August 2018 - Chimera-users - RBVI Mailing Lists

Chimera for mac issue
by Yangfeng Li 13 Aug '18

13 Aug '18

Hello, I installed the latest version of chimera via your website on my mac (macbook air, 2013, hgih sierra). But it doesn't exist in my "application" file. And every time I need to double click chimera dmg file to launch it, which takss a very long long time verifying chimera. That process is different from Windows. I just wonder whether it's normal. Thanks, Yangfeng

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Different center when display coordinates with bonds or ribbon
by 师扬 12 Aug '18

12 Aug '18

Dear chimera developers and users, Recently, I met a very strange issue about displaying coordinates in chimera. I found the helices were off-centered with the map, when I open a well refined PDB file and the map it was refined against, and keep an eye on the helices which is automatically displayed by Ribbon. But actually they are will aligned in COOT. And if I hide Ribbon and showed Atoms/Bonds, they were well-aligned. The attached files show the same region with different displaying modes. And I have tried several versions of chimera, the results were the same. Actually, I want to use Ribbon to display these helices. Does anyone know how to fix it? Thanks in advance! Yang

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Animating peptide bond formation
by Alex Nazlidis 11 Aug '18

11 Aug '18

Dear Chimera users and staff, I've been thinking of ways to animate the formation of a peptide bond between two aminoacids but I haven't come up with a solution. Can you help me out here? :) Thanks in advance, Alex Nazlidis

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problem with electron density map
by kesgin-schaefer＠chemie.uni-hamburg.de 07 Aug '18

07 Aug '18

Dear all, I have a problem with my electron density map: if I load the map in chimera, it will only show a subregion of the map and after "fit to model" the model will not be completely covered (see attachment). Any suggestions about how to solve the problem would be much appreciated. Thanks Steffi

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Problem with FIndHBonds
by Nawel Mele 07 Aug '18

07 Aug '18

Dear Chimera Users I am using hbond command to determine hydrogen bonds between a receptor and multiple compounds with different conformations from a docking simulation. I used a cmd script to automatise the process however I am facing and error that I am not sure to understand. I just pasted follow the part of the reply log where the problem appeared. The problem here is that when I load the compound with the different docked conformations separatly it is not always the same conformation taht has this error so I don't know what is the real problem. Many thanks for your help. Nawel *Finding intermodel H-bondsFinding intramodel H-bondsConstraints relaxed by 0.4 angstroms and 20 degreesModels used: #0 Representative_confo_site_active_minimum_distance_state001.pdb #1 DB08734_1|LigPrep_output_named|sdf|8330|dock5H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):#0 LYS 73.A NZ #1 UNK 1 O1 no hydrogen 2.924 N/A#0 ASN 76.A ND2 #1 UNK 1 N4 no hydrogen 2.398 N/A2 hydrogen bonds foundDB08734_1|LigPrep_output_named|sdf|8330|dock6 openeddonor: #0 ASN 76.A ND2 acceptor: #1 UNK 1 N4Traceback (most recent call last): File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/chimeraInit.py", line 683, in init chimera.openModels.open(a, prefixableType=1) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/chimera/__init__.py", line 1919, in open models = func(filename, *args, **kw) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/ChimeraExtension.py", line 35, in func processCommandFile(cmdFile) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 108, in processCommandFile _processFile(f, emulateRead, filename) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 143, in _processFile if makeCommand(line): File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 69, in makeCommand f(c, args) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/ChimeraExtension.py", line 33, in cmdHBonds specInfo=[("spec", "models", "molecules")]) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 451, in doExtensionFunc extFunc(*tuple(processedArgs), **kw) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/base.py", line 940, in createHBonds interSubmodel=interSubmodel, cacheDA=cacheDA) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/base.py", line 574, in findHBonds (donorAtom, donorHyds) + args):TypeError: accPhiPsi() takes exactly 8 arguments (9 given)Error while processing chimera_input_step2_bug.cmd:TypeError: accPhiPsi() takes exactly 8 arguments (9 given) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/base.py", line 574, in findHBonds (donorAtom, donorHyds) + args):See reply log for Python traceback.* -- Dr Nawel Mele, T: +33 (0) 634443794 (Fr) +44 (0) 7704331840 (UK)

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Re: [Chimera-users] from govinda - How to save coordinates after rotation and translation fitted in cryo em map
by Elaine Meng 05 Aug '18

