- Chimera-users - RBVI Mailing Lists

Ligand Receptor docking
by Shriwas, Pratik 20 Nov '18

20 Nov '18

Hi, I am trying to use UCSF chimera to study ligand-docking interactions. My protein is GLUT1 (4pyp - PDB) and a small molecule called DRB18 .I have used NIH pubchem browser to generate a smiles string for this compound and used the smiles string to generate a 3D structure in chimera. I have found that the compound interacts with protein in central cavity and interacts via hydrogen bonds (depending on parameters). I want to know whether my data is publishable. If docking studies performed using chimera are acceptable. People use softwares like Schrodinger/medusa among others. If you wish to see my work, I can send it in as well via email. Thank you. Regards, Pratik Shriwas Phd Candidate, Molecular and Cellular Biology program, Edison Biotechnology Institute, Ohio University.

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how to make/delete hydrogen bond and delete chains
by Paris Tzou 19 Nov '18

19 Nov '18

Hi, I have a protein-dna complex structure with protomer as A as protein and B as DNA. It is impossible in hbond function to "generate" hbonds between two chains (A and B). One have to parse protein and DNA into two files and load into Chimera as two models. Another question is that, once generated, hbonds cannot be "erased" in the chimera view. And "delete chain ID" cannot really delete one chain from protein-DNA complex. What I am doing is 5MCT, p53-DNA complex. Thanks a lot for your help. Paris

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generating/saving mask files using segmentation
by Uhnsoo Cho 19 Nov '18

19 Nov '18

Hi, I am a beginner and still in the learning phase of chimera. Here is my question. I generated the mask from relion (mask creation) and open the mask in chimera. Using segmentation, I successfully split the mask into three segments and saved them individually. Then, I found that each mask file changes its box size (smaller than the original mask) and failed to run the multi-body refinement in relion. Using relion_image_handler (--new_box), I changed the box size but now the origin is shifted and all three masks are overlapping each other by losing their relative position. Is there a way to save the segmented mask maps by maintaining its original box size and relative position? Thanks. Best, Uhnsoo

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Using headless chimera to create images
by Chemmama, Ilan 19 Nov '18

19 Nov '18

Dear developers, I am trying to create a bunch of images using Chimera. I wrote a script that create the scene using the following steps: mc_frame=str(INPUT_FRAME_NUMBER) rmffile=str("PATH_TO_RMF") runCommand('open '+rmffile) runCommand('set bgcolor white') runCommand('windowsize 1028 1028') runCommand('~set depthCue') runCommand('set projection orthographic') runCommand('wait 2') runCommand('scale 0.75') runCommand('copy file ./Image_'+mc_frame+'.png PNG supersample 3 dpi 300') runCommand('close all') runCommand('stop now’) While the scrips works in the headless version using PDB files, I have not been successful when using RMF files. The images when using the RMF files are just the background color (red when set to red, blue when set to blue) without the structure. I tried also to add the display .2 option as in: runCommand(‘display #0.2’) which corresponds to the RMF beads scene in the model panel. I should add that using the GUI version of chimera, the script works fine and all the images are properly created. Do you have any hints/clues on what could be done to make it work? (I am running the script the full version of chimera but the headless should be more efficient). Thanks, Ilan

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Difference map
by Yangqi Gu 18 Nov '18

18 Nov '18

Dear Chimera users, I am trying to examine two cryo-EM maps and want to know if there is a subtle change between these two. I want to calculate the difference map, is it doable in Chimera? Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

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Can the order of map histograms on Volume Viewer be sorted?
by Jun Ha Song 17 Nov '18

17 Nov '18

Dear RBVI, Sometimes I accidentally open more than 4 maps into UCSF Chimera session without changing the number of histogram that can be shown to some value higher than the default value of first 3 maps. UCSF Chimera places new histogram on the spot where the 1st map used to be, and the histogram order shown on Volume Viewer goes from - 1st map - 2nd map - 3rd map to - 4th map - 2nd map - 3rd map from top to bottom. I know that I can bring back the histogram of 1st map by clicking on Data drop-down menu, but it doesn't bring back the 1st map to the top slot. Is there any way to manually re-sort the order of the histogram so that it would be in the order of their loading (or in the order of their model ID)? Best, Junha Song.

