[PyMOL] About draw_links.py by Dr. Robert Campbell
Hi, I have been trying to use the script draw_links.py at http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ to view links between each pair of c-alpha atoms present in an atom selection. Once I load a PDB (1q16.pdb) and make an atom selection, lets say : PyMOLselect pk1, name CA in resi 5+10+15+12+16 and chain C , on the command-line in pymol, I do : PyMOLrun draw_links.py I wanted to visualise links between all pairs of calpha atoms present in the atom selection, pk1. However I am unable to do that using draw_links.py I am doing: PyMOL draw_links pk1 How can I do this using draw_links.py? Where am I going wrong? - Anasuya Dighe -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ 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] About draw_links.py by Dr. Robert Campbell
Hi Anasuya, On Thu, 21 Feb 2013 17:10:40 +0530 Anasuya Dighe anas...@mbu.iisc.ernet.in wrote: Hi, I have been trying to use the script draw_links.py at http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ to view links between each pair of c-alpha atoms present in an atom selection. Once I load a PDB (1q16.pdb) and make an atom selection, lets say : PyMOLselect pk1, name CA in resi 5+10+15+12+16 and chain C , on the PyMOLcommand-line in pymol, I do : PyMOLrun draw_links.py I wanted to visualise links between all pairs of calpha atoms present in the atom selection, pk1. However I am unable to do that using draw_links.py I am doing: PyMOL draw_links pk1 How can I do this using draw_links.py? Where am I going wrong? Perhaps the instructions are not clear enough, but the script is not designed to automatically draw links between all pairs of C-alphas in a selection. It expects two different selections and it will draw links between the first residue of each selection and then the second and so on. It doesn't therefore make sense to give it the same selection for both because, in your example, it draws a zero-length link between residue 5 and residue 5, and another between residue 10 and residue 10 and so on. You will have to run the script multiple times to get the links you want: draw_links name CA resi 5 and chain C, name CA resi 10 and chain C draw_links name CA resi 5 and chain C, name CA resi 15 and chain C draw_links name CA resi 5 and chain C, name CA resi 12 and chain C Sorry that it doesn't quite do what you were expecting! I designed it for the situation where I have two structures that exhibit a conformational change and I wanted to show how the C-alphas were moving so then it made sense to have the two selections be the same atoms, but in different molecules. 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 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ 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] About draw_links.py by Dr. Robert Campbell
Hi, If you want to draw all bonds for all pairs between two selections, you can just use bond: bond sele and n. ca, sele and n. ca Hope it helps, Tsjerk On Thu, Feb 21, 2013 at 9:19 PM, Robert Campbell robert.campb...@queensu.ca wrote: Hi Anasuya, On Thu, 21 Feb 2013 17:10:40 +0530 Anasuya Dighe anas...@mbu.iisc.ernet.in wrote: Hi, I have been trying to use the script draw_links.py at http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ to view links between each pair of c-alpha atoms present in an atom selection. Once I load a PDB (1q16.pdb) and make an atom selection, lets say : PyMOLselect pk1, name CA in resi 5+10+15+12+16 and chain C , on the PyMOLcommand-line in pymol, I do : PyMOLrun draw_links.py I wanted to visualise links between all pairs of calpha atoms present in the atom selection, pk1. However I am unable to do that using draw_links.py I am doing: PyMOL draw_links pk1 How can I do this using draw_links.py? Where am I going wrong? Perhaps the instructions are not clear enough, but the script is not designed to automatically draw links between all pairs of C-alphas in a selection. It expects two different selections and it will draw links between the first residue of each selection and then the second and so on. It doesn't therefore make sense to give it the same selection for both because, in your example, it draws a zero-length link between residue 5 and residue 5, and another between residue 10 and residue 10 and so on. You will have to run the script multiple times to get the links you want: draw_links name CA resi 5 and chain C, name CA resi 10 and chain C draw_links name CA resi 5 and chain C, name CA resi 15 and chain C draw_links name CA resi 5 and chain C, name CA resi 12 and chain C Sorry that it doesn't quite do what you were expecting! I designed it for the situation where I have two structures that exhibit a conformational change and I wanted to show how the C-alphas were moving so then it made sense to have the two selections be the same atoms, but in different molecules. 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 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ 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] About draw_links.py by Dr. Robert Campbell
in the most recent version of PyMOL, which can render measurement objects with shaders, you can also use the distance command to get a similar result: set use_shaders set dash_gap, 0 distance sele and n. CA, sele and n. CA Cheers, Thomas On Feb 21, 2013, at 10:11 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi, If you want to draw all bonds for all pairs between two selections, you can just use bond: bond sele and n. ca, sele and n. ca Hope it helps, Tsjerk On Thu, Feb 21, 2013 at 9:19 PM, Robert Campbell robert.campb...@queensu.ca wrote: Hi Anasuya, On Thu, 21 Feb 2013 17:10:40 +0530 Anasuya Dighe anas...@mbu.iisc.ernet.in wrote: Hi, I have been trying to use the script draw_links.py at http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ to view links between each pair of c-alpha atoms present in an atom selection. Once I load a PDB (1q16.pdb) and make an atom selection, lets say : PyMOLselect pk1, name CA in resi 5+10+15+12+16 and chain C , on the PyMOLcommand-line in pymol, I do : PyMOLrun draw_links.py I wanted to visualise links between all pairs of calpha atoms present in the atom selection, pk1. However I am unable to do that using draw_links.py I am doing: PyMOL draw_links pk1 How can I do this using draw_links.py? Where am I going wrong? Perhaps the instructions are not clear enough, but the script is not designed to automatically draw links between all pairs of C-alphas in a selection. It expects two different selections and it will draw links between the first residue of each selection and then the second and so on. It doesn't therefore make sense to give it the same selection for both because, in your example, it draws a zero-length link between residue 5 and residue 5, and another between residue 10 and residue 10 and so on. You will have to run the script multiple times to get the links you want: draw_links name CA resi 5 and chain C, name CA resi 10 and chain C draw_links name CA resi 5 and chain C, name CA resi 15 and chain C draw_links name CA resi 5 and chain C, name CA resi 12 and chain C Sorry that it doesn't quite do what you were expecting! I designed it for the situation where I have two structures that exhibit a conformational change and I wanted to show how the C-alphas were moving so then it made sense to have the two selections be the same atoms, but in different molecules. Cheers, Rob -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ 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
