- Chimera-users - RBVI Mailing Lists

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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fixed: error saving scene with independent rotation
by Elaine Meng 31 Jul '18

31 Jul '18

Hi Yanhe, The bug you reported a few days ago has been fixed! I just confirmed that with the current daily build of Chimera, you can now save scenes with independent rotation and use them in the Animation tool and in scripts. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Is there any tool to write some calculated attribute into a header format?
by Sergio Garay 31 Jul '18

31 Jul '18

Hi All! I would like to know: Is there any way or tool to write some calculated attribute into a header format? I want to see the same color values obtained for some a calculated attribute projected onto a sequence. I have read in the chimera list the inverse process: exporting a header from a sequence window to be read as an attribute. Thank you in advance. -- *Sergio GarayDr. en Ciencias BiológicasFacultad de Bioquimica y Cs. BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 - Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54 (342) 4575-221 *

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Fwd: Inquiry for new/re-registration license key_Arifuzzaman Sarder
by Elaine Meng 31 Jul '18

31 Jul '18

> From: Sarder Arifuzzaman <arifpharmju(a)gmail.com> > Subject: Inquiry for new/re-registration license key_Arifuzzaman Sarder > Date: July 31, 2018 at 9:08:53 AM PDT > To: chimera-announce-owner(a)cgl.ucsf.edu > > Hi > Greetings. > This is Arifuzzamman Sarder. I am an earlier user of chimera software tool. Recently I installed the updated version (v1.13). However, I could not draw any chemical structure by inputting canonical smiles or any other chemical ID in this tool. Even it can not capture any chemical structure from PDB, unlikely it is giving us only protein structure. Could you please let me know how can I revive this tool, so that I can use it for molecular docking and chemical structure as well. > Thank you very much in advance. I am looking forward for your response please. > Sincerely > Arifuzzaman, Sarder > PhD research fellow > Chung-Ang University > Mobile: 010-2654-2606 > E-mail: arifpharmju(a)gmail.com <mailto:arifpharmju@gmail.com> > Web: https://sarderarifuzzaman.wixsite.com/arif <https://sarderarifuzzaman.wixsite.com/arif> HI Arifuzzamman Sarder, (forwarding to the proper address for asking Chimera questions: chimera-users(a)cgl.ucsf.edu ) There is no reason it should not work as before. Chimera does not use a license key. For example, in Chimera 1.13, command: open pubchem:12123 (- or -) open smiles:C1CCNC1 …shows a small molecule in sticks, and command: open 2gbp … shows PDB entry 2GBP; protein ribbons with ligand (glucose) as sticks and nearby sidechains as sticks. If you mean that your Chimera 1.13 is not showing small molecules, or not showing sticks, I only have two ideas: (A) graphics/rendering problem of your computer or (B) New Molecules preferences was set to show only ribbons. To check (B), show Preferences from the Favorites menu, then change to category: New Molecules and check that the settings are what you want, and then click Save. The behavior I described is for the default, “smart initial display” true. If you had it false, and also had “show atoms” false, it would not show atoms when you open a structure. If you feel it is a bug, you can use menu: Help… Report a Bug and describe in detail what you did and what the problem is. However, if it is a graphics problem of your computer, it is not something we can fix. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: [Chimera-users] Extracting asymmetric unit
by Tom Goddard 31 Jul '18

31 Jul '18

Hi Martin, Fit an atomic model of the asymmetric unit then use volume zone (Volume Viewer menu entry Feature / Zone) then save the map (Volume Viewer / File / Same Map As…). See the maskZone option description in the volume save command for details https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output> Tom > On Jul 31, 2018, at 7:00 AM, Martin Moncrieffe <mcm35(a)cam.ac.uk> wrote: > > Hi Tom, > > A quick question. I have a helical reconstruction (EM) and would like to extract the density for the asymmetric unit from the map. How does one do this? > > Best. > > __martin > >

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Surface vertex density
by Tom Goddard 31 Jul '18

