September 2014 - Chimera-users - RBVI Mailing Lists

Angle
by Jian Guan 25 Sep '14

25 Sep '14

Hi All, I made two axes for two molecule, and want to measure the angle between them. Let's say, #1 and #2 are the two axes. I used command line of "angle #1 #2" to do that. Question: What is the default angle measurement? The #1 rotate clockwise or anti-clockwise to reach #2? Thanks, Jian

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Castp volume and surface area
by Felipe Vasquez 24 Sep '14

24 Sep '14

Hi, I am using CASTp plugin from Chimera in order to calculate both the volume and surface area of a specific pocket. I noticed that the 'mouth' atoms can be excluded from the visualization, and even the surface area is reported separately for both the pocket and the mouths by CASTp. However, there is only one reported volume. Is that volume considering both the pocket and mouth atoms to make just one general calculation? In addition, where can I find more info about the criteria to define a pocket's mouth? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

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opening a .dx format file as a volume file?
by David A Case 24 Sep '14

24 Sep '14

Hi: Is there a way for chimera to open a .dx file, but to treat the data as volume (density) data, rather than as an electrostatic potential? That is, I'd like the data in the .dx file to be rendered by the Volume Viewer, as if I had opened a CNS/XPLOR or CCP4 map file. Or, do you know of programs that will convert these file formats? (I've written one of my own, but am looking for confirmation that my code is actually correct, and doesn't have some off-by-one grid point or other mistake.) ....thanks!....dave case

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code or psuedo code for unit cell packing
by Bennion, Brian 24 Sep '14

24 Sep '14

Hello I found the unit cell gui to be very useful recently. However I am curious about how the "pack into unit cell" option works. What information in the pdb header is used to translate/rotate a set of monomers each in an individual unit cell and pack them back into the "original cell". Thanks for any help Brian

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soft roll off edges with Zone masks
by Adam Frost 23 Sep '14

23 Sep '14

hi Chimera users We have determined a pseudo-atomic resolution cryoEM density of a helical co-polymer (two unique chains for the repeating hetero-dimer). We would like to compute map-versus-model FSC curves for each of the unique chains. We'd like to use the Zone tool to mask out the relevant density per chain within ~3A or so of the atoms in our atomic model, but we would like the edges of this mask to be appropriately "soft" (whereas right now zone masking appears to employ a hard edge). has anyone already solved this problem? ~Adam

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Swapping aminoacid to a non-standard residue
by Rui Almeida 23 Sep '14

23 Sep '14

Hello all I am trying to change one aminoacid on a PDB file to a nonstandard residue: TYR to nitrotyroine (PDB ligand code: NIY). I tried modifying the structure of the existing aminoacid in the coordinate file to include an NO2 group in the meta position (Structure Editing --> Build Structure --> Modify Structure...), but ANTECHAMBER cannot assign the correct charges afterwards. Command "swapaa" was also ineffective. Is there anyway to modify the residue and assign the correct charges? Thank you in advance, Rui Almeida. -- Rui Almeida Ph.D., Biochemistry REQUIMTE/CQFB - BioInorganic Chemistry Lab Dep. Quimica, Faculdade de Ciencias e Tecnologia, UNL 2829-516 Caparica, PORTUGAL E-mail: rui.almeida(a)fct.unl.pt

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Find Clashes/Contact (or FindHBond) after splitting chains?
by Mark Girvin 19 Sep '14

19 Sep '14

(Apologies if this arrives twice - on rechecking it, the email address that I tried first looked wrong) Hello, A student in our Biochem class (we have them use Chimera, and tell them that this choice is because it is such a well-done program, and has such active support from the developers and mailing list -- thank you all!) was trying to use Tools->Structure Analysis->Find Contacts/Clashes (and FindHBonds, with the same problem) after running split to simplify displaying and hiding the 14 chains in the coordinate file of the oligomer (1avo) that he was working on. Selecting the residues in one chain (now one model), designating them as the first set within Find Clash/Contacts, checking against all other atoms, choosing "contacts" and applying (Find Contacts) gives no contacts (0 contacts on Reply log). But if run before splitting (selecting chain A and running Find Clash/Contact with the same settings) finds many contacts. The same holds true when using FindHBond - works pre-split, but not post-split. I was wondering whether we were doing something wrong, or if this is the expected behaviour? Thanks, - Mark (our work-around was to delete different subsets of chains and save the resulting coordinates as "HeteroDimerDimer.pdb" & "HeteroDimer.pdb" and then work with those, which went fine) - Mark

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Hardware requirements
by Rick Roberts 19 Sep '14

19 Sep '14

Hello, We are on boarding a Physician that will be using Chimera. What are the hardware requirements (processor, video card, memory, etc.) Thanks in advance. Rick Roberts Children's Hospital Los Angeles Pathology and Laboratory Medicine Phone: 323-361-5836 Fax: 323-361-8004 Cell: 818-415-6085

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Find Clashes/Contact (or FindHBond) after splitting chains?
by Mark Girvin 19 Sep '14

19 Sep '14

Hello, A student in our Biochem class (we have them use Chimera, and tell them that this choice is because it is such a well-done program, and has such active support from the developers and mailing list -- thank you all!) was trying to use Tools->Structure Analysis->Find Contacts/Clashes (and FindHBonds, with the same problem) after running split to simplify displaying and hiding the 14 chains in the coordinate file of the oligomer (1avo) that he was working on. Selecting the residues in one chain (now one model), designating them as the first set within Find Clash/Contacts, checking against all other atoms, choosing "contacts" and applying (Find Contacts) gives no contacts (0 contacts on Reply log). But if run before splitting (selecting chain A and running Find Clash/Contact with the same settings) finds many contacts. The same holds true when using FindHBond - works pre-split, but not post-split. I was wondering whether we were doing something wrong, or if this is the expected behaviour? Thanks, - Mark (our work-around was to delete different subsets of chains and save the resulting coordinates as "HeteroDimerDimer.pdb" & "HeteroDimer.pdb" and then work with those, which went fine)

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New Residue-interaction network MD movie plugin
by rswett＠chem.wayne.edu 19 Sep '14

19 Sep '14

Hey all, I'm trying to visualize an RIN from a dynamics run using the new addition to the Trajectory tools. Cytoscape isn't playing nice with launching chimera, so I was wondering how difficult it would be to save the calculated network to load independently in cytoscape? Currently the calculation runs just fine, but I can't save the output. Is there a command line way to do it? Any other suggestions? Rebecca

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Chimera-users September 2014