Re: [PyMOL] Transparency of VASCo surfaces
Hi Gianluigi, that surface is a CGO object, so you need: set cgo_transparency, value, object Hope that helps. Cheers, Thomas Gianluigi Caltabiano wrote, On 04/22/13 18:49: Hi all, I often use VASCo surfaces and I am experiencing a strange behaviour on transparency settings as VASCo surfaces do not respond to: set transparency, value, object Not from the command line, not from the plugin itself. Pymol's surfaces get transparent but not the object corresponding to VASCo surface. I am not sure but I would say it worked to me before. I am on pymol 1.5.0.3 on a Macbook pro 2011 (Pymol Hybrid). Am I missing something? thanks and regards Gianluigi -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ 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] Visualization of the protein-ligand interactions
Dear Pymol users! I want to examine protein-ligand interactions observed in the md trajectory using Pymol. For such task I have 100 snapshots of the protein-ligand complex which I've loaded into the pymol. Now I want to extract from all snapshots 100 ligands as the separate 100 objects and save it in the mol2. Actually I can do such task in the simplest way extracting all ligands in one object but I need as a result 100 mol2 files. Could someone show me example of some script which could do such tasks? Also I'll be very thankful if someone can provide me with some tool which can be used for investigation of the ligand dynamics along MD trajectory ( in particular I want to visualize all binding poses and define all polar contacts along trajectory). For such task I've being used pymol as well as pose view loading snapshots to that programs but that way is not appropriate for analyzing of the ensembles of the binding poses obtained from md run. Thanks for help, James -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ 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] SS in a trajectory
Hi, I have a trajectory file, in which two short helices would merge into one long helix. However, when I play the trajectory in Pymol as cartoon, the long helix would still be shown as two helices with a loop in between. Is there a way to force Pymol to show a long helix for a specific range of frames in a trajectory? Thanks a lot. --Jianghai -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ 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] Visualization of the protein-ligand interactions
I want to examine protein-ligand interactions observed in the md trajectory using Pymol. For such task I have 100 snapshots of the protein-ligand complex which I've loaded into the pymol. Now I want to extract from all snapshots 100 ligands as the separate 100 objects and save it in the mol2. Actually I can do such task in the simplest way extracting all ligands in one object but I need as a result 100 mol2 files. Could someone show me example of some script which could do such tasks? Save all ligands in a multi-mol mol2 file and then split if with fconv -s. http://pc1664.pharmazie.uni-marburg.de/download/fconv Also I'll be very thankful if someone can provide me with some tool which can be used for investigation of the ligand dynamics along MD trajectory ( in particular I want to visualize all binding poses and define all polar contacts along trajectory). For such task I've being used pymol as well as pose view loading snapshots to that programs but that way is not appropriate for analyzing of the ensembles of the binding poses obtained from md run. I usually monitor H-bonds with g_hbond from GROMACS Tools and Salt-Bridges with the respective VMD plugin. Then I make a table with frequences of each polar interaction, pick up a frame that contains as many important interactions as possible, load it in PyMOL and draw dotted lines between the interacting atoms. PS: I didn't know about PoseView plugin, it seems to be a very useful addition to PyMOL :) Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ 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] Visualization of the protein-ligand interactions
Thomas, thanks for help! As I understood fconv can be used for the split several mol2 (or pdb) files which was placed in 1 model to the several pdb files, doesnt it ? In past I forced with some problems with g_hbond. Is there any other way to monitor h bonds along the trajectory (e.g in vmd) ? PoseView is used as the separate software or web server http://poseview.zbh.uni-hamburg.de/poseview ( I mean that I analyze polar interactions both in pymol as well as via pose view). James 2013/4/24 Thomas Evangelidis teva...