- Chimera-users - RBVI Mailing Lists

is the connection present?
by Dmitry 25 Aug '15

25 Aug '15

Dear Colleagues, I have 3d tetramer volume density where I fitted known x-ray structure of monomer (to each unit of tetramer). I want to check the inter-monomeric space, whether there is connections between 2 monomers. Is there a command or script that checks the presence of contacts between bounds of 2 structures? Thank you Sincerely, Dmitry

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Electrostatic Potential Visualization
by Chun, Minju 25 Aug '15

25 Aug '15

Hello, I am an intern working with Chimera, and I was wondering if I was missing a plug-in that calculated electrostatic potential. I attempted to load a dx and cube file to emulate electrostatic potential, but there seemed to be a problem finding/reading the files(perhaps I'm doing this wrong too). I thought that if I calculated electrostatic potential directly with Chimera, I could see electrostatic potential. It says on your website that Chimera can calculate the electrostatic potential with APBS: "electrostatic potential calculated with Adaptive Poisson-Boltzmann Solver<http://www.poissonboltzmann.org/apbs/> (APBS); the APBS<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html> tool in Chimera runs this program via web service provided by the NBCR<http://nbcr.ucsd.edu/>" Do you have a tutorial that goes in more detail in how to calculate potential with APBS? Thank you, Minju Chun

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Flattening of coloured icosahedron
by R.I.Koning＠lumc.nl 24 Aug '15

24 Aug '15

Is it possible to flatten a coloured icosahedron surface? I have an electron density of a virus, and using shape icosahedron and colour icosahedron surface and surface colour I can colour it according to this density. I would really like to generate a flattened icosahedron (compared to the flatten icosahedron command) from the coloured icosahedron surface. In order to get a 2D map of the colours. Is this possible somehow in Chimera? Is it otherwise possible to export the icosahedron with the coloured surfaces and try in another program (like Maya of Cinema4D?). Best regards, Roman Koning

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layering problem
by Joseph Atherton 20 Aug '15

20 Aug '15

Hi! I'm trying to make videos at the moment but I have a problem with layering, as in the model seems to be 'hiding' behind the density even when the density is transparent. This occurs when I set transparency also in the model, even at low transparency (e.g command #19:transparency 5,a,r #0:259-271). See the example attached- the left hand most part of the model, and the ADP is hidden when their transparency is non-zero. Can I prevent this? Cheers, Joe

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Re: [Chimera-users] [chimera-dev] distance measurements
by Elaine Meng 19 Aug '15

19 Aug '15

Hi Feixia! Yes, you could use Chimera to measure all lysine CA-CA distances in many structures, but it would require some scripting to loop through the structures, find the lysines, and do the measurements. There is some information on looping through structures and running Chimera commands here: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> Now, for each structure, you might imagine the script should first find all the lysines and then use the “distance" command on each pairwise combination, substituting in the proper residue numbers. However, there is an easier way with the “findclash” command. You can use it for multiple distance measurement in a single command. For example: open 2gbp findclash :lys@ca test self overlap -1000 log true … will measure all distances among lysine CA atoms in structure 2gbp and list results in the Reply Log (open from Favorites menu). The -1000 in the command says to measure the distance even if the atoms are “overlapping” by -1000 (more than 1000 angstroms apart). The last column in the results is the atom-atom distance, and they are given in order of increasing distance, in this case: 464 contacts atom1 atom2 overlap distance LYS 191.A CA LYS 189.A CA -1.802 5.562 LYS 227.A CA LYS 223.A CA -2.137 5.897 LYS 300.A CA LYS 246.A CA -2.800 6.560 LYS 169.A CA LYS 164.A CA -4.676 8.436 LYS 270.A CA LYS 276.A CA -4.677 8.437 [… several lines removed …] LYS 276.A CA LYS 203.A CA -53.705 57.465 LYS 276.A CA LYS 137.A CA -56.756 60.516 LYS 61.A CA LYS 137.A CA -56.829 60.589 LYS 58.A CA LYS 137.A CA -59.598 63.358 464 contacts The log contents can be saved to a text file, for example see <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003184.html> However, your log would have a huge amount of results for all structures and it might be hard to tell which results go with which structures, so another possibility would be to save a separate file of results for each structure, and in that case your script would need to substitute in an output filename, e.g. findclash :lys@ca test self overlap -1000 saveFile ~/Desktop/2gbp.log See findclash documentation for all the options. Then you can embed the command in the python looping script as described in the first link above. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> 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 18, 2015, at 8:36 AM, Feixia <feixia.chu(a)unh.edu> wrote: > Hi there, > I am interested in retrieving distance information from large dataset in an automatic fashion. For instance, can we use Chimera to get the distances between lysine alpha-carbons of current PDB entries. Presumably, we can download all PDB structures on our local desktop, and just call functions one structure at a time. I wonder if we can do that with Chimera. Your advice will be highly appreciated. > Best, > Feixia

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measure the vertical distance between aromatic planes
by Wang, Bing 19 Aug '15

19 Aug '15

Hi Chimera, Is there a way to measure the vertical distance of two planes in the structure? I do know how to measure the angle between two planes or one line and one plane by the Axes/Planes/Centroids in Chimera. I don't need the distance of two centroid of two planes. I do need the vertical distance of two planes. Could you please show me in detail? Thanks a lot! Bing Wang

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How to select a plane from the command line
by JUAN PABLO REYES VALVERDE 17 Aug '15

17 Aug '15

Dear UCSF Chimera Team: Please, I would much appreciate your advice on the following: First issue: Given a number of planes - calculated/created through the 'define' command - I would like to select one of them, with some command entered at the command line .... How can I do it? The reason why I want to select it through the command line, and not by directly by clicking at it at the axes/planes/centroids table, is because later I would like to use the command inside a runCommand statement, in a Python/IDLE script (with *.py extension) ... Second issue: By the way, do you think this piece of code could work? Assume that the desired plane is already selected .... I want to internally handle the plane as 'p1' in my Python code: p1= chimera.Plane() from chimera import selection p1= selection or perhaps this single instruction ..... p1= chimera.selection Let me try to explain: Within my Python code, I want to have a way to make reference to a plane created by the 'define' command ( should I call it a ' handle'? ... not sure whether it is the correct term ...). Well, I hope that I managed to make it sufficiently clear ... Thanks in advance for your kind attention. Cheers, Juan Dr. Juan Pablo Reyes Valverde Laboratorio de Neurobiología Molecular y Celular (D15) Instituto de Neurobiología UNAM Campus UNAM Juriquilla Boulevard Juriquilla 3001 Querétaro, QRO CP 76230 MÉXICO Tel +52 (442) 2381064

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Charges for PTR+DT
by Amali Guruge 17 Aug '15

17 Aug '15

Dear all, I have to prepare the pdb structure 1K4T to my study. When I do the dock prep process, it gives net charges as, PTR+DT -2 TGP +0 I added charges for standard resides by AMBER ff12SB. For other residues, I added charges by Gasteiger method. My problem is why PTR+DT gives -2 charge? I am not familiar with this one. <http://www.google.lk/intl/en/options/> Can anyone help me? Thank you.

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Modification of ribbon scaling to intersect guide atoms at termini and chain breaks?
by Oliver Clarke 14 Aug '15

14 Aug '15

Suggestion - would it be possible at some point in the future to add a new ribbon scaling option (I guess in Chimera 2.0 or later) so that all internal residues behave like the current “Bspline” scaling, but residues at termini or chain breaks behave like “cardinal” - where the ribbon path exactly intersects the guide atoms? The attached image illustrates the kind of situation this would address - where one wants to show secondary structure in cartoon, but pick out a loop or structural feature of interest in backbone or CA+sidechains, with no ugly discontinuities between the all-atom and ribbon representations. This would allow seamless mixing of nice looking cartoon representation and nice looking backbone or C-alpha+sidechains representation, which I don’t believe is possible at the moment. Cheers, Oliver. Also, in case anyone finds it useful, the following alias applied to a selection or model will generate the CA+sidechains representation depicted below: #Show CA trace with sidechains #Usage: ca_and_sidechains #model_id (or selection/atom-spec) alias ^ca_and_sidechains sel $1; namesel tmp; ~ribbon tmp; ~disp tmp; sel tmp&@CA&protein; repr stick sel; disp sel; setattr m stickScale 1.00 tmp; sel side chain/base.without CA/C1'&tmp; repr stick sel; disp sel; setattr b radius 0.1 sel; color orange tmp; color byhet tmp; sel @CAA |@CB; namesel tmp2; sel tmp&tmp2; repr stick sel; setattr b radius 0.1 sel; sel @CD,N&:pro&tmp; disp sel; repr stick sel; setattr b radius 0.. 1 sel; ~sel

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~select doesn't work on axes?
by Oliver Clarke 14 Aug '15

14 Aug '15

The command "~sel” does not unselect selected axes/planes/centroids - is this intended, and/or is there another way to unselect these objects from the command line? Also, is there a command to undisplay selected axes/planes/centroids? I can only figure out how to do so from the GUI but I would like to do this from the command line, as when you have many axes defined and only want to hide a few it would be easier to have an equivalent of “~disp sel” rather than hunting for the specific axes in the Axes/Planes/Centroids list. Cheers, Oliver.

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