Hello! I'm using Chimera to view DFT optimizations and vibrational modes. I split the large xyz files into multiple small xyz files and load them with the MD tool. Now my question is: can I do the last step from the command line so I could write a script which sets the first and the last frames automatically? Also, is it possible to create the respective movie (as mpeg) in an automated fashion? Thank you, Thomas
Hi Thomas, You can use an MD Movie "metafile" to open your trajectory from the command line -- basically, it's a text file that has all the same info that would otherwise be entered into the MD Movie file input dialog. Contents of "example.meta" could be something like xyz startfile.xyz endfile.xyz and then you could open the trajectory with command: open md:example.meta See the description of metafiles under MD Movie startup and input: <http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie....> If by automatic you mean with a command script, you can use the "movie" command for recording, encoding, etc. and the "coordset" command to play through your trajectory during recording. <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html> <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#content> The "trmovie" example here includes creating a morph trajectory and recording playback of the trajectory. Of course, you wouldn't be doing the morphing part, but the playback and recording would be analogous: <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Aug 3, 2011, at 5:32 AM, Dr. techn. Thomas Mitterfellner wrote:
Hello! I'm using Chimera to view DFT optimizations and vibrational modes. I split the large xyz files into multiple small xyz files and load them with the MD tool.
Now my question is: can I do the last step from the command line so I could write a script which sets the first and the last frames automatically? Also, is it possible to create the respective movie (as mpeg) in an automated fashion? Thank you, Thomas
Hallo I wonder if there is a command in Chimera to show the statistics of the PDBFILE, i.e. number of oxygens, nitrogen atoms, number of rotamers, etc.. Thank you in advance Alex ---------------------------------------------------------------------- Alexander V. Shkumatov, Ph.D. Biological Small Angle Scattering Group EMBL Hamburg Outstation c/o DESY tel: +49 40 89902 178 Building 25A Notkestraße 85 fax: +49 40 89902 149 22603 Hamburg, Germany email: ashkumat@embl-hamburg.de ----------------------------------------------------------------------
Hi Alex, There is nothing exactly like that. However, you could just count oxygens, nitrogens, subsets of residues etc. by making a selection and seeing how many atoms or residues are selected. You could make a selection with commands, for example select O ...would select all oxygens select protein ...would select all protein select :trp ... would select all tryptophan residues or with the menu, for example Select... Chemistry... element... O Select... Structure... protein Select... Residue... TRP Then after something is selected, you could see contents of the selection (how many atoms and residues) by clicking the green magnifying glass near the bottom right corner of the Chimera window, or write a list of the selected atoms or residues to a file or to the Reply Log (Actions... Write List). The status line also reports the number of selected atoms, temporarily. If instead you meant small molecule descriptors (cheminformatics), Chimera does not calculate these for the most part, and other programs would be more suitable. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Aug 4, 2011, at 6:21 AM, Alex Shkumatov wrote:
Hallo I wonder if there is a command in Chimera to show the statistics of the PDBFILE, i.e. number of oxygens, nitrogen atoms, number of rotamers, etc.. Thank you in advance Alex
Hi Elaine That perfectly answers my question. Is there also a way to do selection such as select 0 AND not all waters AND not rotamers. Thank you for reply! Alex On 04.08.2011 18:14, Elaine Meng wrote:
You could make a selection with commands, for example select O ...would select all oxygens select protein ...would select all protein select :trp ... would select all tryptophan residues
or with the menu, for example Select... Chemistry... element... O Select... Structure... protein Select... Residue... TRP
Then after something is selected, you could see contents of the selection (how many atoms and residues) by clicking the green magnifying glass near the bottom right corner of the Chimera window, or write a list of the selected atoms or residues to a file or to the Reply Log (Actions... Write List). The status line also reports the number of selected atoms, temporarily.
-- ---------------------------------------------------------------------- Alexander V. Shkumatov, Ph.D. Biological Small Angle Scattering Group EMBL Hamburg Outstation c/o DESY tel: +49 40 89902 178 Building 25A Notkestraße 85 fax: +49 40 89902 149 22603 Hamburg, Germany email: ashkumat@embl-hamburg.de ----------------------------------------------------------------------
Hi Alex, I believe that the command and menu selection methods automatically omit the rotamers, so you if your waters are named HOH you could just use command sel #0 & ~:hoh I tested that by using the command before and after showing rotamers for some residue, and both gave the same number of atoms and bonds selected. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Aug 4, 2011, at 9:39 AM, Alex Shkumatov wrote:
Hi Elaine
That perfectly answers my question. Is there also a way to do selection such as select 0 AND not all waters AND not rotamers.
Thank you for reply! Alex
On 04.08.2011 18:14, Elaine Meng wrote:
You could make a selection with commands, for example select O ...would select all oxygens select protein ...would select all protein select :trp ... would select all tryptophan residues
or with the menu, for example Select... Chemistry... element... O Select... Structure... protein Select... Residue... TRP
Then after something is selected, you could see contents of the selection (how many atoms and residues) by clicking the green magnifying glass near the bottom right corner of the Chimera window, or write a list of the selected atoms or residues to a file or to the Reply Log (Actions... Write List). The status line also reports the number of selected atoms, temporarily.
participants (3)
-
Alex Shkumatov -
Dr. techn. Thomas Mitterfellner -
Elaine Meng