From: Marcus C. <ma...@bi...> - 2005-11-01 16:10:16
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Hello all, The surface rendering in PyMOL is quite nice, but I cannot separate the "branches" of the surface. That is, I would like to view a large cavity inside of a protein independently from the outer, solvent accessible surface. Is anyone aware of a means to do this? Marcus Collins ***************************************************************************** Marcus D. Collins Gruner Biophysics Group, Cornell University Dept. of Physics, LASSP (h) 607.347.4720 (w) 607.255.8678 (c) 607.351.8650 "You have opened a new door, and I share this with you, for I have been where you are now." ***************************************************************************** |
From: Peter A. M. <pa...@co...> - 2005-11-01 17:37:42
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Hi Marcus, > The surface rendering in PyMOL is quite nice, but I cannot separate the > "branches" of the surface. That is, I would like to view a large cavity > inside of a protein independently from the outer, solvent accessible > surface. Is anyone aware of a means to do this? The easiest way I'm aware of is to select the residues involved on the surface of your cavity, and then do show surface, [selection]. Pete Pete Meyer Fu Lab BMCB grad student Cornell University |
From: <gre...@un...> - 2005-11-02 06:45:27
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Have you tried to simply use your mouse wheel? This will change the clipping view. |
From: Eric Z. <zo...@ca...> - 2005-11-02 19:41:03
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Marcus, Here is one way (courtesy Kyle Lassila): Check out VOIDOO: http://xray.bmc.uu.se/usf/voidoo.html Then: Use VOIDOO to make a map of the cavity. That gives a map in one of the electron density formats, .ezd. Then use MAPMAN (also found as Uppsala Software Factory) to convert to .ccp4 so that pymol can read it. Load the map with "load filename.ccp4". View the map with "isomesh msh1,filename,1.0" mapman input file: RE m1 cavity_1.ezd NEWEZD WR m1 cavity_1.ccp4 CCP4 QU sample voidoo input file: c n voidoo_etc/cavity.lib design.pdb 0.75 1.2 20 1.05 1 y 49.1 32.7 46.5 n cavity.log y 10 o 0.90 15 0.05 0.05 n y cavity 0.2 n Eric Marcus Collins wrote: > Hello all, > > The surface rendering in PyMOL is quite nice, but I cannot separate the > "branches" of the surface. That is, I would like to view a large cavity > inside of a protein independently from the outer, solvent accessible > surface. Is anyone aware of a means to do this? > > Marcus Collins > > ***************************************************************************** > > Marcus D. Collins > Gruner Biophysics Group, Cornell University Dept. of Physics, LASSP > (h) 607.347.4720 (w) 607.255.8678 (c) 607.351.8650 > "You have opened a new door, and I share this with you, > for I have been where you are now." > ***************************************************************************** > > > > ------------------------------------------------------- > SF.Net email is sponsored by: > Tame your development challenges with Apache's Geronimo App Server. > Download > it for free - -and be entered to win a 42" plasma tv or your very own > Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Sebastien M. <seb...@ig...> - 2005-11-03 07:49:10
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> Marcus, > Here is one way (courtesy Kyle Lassila): > Check out VOIDOO: > http://xray.bmc.uu.se/usf/voidoo.html >=20 > Then: > Use VOIDOO to make a map of the cavity. That gives a > map in one of the electron density formats, .ezd. Then use MAPMAN (als= o=20 > found as Uppsala Software Factory) to > convert to .ccp4 so that pymol can read it. >=20 > Load the map with "load filename.ccp4". > View the map with "isomesh msh1,filename,1.0" >=20 > mapman input file: > RE m1 cavity_1.ezd NEWEZD > WR m1 cavity_1.ccp4 CCP4 > QU >=20 > sample voidoo input file: > c > n > voidoo_etc/cavity.lib > design.pdb > 0.75 > 1.2 > 20 > 1.05 > 1 > y > 49.1 32.7 46.5 > n > cavity.log > y > 10 > o > 0.90 > 15 > 0.05 > 0.05 > n > y > cavity > 0.2 > n >=20 > Eric Hi Marcus, You can install the CASTp plugin for PyMOL : http://cast.engr.uic.edu/cast/?mode=3DCASTpyMOL CASTp (http://cast.engr.uic.edu/cast/) is "Computed Atlas of Surface=20 Topography of proteins" and analyzes the "Anatomy of Protein Pockets and=20 Cavities". So, with the plugin, you can get every cavities (pockets), CASTp has=20 predicted, automatically. I hope this will help you. >> Hello all, >> >> The surface rendering in PyMOL is quite nice, but I cannot separate=20 >> the "branches" of the surface. That is, I would like to view a large=20 >> cavity inside of a protein independently from the outer, solvent=20 >> accessible surface. Is anyone aware of a means to do this? >> >> Marcus Collins >> >> **********************************************************************= *******=20 >> >> Marcus D. Collins >> Gruner Biophysics Group, Cornell University Dept. of Physics, LAS= SP >> (h) 607.347.4720 (w) 607.255.8678 (c) 607.351.8650 >> "You have opened a new door, and I share this with you, >> for I have been where you are now." >> **********************************************************************= *******=20 --=20 S=E9bastien Moretti http://www.igs.cnrs-mrs.fr/ CNRS - IGS 31 chemin Joseph Aiguier 13402 Marseille cedex |
From: Bingding H. <bh...@bi...> - 2005-11-07 11:37:56