@gmail.com I want to examine protein-ligand interactions observed in the md trajectory using Pymol. For such task I have 100 snapshots of the protein-ligand complex which I've loaded into the pymol. Now I want to extract from all snapshots 100 ligands as the separate 100 objects and save it in the mol2. Actually I can do such task in the simplest way extracting all ligands in one object but I need as a result 100 mol2 files. Could someone show me example of some script which could do such tasks? Save all ligands in a multi-mol mol2 file and then split if with fconv -s. http://pc1664.pharmazie.uni-marburg.de/download/fconv Also I'll be very thankful if someone can provide me with some tool which can be used for investigation of the ligand dynamics along MD trajectory ( in particular I want to visualize all binding poses and define all polar contacts along trajectory). For such task I've being used pymol as well as pose view loading snapshots to that programs but that way is not appropriate for analyzing of the ensembles of the binding poses obtained from md run. I usually monitor H-bonds with g_hbond from GROMACS Tools and Salt-Bridges with the respective VMD plugin. Then I make a table with frequences of each polar interaction, pick up a frame that contains as many important interactions as possible, load it in PyMOL and draw dotted lines between the interacting atoms. PS: I didn't know about PoseView plugin, it seems to be a very useful addition to PyMOL :) Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ 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 -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ 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] Fwd: Visualization of the protein-ligand interactions
As I understood fconv can be used for the split several mol2 (or pdb) files which was placed in 1 model to the several pdb files, doesnt it ? fconv can do miracles :) check it out ! fconv -h In past I forced with some problems with g_hbond. Is there any other way to monitor h bonds along the trajectory (e.g in vmd) ? In contrast, I encountered problems with the H-bonds VMD plugin, that's why I resorted to g_hbond. Beware that g_hbonds will count the frequencies of salt-bridges too. PoseView is used as the separate software or web server http://poseview.zbh.uni-hamburg.de/poseview ( I mean that I analyze polar interactions both in pymol as well as via pose view). If you find a way to draw the most important protein-ligand interactions throughout the trajectory with PoseView, then I would be very interested to know how. James 2013/4/24 Thomas Evangelidis teva...@gmail.com I want to examine protein-ligand interactions observed in the md trajectory using Pymol. For such task I have 100 snapshots of the protein-ligand complex which I've loaded into the pymol. Now I want to extract from all snapshots 100 ligands as the separate 100 objects and save it in the mol2. Actually I can do such task in the simplest way extracting all ligands in one object but I need as a result 100 mol2 files. Could someone show me example of some script which could do such tasks? Save all ligands in a multi-mol mol2 file and then split if with fconv -s. http://pc1664.pharmazie.uni-marburg.de/download/fconv Also I'll be very thankful if someone can provide me with some tool which can be used for investigation of the ligand dynamics along MD trajectory ( in particular I want to visualize all binding poses and define all polar contacts along trajectory). For such task I've being used pymol as well as pose view loading snapshots to that programs but that way is not appropriate for analyzing of the ensembles of the binding poses obtained from md run. I usually monitor H-bonds with g_hbond from GROMACS Tools and Salt-Bridges with the respective VMD plugin. Then I make a table with frequences of each polar interaction, pick up a frame that contains as many important interactions as possible, load it in PyMOL and draw dotted lines between the interacting atoms. PS: I didn't know about PoseView plugin, it seems to be a very useful addition to PyMOL :) Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ 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] sculpt settings
Where I can find documentation about the exact meaning of all the settings related to the sculpt function? In particular what the sculpt_field_mask setting does? I am trying to sculpt the sidechaiin of a particular residue while protecting the rest of the structure. Which are the bet parameters to try to move the sidechain while avoiding clashes/bumps? Thanks. -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ 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] SS in a trajectory
If none suggests a solution in PyMOL ten use sscache.tcl script in VMD to update the SS at every frame. Thomas On 24 April 2013 17:31, Jianghai Zhu j...@idi.harvard.edu wrote: Hi, I have a trajectory file, in which two short helices would merge into one long helix. However, when I play the trajectory in Pymol as cartoon, the long helix would still be shown as two helices with a loop in between. Is there a way to force Pymol to show a long helix for a specific range of frames in a trajectory? Thanks a lot. --Jianghai -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ 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 -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ 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] SS in a trajectory