05 Aug '18

Dear Govinda, Please see the User’s Guide page on saving your data, and the links therein: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html> …including Save PDB <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> ...write command <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> …saving after fitting <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting> It is recommended to send questions to chimera-users(a)cgl.ucsf.edu (CC’d here). You can also use Chimera menu: Help… Search Documentation. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 4, 2018, at 11:22 AM, Govindasamy, Lakshmanan <lgovin(a)pennmedicine.upenn.edu> wrote: > > Dear Dr.Meng, > > How to save the coordinates in chimera after fitting into cryo em map. > i am having difficulty in save the coordinates > Please educate me how to save coordinates. > > thanks > govinda

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question
by 许东 04 Aug '18

04 Aug '18

Dear editors: thank you for your excellent work. I had a problem. After i built my protein model, it was shown in software as:but when i tried to save the result, the output was displayed as so could you tell me how to solve this problem? look forward to your reply, thank you

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Error from running headless Chimera
by Zhe Wang 03 Aug '18

03 Aug '18

Hi, I am trying to using headless Chimera on RedHat linux server 7.3 to produce some images. But I end up with a segmentation fault. Does anyone have an idea how it comes to this? The headless chimera is from https://www.cgl.ucsf.edu/chimera/download.html (64-bit daily build). The test code was taken without changes from https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html. Any ideas will be appreciated. Best, Zhe PS: OSMesa 11.2.2 has been installed. Executing chimera_surface.py... Processing 6c7m.pdb Opening 6c7m.pdb... #0, chain A: kemp eliminase KE07 6c7m.pdb opened Center of rotation: 0.867528 -1.77985 11.157 /software/chimera_headless/bin/mscalc 1.400000 2.000000 1 MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk Copyright M.F. Sanner (March 2000) Compilation flags Surface 6c7m.pdb, category main, probe radius 1.4, vertex density 2 12 connected surface components Total solvent excluded surface area = 10612 component areas = 10035.4, 126.971, 97.9893, 90.9594, 38.157, 36.4953, 34.1487, 33.7557, 32.681, 30.3253, 29.9037, 25.222 Total solvent accessible surface area = 11324.6 component areas = 11265.5, 25.8506, 19.8737, 10.3135, 0.685134, 0.778238, 0.522429, 0.365982, 0.314644, 0.177358, 0.178001, 0.00214196 Surface 6c7m.pdb, category main has 12 components /software/chimera_headless/bin/mscalc 1.400000 10.000000 1 MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk Copyright M.F. Sanner (March 2000) Compilation flags RESTART FROM TRI: 1 radius of atom 5 goes from 1.880000 to 1.980000 radius of atom 6 goes from 1.880000 to 1.980000 radius of atom 1569 goes from 1.420000 to 1.520000 Partial mode /software/chimera_headless/bin/mscalc 1.400000 10.000000 0 MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk Copyright M.F. Sanner (March 2000) Compilation flags RESTART FROM TRI: 1 radius of atom 5 goes from 1.880000 to 1.980000 radius of atom 6 goes from 1.880000 to 1.980000 radius of atom 1569 goes from 1.420000 to 1.520000 Partial mode Calculation of some surface components failed. A single component of the surface was calculated correctly - the failure occurred for disconnected additional components such as inside bubbles. If the desired surface is already shown, there is no need for concern. However, if it is not shown, see below for possible fixes. Surface calculation frequently fails for large, multi-chain structures. The calculation may be successful if the chains are treated individually, by using the "split" command before generating a surface. If splitting is not desired or the structure is already a single chain, changing molecular surface parameters in the Selection Inspector or (before surface creation) the New Surfaces category of Preferences may allow the calculation to succeed. More details are given at http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html Surface 6c7m.pdb, category main, probe radius 1.4, vertex density 10 1 connected surface components Total solvent excluded surface area = 10036.7 Total solvent accessible surface area = 11266.5 Surface 6c7m.pdb, category main has 1 components Rendering high resolution image... Segmentation fault

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Activation buttons (namely "All")
by Eric Pettersen 01 Aug '18

01 Aug '18

Hi all, The activation buttons below the command line have an “All” button that works much the same way as the “activate all” button in the Model Panel works: if you check it on, then all models are activated for motion; if you check it off then the previous activation states are restored. It has been suggested that the behavior could instead be that when checked off all models would be deactivated (making it easier in some cases to go from moving all models to moving just one). I’m trying to find out if any users make strong use of the current behavior of that button and wouldn’t want it changed. Conversely, I wouldn’t mind hearing people who would really like to see the behavior switched. Regardless of the outcome of the discussion, the behavior of the corresponding Model Panel button would remain the same for a couple of reasons: 1) when clicked, the text of the button changes to “restore activities” so there’s less chance of confusion, and 2) there’s a separate “deactivate” button. I will interpret lack of feedback as “sure, go ahead”. :-) —Eric Eric Pettersen UCSF Computer Graphics Lab

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Chimera-users August 2018