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Dear all, I download CASTpyMOL.pyc and put it in the right folder. Now I want to use it for detecting cavity for 50 proteins. I don't want to do that one after one by hand. Is it possible to write a python (pymol) script to do that automatically? Thanks a lot! Regards Bingding Sebastien Moretti wrote: Dear Bingding, CASTp cavities are pre-computed for most of PDB entries. So, you could create a PyMOL script (.pml) which could look like that: "call the CASTp plugin for xxxx" ? save xxxx.pdb reinitialize "call the CASTp plugin for yyyy" ? ... With this kind of script you could be able to get the cavities for your 50 proteins with only one PyMOL execution. Nevertheless, I don't know how to call the CASTp plugin from a PyMOL script. And how to save all cavities as distinct pdb files. But I know that that is possible. Only the PyMOL mailing list or Wiki are able to help you now. > > Hi Marcus, > You can install the CASTp plugin for PyMOL : > http://cast.engr.uic.edu/cast/?mode=CASTpyMOL > > CASTp (http://cast.engr.uic.edu/cast/) is "Computed Atlas of Surface > Topography of proteins" and analyzes the "Anatomy of Protein Pockets > and Cavities". > So, with the plugin, you can get every cavities (pockets), CASTp has > predicted, automatically. > > I hope this will help you. > >>> Hello all, >>> >>> The surface rendering in PyMOL is quite nice, but I cannot separate >>> the "branches" of the surface. That is, I would like to view a >>> large cavity inside of a protein independently from the outer, >>> solvent accessible surface. Is anyone aware of a means to do this? >>> >>> Marcus Collins >>> >>> ***************************************************************************** >>> >>> Marcus D. Collins >>> Gruner Biophysics Group, Cornell University Dept. of Physics, >>> LASSP >>> (h) 607.347.4720 (w) 607.255.8678 (c) 607.351.8650 >>> "You have opened a new door, and I share this with you, >>> for I have been where you are now." >>> ***************************************************************************** >> >> > -- Bingding Huang PhD student Bioinformatics group Biotec & Department of Computing Tazberg 47, 01307 TU Dresden, Germany Tel: 0049 351 46340064 (Office) Tel: 0049 351 4403368 (Home) Fax: 0049 351 46340061 Web: http://www.biotec.tu-dresden.de/~bhuang E-mail: bh...@bi... |
From: Andrea S. <and...@gm...> - 2005-11-07 23:29:38
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what about Caver: http://loschmidt.chemi.muni.cz/caver/concept.php very nice and it works very well andrea 2005/11/7, Bingding Huang <bh...@bi...>: > > Dear all, > > I download CASTpyMOL.pyc and put it in the right folder. > Now I want to use it for detecting cavity for 50 proteins. I don't want > to do that one after one by hand. > Is it possible to write a python (pymol) script to do that automatically? > > Thanks a lot! > > Regards > Bingding > > > > > > Sebastien Moretti wrote: > > Dear Bingding, > CASTp cavities are pre-computed for most of PDB entries. > > So, you could create a PyMOL script (.pml) which could look like that: > "call the CASTp plugin for xxxx" ? > save xxxx.pdb > reinitialize > "call the CASTp plugin for yyyy" ? > ... > > With this kind of script you could be able to get the cavities for your > 50 proteins with only one PyMOL execution. > Nevertheless, I don't know how to call the CASTp plugin from a PyMOL > script. And how to save all cavities as distinct pdb files. > But I know that that is possible. > > Only the PyMOL mailing list or Wiki are able to help you now. > > > > > > Hi Marcus, > > You can install the CASTp plugin for PyMOL : > > http://cast.engr.uic.edu/cast/?mode=3DCASTpyMOL > > > > CASTp (http://cast.engr.uic.edu/cast/) is "Computed Atlas of Surface > > Topography of proteins" and analyzes the "Anatomy of Protein Pockets > > and Cavities". > > So, with the plugin, you can get every cavities (pockets), CASTp has > > predicted, automatically. > > > > I hope this will help you. > > > >>> Hello all, > >>> > >>> The surface rendering in PyMOL is quite nice, but I cannot separate > >>> the "branches" of the surface. That is, I would like to view a > >>> large cavity inside of a protein independently from the outer, > >>> solvent accessible surface. Is anyone aware of a means to do this? > >>> > >>> Marcus Collins > >>> > >>> *********************************************************************= ******** > >>> > >>> Marcus D. Collins > >>> Gruner Biophysics Group, Cornell University Dept. of Physics, > >>> LASSP > >>> (h) 607.347.4720 (w) 607.255.8678 (c) 607.351.8650 > >>> "You have opened a new door, and I share this with you, > >>> for I have been where you are now." > >>> *********************************************************************= ******** > >> > >> > > > > > -- > Bingding Huang > PhD student > Bioinformatics group > Biotec & Department of Computing > Tazberg 47, 01307 > TU Dresden, Germany > > Tel: 0049 351 46340064 (Office) > Tel: 0049 351 4403368 (Home) > Fax: 0049 351 46340061 > Web: http://www.biotec.tu-dresden.de/~bhuang > E-mail: bh...@bi... > > > > ------------------------------------------------------- > SF.Net email is sponsored by: > Tame your development challenges with Apache's Geronimo App Server. Downl= oad > it for free - -and be entered to win a 42" plasma tv or your very own > Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- "La conoscenza libera il genere umano dalla superstizione" J. Watson |