I load all files into PyMOL, I observe that the required RAM of PyMOL >>> (MacOS X 10.6) increases by roughly this amount. >>> When I delete all objects, the RAM requirement remains the same and when >>> I then reload all structures, the RAM requirement increases even further. >>> I'm currently using PyMOL to batch process a number of files where a >>> structure is loaded, modified and then deleted again from the objects >>> list. This then results in RAM requirements of over 1GB and together >>> with other applications, I run out of memory. >>> Is there a way I can prevent PyMOL from behaving this way? >>> >>> Best regards and thanks for any help >>> Martin >>> >>> >>> ------------------------------------------------------------------------------ >>> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial >>> Remotely access PCs and mobile devices and provide instant support >>> Improve your efficiency, and focus on delivering more value-add services >>> Discover what IT Professionals Know. Rescue delivers >>> http://p.sf.net/sfu/logmein_12329d2d >>> _______________________________________________ >>> PyMOL-users mailing list (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >> >> >> > -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Martin H. <ma...@bl...> - 2012-12-20 16:20:22
|
I'll give it a try with the newer versions. I just checked, and I believe I'm doing some cleaning up. Sure, I posted the scripte on this pastebin: http://pastebin.com/mC6Rs6wk Sorry for the layout (all pretty in development). In production, the script is invoked from the "frag" function. Martin On 20.12.12 17:05, Jason Vertrees wrote: > Martin, > > That sounds like a memory leak in v1.3. Can you try a newer version of > PyMOL and let us know if it still happens? We've fixed lots of bugs > since v1.3. > > Also, is your script simply iterating over structures and deleting > them when done? You sure you're not missing a cleanup step somewhere? > (Any chance we can see the script or a stub of it?) > > Cheers, > > -- Jason > > On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger <ma...@bl...> wrote: >> Hi Jason, >> I'm using PyMOL 1.3. >> >> Best regards >> Martin >> >> >> >> >> >> On 20.12.12 15:53, Jason Vertrees wrote: >>> Hi Martin, >>> >>> Which version of PyMOL are you using? >>> >>> Cheers, >>> >>> -- Jason >>> >>> On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger <ma...@bl...> wrote: >>>> Dear PyMOL users >>>> In a directory are PDB files of combined size equal to around 3MB. When >>>> I load all files into PyMOL, I observe that the required RAM of PyMOL >>>> (MacOS X 10.6) increases by roughly this amount. >>>> When I delete all objects, the RAM requirement remains the same and when >>>> I then reload all structures, the RAM requirement increases even further. >>>> I'm currently using PyMOL to batch process a number of files where a >>>> structure is loaded, modified and then deleted again from the objects >>>> list. This then results in RAM requirements of over 1GB and together >>>> with other applications, I run out of memory. >>>> Is there a way I can prevent PyMOL from behaving this way? >>>> >>>> Best regards and thanks for any help >>>> Martin >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial >>>> Remotely access PCs and mobile devices and provide instant support >>>> Improve your efficiency, and focus on delivering more value-add services >>>> Discover what IT Professionals Know. Rescue delivers >>>> http://p.sf.net/sfu/logmein_12329d2d >>>> _______________________________________________ >>>> PyMOL-users mailing list (PyM...@li...) >>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> Archives: http://www.mail-archive.com/pym...@li... >>> >>> > > |
From: Gianluigi C. <chi...@ya...> - 2012-12-21 08:53:15
|
I have the same problem since pymol 1.5, mainly with the hybrid (I can reach 10GB of ram memory with relatively small sessions). I'm on MAC OS 10.7.5 and pymol version 1.5.0.3. I had to renounce working with Hybrid unless I really need some plug-in. Gianluigi ________________________________ Da: Jason Vertrees <jas...@sc...> A: Martin Hediger <ma...@bl...> Cc: "pym...@li..." <pym...@li...> Inviato: Giovedì 20 Dicembre 2012 17:05 Oggetto: Re: [PyMOL] Memory not released after load and delete of structure Martin, That sounds like a memory leak in v1.3. Can you try a newer version of PyMOL and let us know if it still happens? We've fixed lots of bugs since v1.3. Also, is your script simply iterating over structures and deleting them when done? You sure you're not missing a cleanup step somewhere? (Any chance we can see the script or a stub of it?) Cheers, -- Jason On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger <ma...@bl...> wrote: > Hi Jason, > I'm using PyMOL 1.3. > > Best regards > Martin > > > > > > On 20.12.12 15:53, Jason Vertrees wrote: >> >> Hi Martin, >> >> Which version of PyMOL are you using? >> >> Cheers, >> >> -- Jason >> >> On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger <ma...@bl...