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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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rename a residue?
by Julian Tirado-Rives 18 Jun '14

18 Jun '14

Dear Chimera team, thanks for all the work you put in into a very, very, useful program. I just have a question that I am hoping is just my inability to find the proper command ... is there a way to rename a residue before writing a PDB? I often use chimera as pre-preparation step before getting into some particular calculation packages, which often require different names for residues to indicate tautomers, protonation, etc. and it would be nice to do it from chimera rather than take the PDB's through a rather annoying set of scripts, sed's, or even text editors! Thanks in advance, - Julian - -- ----------------------------------------------------------------- | Julian Tirado-Rives | | | Department of Chemistry | Phone: (203)432-3356 | | Yale University | Fax: (203)432-6144 | | P. O. Box 208107 | email: Julian.Tirado-Rives(a)yale.edu | | New Haven, CT 06520-8107 | | -----------------------------------------------------------------

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Attaching a Probe to Modify an Existing Amino Acid
by Shana Burstein 18 Jun '14

18 Jun '14

Hello, I am an undergraduate student at Haverford College and I am attempting to attach thiocyanate probes onto different sites along a protein by first replacing the existing amino acid with a cysteine and then by adding a C and N onto the S- of the Cys residue. I know it is possible to carry this out manually using Tools>Structure Editing>Modify Structure, but I am hoping to automate this process by calling an external .py script that will primarily contain a list of preexisting Chimera commands. I have been successful at converting the targeted amino acid to Cys using "swapaa," building a CN residue called MSCN (using the createMolecule.py as a guide), combining the two models into one ("combine selected close True") and forming a bond between the Cys S and CN C atoms ("bond"). At this point, I am seeking help in automating the renaming of the modified residue to MSCN. Currently, Chimera sees this residue as two different separate residues called CYS and MSCN. Is there a way to combine these two structures so that the label corresponds to MSCN and the residue number corresponds to CYS? Sincerely, Shana Burstein Haverford College '15

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delete atoms based on their coordinates
by Aranha, Michelle 18 Jun '14

18 Jun '14

Hi , I wanted to know if there is a way in chimera to select and delete atom/atoms based on their position/coordinates in the simulation box. For example delete water 150 at (x, y, z). I tried zone sel, but I couldnt get it to work. Regards, Michelle ?

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