tag:blogger.com,1999:blog-3599722177679860131.post8966776495701073272..comments2024-01-03T10:01:29.738+01:00Comments on Chemical Quantum Images: Molecular dynamics movieFelixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.comBlogger2125tag:blogger.com,1999:blog-3599722177679860131.post-8217488833446902332008-06-26T13:05:00.000+01:002008-06-26T13:05:00.000+01:00hi, actually what I start out with is a multi-reco...hi, actually what I start out with is a multi-record xyz. molden for example will read that but pymol only reads the first entry. but it's very convenient to just make a multiple sdf with babel<BR/><BR/>I think the frames are correct, something like 30 frames per second. one frame is 0.5 fs in the simulation. so you have it slowed down by about 10^14. google changed the resolution I think, but I don't know if that should be a problemFelixhttps://www.blogger.com/profile/05138335803929997277noreply@blogger.comtag:blogger.com,1999:blog-3599722177679860131.post-50132929019975916142008-06-26T12:45:00.000+01:002008-06-26T12:45:00.000+01:00SDF are multi-record files and Pymol handles them ...SDF are multi-record files and Pymol handles them by loading every molecule record into a separate state. You can also make yourself a trajectory file without using open babel. PDB also can have multiple records. Assuming you have some single-record files (let's say XYZ) like this:<I><BR/>molecule001.xyz<BR/>molecule002.xyz<BR/>...<BR/>molecule100.xyz</I><BR/>that are located in <I>/some/path/to/a/directory</I><BR/>Now you simply go from the Pymol console to that directory<BR/><B>cd /some/path/to/a/directory</B><BR/>and then load every file into the same object but specifying different states. This can be done by hand, but for many files it's better to use a loop like this (single line):<BR/><B>for idx in range(1,100):cmd.load("molecule%03d.xyz"%idx,"molecule")</B><BR/>Now you have a multi-record object to make a movie. If you wish you can save it also on the disk, by overriding de default settings:<BR/><B>save multirecord.pdb, (all), state=-1</B><BR/><BR/>PS. Nice movie, but it's a bit hypnotic - I watched it about 3-4 times and still can't get enough ]:) You really got here the right frames per second settings.Lightnirhttps://www.blogger.com/profile/16789348893952913132noreply@blogger.com