31 Jul '18

For a density map you can control the number of surface triangles and vertices by choosing the subsampling “step” size in the Volume Viewer dialog. Step 2 will use every other grid point along x,y,z axes and result in a coarser mesh. For molecular surfaces computed from atoms, change the vertex density as described here http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005889.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005889.html> Tom > On Jul 31, 2018, at 5:53 AM, ⁨עמיחי הולצר⁩ wrote: > > And another question - there is "Surface and Mesh options" under the "Features" tab, so one can control the smoothing of the surface, thickness, etc. How can I control the number of nodes of the surface? I mean, I want the mesh not to be so dense. Is it possible? > > Thanks again! > > 2018-07-31 13:38 GMT+03:00 עמיחי הולצר : > When I save it as OBJ file, how can I watch it in chimera again as a molecule with "atoms" and "bonds" (like CONECT line in pdb file)? > I see that OBJ file look like a xml file, and contains coordinates and edges, but does it reflect the mesh? > > Thanks, > Amichai > > 2018-07-30 19:37 GMT+03:00 Tom Goddard : > Hi Amichai, > > Chimera computes density map isosurfaces using the marching cubes algorithm. It can be saved in various file formats for example OBJ, others are described with the export command > > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html> > > Tom > > >> On Jul 29, 2018, at 3:06 AM, ⁨עמיחי הולצר⁩wrote: >> >> Hi Chimera support, >> >> I have 2 questions: >> >> 1. How does Chimera calculate the mesh from the density map? >> >> 2. How can I save the mesh as a file? >> >> Thanks a lot, >> Amichai Holzer >> Huji >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev> > >

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Re: [Chimera-users] [chimera-dev] Save density map as a mesh
by Tom Goddard 31 Jul '18

31 Jul '18

If you want to save atoms, bonds and surfaces and load them into Chimera later, then save a session, menu File / Save Session As…. Tom > On Jul 31, 2018, at 3:38 AM, ⁨עמיחי הולצר⁩ <⁨amiholz(a)gmail.xn--com-yx0a> wrote: > > When I save it as OBJ file, how can I watch it in chimera again as a molecule with "atoms" and "bonds" (like CONECT line in pdb file)? > I see that OBJ file look like a xml file, and contains coordinates and edges, but does it reflect the mesh? > > Thanks, > Amichai > > 2018-07-30 19:37 GMT+03:00 Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>>: > Hi Amichai, > > Chimera computes density map isosurfaces using the marching cubes algorithm. It can be saved in various file formats for example OBJ, others are described with the export command > > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html> > > Tom > > >> On Jul 29, 2018, at 3:06 AM, ⁨עמיחי הולצר⁩ <⁨amiholz(a)gmail.com <mailto:amiholz@gmail.com>⁩> wrote: >> >> Hi Chimera support, >> >> I have 2 questions: >> >> 1. How does Chimera calculate the mesh from the density map? >> >> 2. How can I save the mesh as a file? >> >> Thanks a lot, >> Amichai Holzer >> Huji >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev> > >

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display floating XYZ axes
by Pranav Shah 27 Jul '18

27 Jul '18

Dear Chimera Users and Devs, Is there a possibility to display the XYZ axes *a la* coot in chimera, so that one can keep a track of the direction of the views in the window? Cheers, Pranav -- Pranav Shah Postdoctoral Research Fellow. Hogle Lab Harvard Medical School 240 Longwood Avenue Boston, MA 02115 (617) 432-4360 (fax) (617) 432-3839 (lab)

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(no subject)
by Yanhe Zhao 26 Jul '18

26 Jul '18

Hi, This is Yanhe. I want to make movies of side-by side rotaing structures, I set "center of rotation method" to "independent", when I try to save the scenes, chimera give error report as attached file shown. what should I do now? I really appreciate it if you can do me the favor. Best, Yanhe

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Removing structure segment and connecting the edges with dashed line
by Ahmad Khalifa 26 Jul '18

26 Jul '18

Hello, Selecting a segment of a structure and deleting it does remove that segment, but the ends are not connected. How to do the same and make the edges connected with a dashed line? Best regards.

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Problem with minimizing structure
by Renee Arias 26 Jul '18

26 Jul '18

Hello all, I am having a problem with the minimizing structure function in Chimera. I am just trying to change a single residue on a very small protein (88 residues), but I keep getting the error: No MMTK name for atom "H1" in standard residue "GLN". Previous message boards seem to just point to bug fixes in Chimera, but I am running the newest version available for Windows 10. I would appreciate any help! Thanks so much, Renee

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Click-and-drag selection still not working for chimera in Mac OSX....any plans for improvement
by Carmen Bayly 26 Jul '18

26 Jul '18

Hello Chimera users, I'm working with Chimera on an OSX 10.12.2 (intel core processor). I noticed that the click-and-drag selection function doesn't work, and saw a bug report from 2015 explaining it was because of the intel processor. However, it's 2018 now - does anyone know any fixes besides the wire display style? Thanks, Carmen

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action of labels
by Yanhe Zhao 26 Jul '18

26 Jul '18

To whom may concern, This is Yanhe Zhao, from ut southwestern medical center. After I add the 2D labels, i know how to move them, but could I rotate them? I really appreciate if someone can do me the favor. Best, Yanhe

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Aligning structure based on a specific secondary structure
by Ahmad Khalifa 25 Jul '18

25 Jul '18

Hello, All the options I see in Matchmaker is based on aligning whole chains. Is it possible to align structures based on a specific secondary structure, like a specific alpha helix for example? How to do so? Thanks in advance.

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How to place two identical proteins "near" each other
by Marla DeKlotz 24 Jul '18

24 Jul '18

I am trying to prepare a pdb to use in Rosetta docking. I need to place two copies of the same protein "near" each other, in roughly the alignment they should have after they dock together. Chimera seems to always overlay the two copies and I can't figure out a way to separate them and move/rotate each one independently. I don't want a tile view, I need them to have a real relationship in space so Rosetta knows where to "aim" its docking protocol. Thanks, Marla

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Including halogen atoms in findHBond tool?
by Nawel Mele 23 Jul '18

23 Jul '18

Dear Chimera users, I am looking for hydrogen bonds between a receptor and an ensemble of docked ligands with different structures including halogen atoms. I would like to know if there is a way to include halogen atoms in the hydrogen bond (findHBond) facility ? Best regards, Nawel -- Dr Nawel Mele, T: +33 (0) 634443794 (Fr) +44 (0) 7704331840 (UK)

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Question about disulfide bonds and energy minimization
by Steven Douglas Aird 23 Jul '18

23 Jul '18

Dear Elaine, For the first time in about three years, I need to do a little more modeling. We sequenced an NADase and I used Galaxy to create a model using a known CD38 structure as a template (attached). Chimera displayed everything, but the disulfide bonds, of course. So I entered the specifications for those manually into the PDB file (attached). Two of the disulfides displayed properly, but four appear as thin dashed lines. At least one, at the C-terminus is clearly way too long. I tried to do an energy minimization, but while Chimera executed the steps, nothing in the structure moved. It used to be that one could watch the structure flex as it assumed the most energetically favorable conformation, but not this time, yet some of the disulfide bond lengths are clearly wrong. I also tried to use the set length command, in the forms: set length 2.05 / Set Length [2.05] but Chimera does not like either of these commands. If the manual included examples of the command format for each command, that would be really useful, because it is not clear where the syntax problem lies. As always, thanks for your help! Sincerely yours, Steve Steven D. Aird Technical Editor Faculty Affairs Office Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son Kunigami-gun, Okinawa-ken Japan 904-0495 Phone: 098-982-3584 Cell: 080-4154-9504 Email: steven.aird(a)oist.jp<mailto:steven.aird@oist.jp>

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Morph Conformations tool doesn't produce a model with ribbons + *atoms*.
by Alex Nazlidis 22 Jul '18

22 Jul '18

Hello, I am trying to use morph conformation tool to produce a morph in a ribbon + atoms representation. While my 2 models are represented exactly as I want, when I create the morph the atoms diasappear and I'm left with the ribbon representation. Is there a way to create what I want? Regards, Alex

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Truncating fitted structures using a map mask
by Ahmad Khalifa 20 Jul '18

20 Jul '18

Hello, I have a tubulin lattice (sheet) fitted into a microtubule map. I want to generate a structure that has only one dimer, surrounded by only fragments from the other dimers on the top, bottom and sides. Is there a way to do that in chimera? Regards.

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Problems with V1.13
by Stefan Kunert 20 Jul '18

20 Jul '18

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