> wrote: >>> >>> Dear PyMOL users >>> In a directory are PDB files of combined size equal to around 3MB. When >>> I load all files into PyMOL, I observe that the required RAM of PyMOL >>> (MacOS X 10.6) increases by roughly this amount. >>> When I delete all objects, the RAM requirement remains the same and when >>> I then reload all structures, the RAM requirement increases even further. >>> I'm currently using PyMOL to batch process a number of files where a >>> structure is loaded, modified and then deleted again from the objects >>> list. This then results in RAM requirements of over 1GB and together >>> with other applications, I run out of memory. >>> Is there a way I can prevent PyMOL from behaving this way? >>> >>> Best regards and thanks for any help >>> Martin >>> >>> >>> ------------------------------------------------------------------------------ >>> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial >>> Remotely access PCs and mobile devices and provide instant support >>> Improve your efficiency, and focus on delivering more value-add services >>> Discover what IT Professionals Know. Rescue delivers >>> http://p.sf.net/sfu/logmein_12329d2d >>> _______________________________________________ >>> PyMOL-users mailing list (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >> >> >> > -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) Jas...@sc... (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d _______________________________________________ PyMOL-users mailing list (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |
From: Thomas H. <tho...@sc...> - 2012-12-21 16:31:53
|
Hi Gianluigi and Martin, thanks for reporting, this is a serious issue and we are looking into it. As far as we can reproduce, it's related to the undo feature. Adding this to your scripts should help: cmd.set("suspend_undo", 1) Cheers, Thomas On Dec 21, 2012, at 9:53 AM, Gianluigi Caltabiano <chi...@ya...> wrote: > I have the same problem since pymol 1.5, mainly with the hybrid (I can reach 10GB of ram memory with relatively small sessions). I'm on MAC OS 10.7.5 and pymol version 1.5.0.3. > I had to renounce working with Hybrid unless I really need some plug-in. > > Gianluigi > > > Da: Jason Vertrees <jas...@sc...> > A: Martin Hediger <ma...@bl...> > Cc: "pym...@li..." <pym...@li...> > Inviato: Giovedì 20 Dicembre 2012 17:05 > Oggetto: Re: [PyMOL] Memory not released after load and delete of structure > > Martin, > > That sounds like a memory leak in v1.3. Can you try a newer version of > PyMOL and let us know if it still happens? We've fixed lots of bugs > since v1.3. > > Also, is your script simply iterating over structures and deleting > them when done? You sure you're not missing a cleanup step somewhere? > (Any chance we can see the script or a stub of it?) > > Cheers, > > -- Jason > > On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger <ma...@bl...> wrote: > > Hi Jason, > > I'm using PyMOL 1.3. > > > > Best regards > > Martin > > > > > > > > On 20.12.12 15:53, Jason Vertrees wrote: > >> > >> Hi Martin, > >> > >> Which version of PyMOL are you using? > >> > >> Cheers, > >> > >> -- Jason > >> > >> On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger <ma...@bl...> wrote: > >>> > >>> Dear PyMOL users > >>> In a directory are PDB files of combined size equal to around 3MB. When > >>> I load all files into PyMOL, I observe that the required RAM of PyMOL > >>> (MacOS X 10.6) increases by roughly this amount. > >>> When I delete all objects, the RAM requirement remains the same and when > >>> I then reload all structures, the RAM requirement increases even further. > >>> I'm currently using PyMOL to batch process a number of files where a > >>> structure is loaded, modified and then deleted again from the objects > >>> list. This then results in RAM requirements of over 1GB and together > >>> with other applications, I run out of memory. > >>> Is there a way I can prevent PyMOL from behaving this way? > >>> > >>> Best regards and thanks for any help > >>> Martin > > -- > Jason Vertrees, PhD > Director of Core Modeling Product Management > Schrödinger, Inc. > > (e) Jas...@sc... > (o) +1 (603) 374-7120 -- Thomas Holder PyMOL Developer Schrödinger Contractor |
From: Martin H. <ma...@bl...> - 2012-12-22 16:14:04
|
Hi Thomas, thanks for the feedback. I would like to point out that I observe this with version PyMOL 1.3 (also Hybrid), where, correct me if I'm wrong, there is no undo feature available (at least I have never used or seen it here). To me this would mean, the problem has to be with something else (possibly in addition to undo). To perfectly reproduce my situation, you can run the script that I posted on pastebin (http://pastebin.com/mC6Rs6wk). Let me know if you need some guidance with all the variables, I'm sorry for the terrible code. I can also send you the PDB file I used when I got into this problem, then you dont need to adjust any variables. Best regards Martin On 21.12.12 17:31, Thomas Holder wrote: > Hi Gianluigi and Martin, > > thanks for reporting, this is a serious issue and we are looking into it. > > As far as we can reproduce, it's related to the undo feature. Adding this to your scripts should help: > > cmd.set("suspend_undo", 1) > > Cheers, > Thomas > > On Dec 21, 2012, at 9:53 AM, Gianluigi Caltabiano <chi...@ya...> wrote: > >> I have the same problem since pymol 1.5, mainly with the hybrid (I can reach 10GB of ram memory with relatively small sessions). I'm on MAC OS 10.7.5 and pymol version 1.5.0.3. >> I had to renounce working with Hybrid unless I really need some plug-in. >> >> Gianluigi >> >> >> Da: Jason Vertrees <jas...