- Chimera-users - RBVI Mailing Lists

measure rotation command questions
by Joseph Atherton 15 Aug '16

15 Aug '16

Hi, When I use the command 'measure rotation' I get a matrix in the reply log. 1) The fourth column is 'translation'. At most the translation I see is 5 Angstrom, so how do I get these numbers (see below)? I also have a shift along axis reported, which seems a more reasonable number, but what if the shift is in a a different vector to the axis? 2) I can get depiction of the rotation axis, but can I also get a depiction of the translation vector? Cheers, Joe Position of model2 (#20) relative to model1.pdb (#1) coordinates: Matrix rotation and translation 0.98820614 -0.14982292 -0.03165001 43.44553134 0.14930460 0.98862441 -0.01816347 -23.90940685 0.03401127 0.01322376 0.99933396 -9.65968865 Axis 0.10195507 -0.21328736 0.97165512 Axis point 180.93496764 275.63881775 0.00000000 Rotation angle (degrees) 8.85455905 Shift along axis 0.14318049

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chimera crashing upon opening of trajectory
by Natesh Singh 12 Aug '16

12 Aug '16

Dear Sir/Madam, I am unable to open a trajectory (50 ns and about 25 gb size) in a chimera GUI. I am getting a python crash error after some time of initial message of 'reading PDB...' and then chimera shuts down. Is it the large file size that is causing the python to crash? Looking forward for the guidance. Best regards, Natesh

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Re: [Chimera-users] Selecting specific atoms in MD Movie
by Thomas Faour (x2013gua) 12 Aug '16

12 Aug '16

Hi Elaine, I thought about sending the data but was hoping there was an easy solution to something I was doing wrong... Which there was! Using :52.water worked perfectly. Thanks a ton! Thomas On Aug 12, 2016 14:49, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: Hi Thomas, It's difficult to answer questions like this without the data... I only have one low-confidence guess, which is to try :52.water instead of :52 ...as mentioned in the "subcategories" section of <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> If that doesn't work, you would have to send us the data (or a smaller sample, if possible). You could send it to just me if you don't want to send to the whole list. 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 11, 2016, at 4:46 PM, Thomas Faour (x2013gua) <x2013gua(a)stfx.ca> wrote: > Hello there, > > I study water/ice systems and I have an algorithm which reads my trajectories and tell me if a certain water molecule can be considered "liquid", "hexagonal ice" or "cubic ice". So I can label each molecule at each frame as such. I am hoping to be able to use this data to create a movie where each group is coloured differently, and should a molecule change groups be re-coloured accordingly. > > I attempted this by running a PER-FRAME script which reads my labels from a data file, and colours the molecules. However I ran into a problem, running either of the following commands: > > colour blue,a :52 > select :52 > > in the PER-FRAME script, or even just on the command line during an MD Movie does NOT work for me. This works for a single configuration file, but not during a movie. The command: > > color blue,a @OW > > however does work. I am currently using XTC trajectories, in case that is relevant. > > What might fix my problem? Or is there a better way I could be doing this? > Cheers, > Thomas

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Selecting specific atoms in MD Movie
by Thomas Faour (x2013gua) 12 Aug '16

12 Aug '16

Hello there, I study water/ice systems and I have an algorithm which reads my trajectories and tell me if a certain water molecule can be considered "liquid", "hexagonal ice" or "cubic ice". So I can label each molecule at each frame as such. I am hoping to be able to use this data to create a movie where each group is coloured differently, and should a molecule change groups be re-coloured accordingly. I attempted this by running a PER-FRAME script which reads my labels from a data file, and colours the molecules. However I ran into a problem, running either of the following commands: colour blue,a :52 select :52 in the PER-FRAME script, or even just on the command line during an MD Movie does NOT work for me. This works for a single configuration file, but not during a movie. The command: color blue,a @OW however does work. I am currently using XTC trajectories, in case that is relevant. What might fix my problem? Or is there a better way I could be doing this? Cheers, Thomas

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APBS mobile ion option
by Eita Sasaki 12 Aug '16

12 Aug '16

Hi, I'd like to run APBS command with mobile ions (150 mM NaCl). I tried the following command, but it did not work. apbs molecule #1 ion true _posion 1,0.15,1.16 _negion -1,0.15,1.67 If I typed just "apbs molecule #1" it works (without mobile ions). I am wondering my command was perhaps wrong but don't know the right one. I hope you could help me to solve the problem Thank you in advance. Eita

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(no subject)
by Karel W. F. de Pourcq 09 Aug '16

09 Aug '16

Dear Chimera team: I am a student of a Msc. in Bioinformatics at the Autonomous University of Barcelona. I am using Chimera to prepare visual representations of molecular events, and I write in order to ask if there is a straightforward way in which to: a) Create a sphere of a certain diameter: Yes, I found how to do it already: with the "shape" command. This is solved. b) In an orderly and distributed way, cover that sphere with a number of copies of a molecule chain, anchored over the sphere's surface by one of their ends (and the other end of the molecule protruding towards the outside). I believe I could do it manually for a small system. Is there some kind or automated and more convenient way to do this for a large sphere, linking its surface with hundreds of molecules of -for instance- dodecane? I could not find explicitly a way to do something similar to what I am trying to do. I attach an image of a 2-d representation of something similar to what I would like to represent. The difference is that I would like to cover the surface. [image: Imágenes integradas 1] I thank you a lot in advance for your time. Kind greetings from Barcelona, Spain, Karel De Pourcq

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chimera minimize script
by Bylund, Tatsiana (NIH/NIAID) [F] 09 Aug '16

09 Aug '16

Dear all, I need to minimize a lot of protein complexes and am trying to do it with a script. I have a protein complex structure without Hydrogens, but when they are added in Chimera, it outputs error Non-standard atom names: ASN HA2 (:33.K@HA2) ASN HA3 (:33.K@HA3) Total charge for #0: 32.039 Total charge for #0: 32.039 The following residues had non-integral charges: :33.K 0.039 Correct charges are unknown for 2 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log Dock prep finished Error while processing chimera_mini.py: No MMTK name for atom "HA3" in standard residue "ASN" When I delete residue K 33 (which DOES NOT have H in pub file) chimera runs minimization. Would you have any suggestions? Thank you! Kind regards, Tatsiana

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UCSF
by Amali Guruge 05 Aug '16

05 Aug '16

Dear All, What is UCSF referring to? Is it University of California San Francisco ? Thank you.

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Volume and mesh data simultaneously? Coordinate space is different
by Marvin Albert 03 Aug '16

03 Aug '16

Hi all, I process 3d objects and want to visualise them as meshes and volumes simultaneously. However, when I load them into chimera the coordinates of the two are different (meaning they don’t overlap). Is there an obvious reason for this? Would the volume viewer show a .tif file with different coordinates than chimera shows the .wrl mesh? (this tiny cube exemplifies my problem: http://www.filedropper.com/cube_3 <http://www.filedropper.com/cube_3>) Thanks a lot in advance, Marvin

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precalculated void representation as surface
by Michalska, Karolina M. 03 Aug '16

03 Aug '16

Hi, I have a precalculated cavity represented as a grid in the pdb format, where “atoms” are spaced by 0.3 A. What would be the option to visualize this as a surface? I can easily show it as point or spheres, but I cannot display it as surface. I appreciate your help, Karolina

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