June 2014 - Chimera-users - RBVI Mailing Lists

Rainbow by secondary structural element?
by Oliver Clarke 26 Jun '14

26 Jun '14

Hi all, Currently, the rainbow function can operate at the levels of per residue, per chain or per model. I was wondering whether it would be feasible in a future release to add an additional level, coloring per secondary structural element? This would be particularly handy for structures of membrane proteins, where it is often desirable to color each helix/strand a different color, while not varying the color along the helix (and not coloring residues in loops etc). Even better would be to have separate “rainbow helix” “rainbow strand” and “rainbow secstruc” commands for finer control, but this is probably not really necessary. Cheers, Oliver.

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Color by height from surface?
by Oliver Clarke 25 Jun '14

25 Jun '14

Hi all, I’m wondering if there is any way to use scolor to color by height from another surface rather than from a plane, axis or point? Specifically, I’d like to color a molecular surface by distance from the surface of the low-res model generated using multi-scale models, in order to highlight cavities in the surface of the protein. Best, Oliver.

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Chimera scripting with --nogui can't write pdb files
by rswett＠chem.wayne.edu 24 Jun '14

24 Jun '14

Hey guys, i've been trying to put together a command line only set of scripts that will do some selection processing and save a pdb without going through the gui. If I use the command chimera --nogui --script close.py pdb1.pdb pdb2.pdb where close.py contains select #0 za<3 & #1:HOH write selected 1 output.pdb I should get the residues that match that selection criteria saved as the pdb output.pdb, correct? I get SyntaxError: invalid syntax for line 2 even though this works OUTSIDE a script. as in, if I just run chimera command line and enter those commands sequentially, it works. I also noticed that within the gui I need "#1" and outside it only works with '1" as the model number. I've also tried doing this with a python script: chimera --nogui --nostatus --script "close.py pdb1.pdb pdb2.pdb output.pdb" this should pass whatever I enter as $1 $2 $3 as arguments to my script, correct? So close.py for this version contains open (sys.argv[1]) open (sys.argv[2]) select #0 za<3 & #1:CVX write selected 1 (sys.argv[3]) which also pukes on the pdb write. I couldn't find any other way to write a pdb using python syntax, I assume the way i'm doing it is wrong, but I couldn't find a write.pdb function during my digging. Does anyone have suggestions for writing a pdb based on a selection without going through the gui? I plan on batching this up for a huge number of files and directories and going through the gui would be far too time consuming. Rebecca

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making capsid map from asymmetry unit.
by Jian Guan 24 Jun '14

24 Jun '14

Dear All, I want to make a capsid map from asymmetry unit. The PDB ID is 3iyj, the L1 protein of BPV. The BPV is a T=7, icosahedral capsid. Does anybody know how to make it? Thanks a lot. Sincerely yours, Jian

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side view crash
by m.maletta＠nki.nl 23 Jun '14

23 Jun '14

Dear all, I installed the latest stable Chimera 1.9 on a 64bit ubuntu precise 12.04 and I noticed that every time I try to use the side-view applet, in the viewing control, Chimera just crash. Other function seems to work just fine. I should add that on the same machine the Chimera 1.6 does not crash. Can anyone share a similar experience in Linux? chimera Segmentation fault (core dumped) Any hint what may be the problem? Best Max __________________________________ Massimiliano Maletta post-doc in NKI Netherlands Cancer Institute -Antoni van Leeuwenhoek Hospital Plesmanlaan 121 B6 1066CX Amsterdam group of Peter Peters www.nki.nl/research/peters/ | www.necen.nl m.maletta(a)nki.nl Tel : +31 20 512 2022 Fax : +31 20 512 2029

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Icosahedral model
by 李智海 20 Jun '14

20 Jun '14

Hi， I have a density map of an icosahedral capsid, and now i want to make a icosahedral model to represent the capsid. In this model, every corner represent a capsomere. what can i do to display this in Chimera ? Do I require any plug-in? Thank you！ Best wishes! Zhihai Li School of Life Sciences, Xiamen University. Xiang'an Road(South), Xiang'an District, Xiamen City, Fujian Province, China.

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Fwd: CCL: Coordinate system rotation
by Elaine Meng 19 Jun '14

19 Jun '14

On Jun 19, 2014, at 8:33 AM, "Radoslaw Kaminski rkaminski.rk,+,gmail.com" <owner-chemistry(a)ccl.net> wrote: > Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk]=[gmail.com] > Dear All, > > A trivial question. I have a XYZ file with a molecule in some coordinate > system. I would like to have a Z axis be in a certain direction along A...B > atoms. Is there any program that can easily change my coordinate system by > choosing some 3 atoms? I can of course do all transformations by hand (for > example in Excel) but its tedious. I know that ADF is capable of transforming > the coordinates to some specified coordination system (Prof. Baerends' CCL post > from several years ago), but is there any other program that can just make such > transformations quickly? > > Thanks in advance, > Radek From: Elaine Meng <meng(a)cgl.ucsf.edu> Subject: Re: CCL: Coordinate system rotation Date: June 19, 2014 9:57:00 AM PDT Hi Radek, With Chimera you could align 2 atoms front->back and then save a PDB file with the transformed coordinates. Not sure if that is exactly what you needed, or whether it is quick enough, but you could automate looping through multiple files with a little bit of Python. (1) open XYZ file (e.g. menu File…Open, choose file.xyz, or command "open file.xyz") <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/xyz.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/open.html> That will automatically assign unique atom names by element and order in file, for example the first C will be C1, the first N will be N1. (2) use "align" command to put atoms A,B in center of view along the line of sight (laboratory Z axis) with A in front and B in back (e.g.: align @c1@o1) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/align.html> (3) save PDB with transformed coordinates (e.g. menu File…Save PDB, un-check "use untransformed coordinates" or command something like "write #0 file.pdb") <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> (4) close structure (e.g. command "close #0" or "close all") … if multiple structures to process, loop back to step 1. See here for writing looping scripts for Chimera: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.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

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split
by John Mercer 19 Jun '14

19 Jun '14

Hi All, I understand the use of split as outlined in the tutorial describing how to find the contact region between two chains. file:///Applications/Bioinformatics/Chimera.app/Contents/Resources/share/chimera/helpdir/UsersGuide/frametut.html I don’t know the proper syntax for models with more than two chains, e. g. A, B, C, D, and E where you might like to split the model either as: A, B, D, and E in one group C in the other or A, B, and D in one group and C and E in the other. I would be grateful for a recommendation for the correct syntax to use in the argument list to form two groups to identify the contact surface after further processing (in the same manner as the tutorial). Thanks, -John

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STL Resolution Issues
by Eric Bell 19 Jun '14

19 Jun '14

Hello, I am trying to change the resolution of the atoms for a large molecule packing, but no matter how I change the zoom or the subdivisions property in the viewing effects, it seems to always produce the same filesize (~900 MB, not something our software can handle). Is this a bug or is it something that I'm doing incorrectly? I'm running on a mac, and I have tested this both with a .mol2 and .pdb file. Thanks, Eric

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how to tranfer a .mrc file to .mtz file
by #ZHANG HAIPING# 18 Jun '14

18 Jun '14

Dear chimera user: I have a .mrc file generated by chimera, now I want to convert it to .mtz formate, so I can load to coot, and examine the structure in details. Can anyone tell me how to convert .mrc to .mtz? Best regards, Haiping

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Chimera-users June 2014