@sc...> >> A: Martin Hediger <ma...@bl...> >> Cc: "pym...@li..." <pym...@li...> >> Inviato: Giovedì 20 Dicembre 2012 17:05 >> Oggetto: Re: [PyMOL] Memory not released after load and delete of structure >> >> Martin, >> >> That sounds like a memory leak in v1.3. Can you try a newer version of >> PyMOL and let us know if it still happens? We've fixed lots of bugs >> since v1.3. >> >> Also, is your script simply iterating over structures and deleting >> them when done? You sure you're not missing a cleanup step somewhere? >> (Any chance we can see the script or a stub of it?) >> >> Cheers, >> >> -- Jason >> >> On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger <ma...@bl...> wrote: >>> Hi Jason, >>> I'm using PyMOL 1.3. >>> >>> Best regards >>> Martin >>> >>> >>> >>> On 20.12.12 15:53, Jason Vertrees wrote: >>>> Hi Martin, >>>> >>>> Which version of PyMOL are you using? >>>> >>>> Cheers, >>>> >>>> -- Jason >>>> >>>> On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger <ma...@bl...> wrote: >>>>> Dear PyMOL users >>>>> In a directory are PDB files of combined size equal to around 3MB. When >>>>> I load all files into PyMOL, I observe that the required RAM of PyMOL >>>>> (MacOS X 10.6) increases by roughly this amount. >>>>> When I delete all objects, the RAM requirement remains the same and when >>>>> I then reload all structures, the RAM requirement increases even further. >>>>> I'm currently using PyMOL to batch process a number of files where a >>>>> structure is loaded, modified and then deleted again from the objects >>>>> list. This then results in RAM requirements of over 1GB and together >>>>> with other applications, I run out of memory. >>>>> Is there a way I can prevent PyMOL from behaving this way? >>>>> >>>>> Best regards and thanks for any help >>>>> Martin >> -- >> Jason Vertrees, PhD >> Director of Core Modeling Product Management >> Schrödinger, Inc. >> >> (e) Jas...@sc... >> (o) +1 (603) 374-7120 |
From: Gianluigi C. <chi...@ya...> - 2013-01-21 16:41:24
|
The suspension of undo doesn't have any effect on my accumulation of GB when working with Hybrid PyMol... Gianluigi ________________________________ Da: Thomas Holder <tho...@sc...> A: pym...@li... Inviato: Venerdì 21 Dicembre 2012 17:31 Oggetto: Re: [PyMOL] Memory not released after load and delete of structure Hi Gianluigi and Martin, thanks for reporting, this is a serious issue and we are looking into it. As far as we can reproduce, it's related to the undo feature. Adding this to your scripts should help: cmd.set("suspend_undo", 1) Cheers, Thomas On Dec 21, 2012, at 9:53 AM, Gianluigi Caltabiano <chi...@ya...> wrote: > I have the same problem since pymol 1.5, mainly with the hybrid (I can reach 10GB of ram memory with relatively small sessions). I'm on MAC OS 10.7.5 and pymol version 1.5.0.3. > I had to renounce working with Hybrid unless I really need some plug-in. > > Gianluigi > > > Da: Jason Vertrees <jas...@sc...> > A: Martin Hediger <ma...@bl...> > Cc: "pym...@li..." <pym...@li...> > Inviato: Giovedì 20 Dicembre 2012 17:05 > Oggetto: Re: [PyMOL] Memory not released after load and delete of structure > > Martin, > > That sounds like a memory leak in v1.3. Can you try a newer version of > PyMOL and let us know if it still happens? We've fixed lots of bugs > since v1.3. > > Also, is your script simply iterating over structures and deleting > them when done? You sure you're not missing a cleanup step somewhere? > (Any chance we can see the script or a stub of it?) > > Cheers, > > -- Jason > > On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger <ma...@bl...> wrote: > > Hi Jason, > > I'm using PyMOL 1.3. > > > > Best regards > > Martin > > > > > > > > On 20.12.12 15:53, Jason Vertrees wrote: > >> > >> Hi Martin, > >> > >> Which version of PyMOL are you using? > >> > >> Cheers, > >> > >> -- Jason > >> > >> On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger <ma...@bl...> wrote: > >>> > >>> Dear PyMOL users > >>> In a directory are PDB files of combined size equal to around 3MB. When > >>> I load all files into PyMOL, I observe that the required RAM of PyMOL > >>> (MacOS X 10.6) increases by roughly this amount. > >>> When I delete all objects, the RAM requirement remains the same and when > >>> I then reload all structures, the RAM requirement increases even further. > >>> I'm currently using PyMOL to batch process a number of files where a > >>> structure is loaded, modified and then deleted again from the objects > >>> list. This then results in RAM requirements of over 1GB and together > >>> with other applications, I run out of memory. > >>> Is there a way I can prevent PyMOL from behaving this way? > >>> > >>> Best regards and thanks for any help > >>> Martin > > -- > Jason Vertrees, PhD > Director of Core Modeling Product Management > Schrödinger, Inc. > > (e) Jas...@sc... > (o) +1 (603) 374-7120 -- Thomas Holder PyMOL Developer Schrödinger Contractor ------------------------------------------------------------------------------ LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d _______________________________________________ PyMOL-users mailing list (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |