Re: [PyMOL] choice of color in util.cbc
Hi Charles, The `first_color` argument is only active with `legacy=1`. util.cbc 6uwz, first_color=1, legacy=1 Other options for coloring by chain: spectrum chain, rainbow, 6uwz spectrum chain, blue green red yellow, 6uwz Hope that helps. Cheers, Thomas > On Jul 14, 2020, at 7:18 PM, Chen, Qiang wrote: > > Hi, Pymol Users > > Is it possible to choose different color pattern when using util.cbc? > > Wiki says I could use the following to choose the first_color > > util.cbc 6uwz, first_color=1, quiet=0 > > 6uwz is just an example of a pentameric protein. > > However, there is no change when specify any other number for first_color. It > always starts with cyan on the first chain. > > I know I can color the chain individually. I am just puzzled that util.cbc > behaves this way. > > I am using open-source pymol2.5.0a0 running on windows 10. > > Thanks! > > Charles > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Reading Cell Dimensions from GROMACS XTC file
Hi Dan, Showing different cells for each state is currently not implemented, but I think it would not be too difficult to add support for that. I've opened a feature request ticket: https://github.com/schrodinger/pymol-open-source/issues/114 Cheers, Thomas > On Jul 13, 2020, at 4:20 PM, Daniel Kozuch wrote: > > Hello, > > I would like to load a GROMACS xtc trajectory and visualize the (changing) > cell size. > > My current workflow is: > > load sim.pdb > load_traj sim.xtc, sim > show cell > > This shows a cell/box but it is the wrong size and does not update every > frame. Is there some way to load the proper cell dimensions? > > Best regards, > Dan Kozuch > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] choice of color in util.cbc
Thanks! This works well. "Spectrum chain" is more flexible and powerful in this case. Charles From: Thomas Holder Sent: Tuesday, July 14, 2020 2:24 PM To: Chen, Qiang Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] choice of color in util.cbc Hi Charles, The `first_color` argument is only active with `legacy=1`. util.cbc 6uwz, first_color=1, legacy=1 Other options for coloring by chain: spectrum chain, rainbow, 6uwz spectrum chain, blue green red yellow, 6uwz Hope that helps. Cheers, Thomas > On Jul 14, 2020, at 7:18 PM, Chen, Qiang wrote: > > Hi, Pymol Users > > Is it possible to choose different color pattern when using util.cbc? > > Wiki says I could use the following to choose the first_color > > util.cbc 6uwz, first_color=1, quiet=0 > > 6uwz is just an example of a pentameric protein. > > However, there is no change when specify any other number for first_color. It > always starts with cyan on the first chain. > > I know I can color the chain individually. I am just puzzled that util.cbc > behaves this way. > > I am using open-source pymol2.5.0a0 running on windows 10. > > Thanks! > > Charles > ___ > PyMOL-users mailing list > Archives: > https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.netdata=02%7C01%7Cqic8%40pitt.edu%7C7fa17ea9f1c74b8091a208d828232bad%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637303478808757916sdata=4LxB2rIRWc%2F46YtcoayR7%2Bg48nlegyee7IVfjGGKdnc%3Dreserved=0 > Unsubscribe: > https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribedata=02%7C01%7Cqic8%40pitt.edu%7C7fa17ea9f1c74b8091a208d828232bad%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637303478808757916sdata=tcPJS4ItBU%2BMofo9oscHVA%2FhTOE4%2FN%2FpUD5ehSbzXIU%3Dreserved=0 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] choice of color in util.cbc
Hi, Pymol Users Is it possible to choose different color pattern when using util.cbc? Wiki says I could use the following to choose the first_color util.cbc 6uwz, first_color=1, quiet=0 6uwz is just an example of a pentameric protein. However, there is no change when specify any other number for first_color. It always starts with cyan on the first chain. I know I can color the chain individually. I am just puzzled that util.cbc behaves this way. I am using open-source pymol2.5.0a0 running on windows 10. Thanks! Charles ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] Pymol Will Not Open PDBs on a New HDD
Hi, I recently moved my documents to a new hard drive disk. Interestingly, Pymol will not open any pdb's in the new location. When the same file was moved outside the new disk the problem goes away. Other visualization programs, e.g. Chimera, work fine. I'm working on Ubunut 20.04, and I'm using Pymol 2.41. The error I get is not specific: Error: failed to open file "/folder_directory/name.pdb Error: Argument processing aborted due to exception (above). Any ideas what's happening? --Mike ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