Hi, On Wed, 2013-04-24 10:31 EDT, Jianghai Zhu j...@idi.harvard.edu wrote: Hi, I have a trajectory file, in which two short helices would merge into one long helix. However, when I play the trajectory in Pymol as cartoon, the long helix would still be shown as two helices with a loop in between. Is there a way to force Pymol to show a long helix for a specific range of frames in a trajectory? Thanks a lot. When you load the trajectory, use the discrete flag to have PyMOL computer the secondary structure for each state . load trajectory.pdb, discrete=1 I'm assuming you are loading a multi-model .PDB file as the trajectory. If you are using the load_traj command to load an AMBER trajectory, there is no similar option. 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 -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ 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] Fwd: Visualization of the protein-ligand interactions
Thomas, actually I used very routine way. Firstly I've extract conformers of protein-ligand complexes from the trajectory. Than I've loaded it into pymol and visualize possible interactions. Than I've selected most representative conformers and loaded it separately into pose view to obtain 2D maps. I understand that its very routine but I had not any other alternatives. By the way during usage of the g_hbond with the below flags g_hbond -f fitted.trr -s complex.gro -n index.ndx -hbm ./hb/hbmap.xpm -life ./hb/hblife.xvg In the index file I've specified ligand and protein as two groups. should I define second group more accurately ( e.g only possible amino acids from the ligand binding pocket) ? I've forced with the problem of the interpretation of the hbmap. As I understood that could be used for the monitoring of the h-bond occurring and breaking between protein and ligand during MD run. How it could be visualize to observe particular amino-acids on the first (protein) group which contribute to H-bonds ? James 2013/4/24 Thomas Evangelidis teva...@gmail.com As I understood fconv can be used for the split several mol2 (or pdb) files which was placed in 1 model to the several pdb files, doesnt it ? fconv can do miracles :) check it out ! fconv -h In past I forced with some problems with g_hbond. Is there any other way to monitor h bonds along the trajectory (e.g in vmd) ? In contrast, I encountered problems with the H-bonds VMD plugin, that's why I resorted to g_hbond. Beware that g_hbonds will count the frequencies of salt-bridges too. PoseView is used as the separate software or web server http://poseview.zbh.uni-hamburg.de/poseview ( I mean that I analyze polar interactions both in pymol as well as via pose view). If you find a way to draw the most important protein-ligand interactions throughout the trajectory with PoseView, then I would be very interested to know how. James 2013/4/24 Thomas Evangelidis teva...@gmail.com I want to examine protein-ligand interactions observed in the md trajectory using Pymol. For such task I have 100 snapshots of the protein-ligand complex which I've loaded into the pymol. Now I want to extract from all snapshots 100 ligands as the separate 100 objects and save it in the mol2. Actually I can do such task in the simplest way extracting all ligands in one object but I need as a result 100 mol2 files. Could someone show me example of some script which could do such tasks? Save all ligands in a multi-mol mol2 file and then split if with fconv -s. http://pc1664.pharmazie.uni-marburg.de/download/fconv Also I'll be very thankful if someone can provide me with some tool which can be used for investigation of the ligand dynamics along MD trajectory ( in particular I want to visualize all binding poses and define all polar contacts along trajectory). For such task I've being used pymol as well as pose view loading snapshots to that programs but that way is not appropriate for analyzing of the ensembles of the binding poses obtained from md run. I usually monitor H-bonds with g_hbond from GROMACS Tools and Salt-Bridges with the respective VMD plugin. Then I make a table with frequences of each polar interaction, pick up a frame that contains as many important interactions as possible, load it in PyMOL and draw dotted lines between the interacting atoms. PS: I didn't know about PoseView plugin, it seems to be a very useful addition to PyMOL :) Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ 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 -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt!