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How can I export the list of hydrogen bonding and clash/contact?
by Paris Tzou 15 Nov '18

15 Nov '18

Hi, I have a structure of protein-DNA complex. How can I export the list of hydrogen bonding and clash/contact, please? Thanks a lot, Paris

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Re: [Chimera-users] Fwd: Re: How to correct this error: ~/usr/chimera-1.12/lib/libgomp.so.1: version `GOMP_4.0' not found (required by /usr/lib/libopenbabel.so.4)
by Francois Berenger 15 Nov '18

15 Nov '18

On 11/15/18 9:51 AM, Francois Berenger wrote: > > > -------- Original Message -------- > Subject: Re: [Chimera-users] How to correct this error: > ~/usr/chimera-1.12/lib/libgomp.so.1: version `GOMP_4.0' not found > (required by /usr/lib/libopenbabel.so.4) > Date: 14/11/2018 18:42 > From: Greg Couch <gregc(a)cgl.ucsf.edu> > To: Francois Berenger <mlists(a)ligand.eu>, chimera > <chimera-users(a)cgl.ucsf.edu> > > That looks like a problem between libopenbabel and Chimera. The bug is > that libopenbabel.so was compiled with a newer compiler than what > Chimera was compiled with. You can try renaming > chimera-1.12/lib/libgomp.so.1 (eg., to libgomp.so.1.save) to see if it > fixes the problem. Yes, this workaround works: mv ~/usr/chimera-1.13/lib/libgomp.so.1.bck ~/usr/chimera-1.13/lib/libgomp.so.1.bck And I also needed to issue that one: mv ~/usr/chimera-1.13/lib/libz.so.1 ~/usr/chimera-1.13/lib/libz.so.1.bck > While I consider this a bug with the Python > openbabel package, it should be bundling and using a libopenbabel.so > that is compatible with the Python "manylinux1" ABI (based on CentOS 5), > we will investigate incorporating a workaround. Thanks a lot. Francois. > -- Greg > > > On 11/13/2018 5:53 PM, Francois Berenger wrote: >> Hello, >> >> On a Ubuntu 18.04.1 LTS, I get this error message when I start chimera. >> >> Is there a known fix? >> >> Am I running a too old version of chimera or should I run >> a version specially compiled for Ubuntu computers? >> >> Here is the full error message: >> --- >> # chimera >> Error while importing plipgui from >> /home/berenger/.local/lib/python2.7/site-packages: >> Traceback (most recent call last): >> File >> "/home/berenger/usr/chimera-1.12/share/chimera/extension/base.py", >> line 349, in _importExtension >> __import__(module) >> File >> "/home/berenger/.local/lib/python2.7/site-packages/plipgui/ChimeraExtension.py", >> line 8, in <module> >> from plipgui.core import cmd_plip, cmd_unplip >> File >> "/home/berenger/.local/lib/python2.7/site-packages/plipgui/core.py", >> line 50, in <module> >> from plip.modules.preparation import PDBComplex >> File >> "/home/berenger/.local/lib/python2.7/site-packages/plip/modules/preparation.py", >> line 13, in <module> >> from .detection import * >> File >> "/home/berenger/.local/lib/python2.7/site-packages/plip/modules/detection.py", >> line 12, in <module> >> from .supplemental import * >> File >> "/home/berenger/.local/lib/python2.7/site-packages/plip/modules/supplemental.py", >> line 26, in <module> >> import pybel >> File "/home/berenger/.local/lib/python2.7/site-packages/pybel.py", >> line 53, in <module> >> import openbabel as ob >> File >> "/home/berenger/.local/lib/python2.7/site-packages/openbabel.py", line >> 21, in <module> >> _openbabel = swig_import_helper() >> File >> "/home/berenger/.local/lib/python2.7/site-packages/openbabel.py", line >> 20, in swig_import_helper >> return importlib.import_module('_openbabel') >> File >> "/home/berenger/usr/chimera-1.12/lib/python2.7/importlib/__init__.py", >> line 37, in import_module >> __import__(name) >> ImportError: /home/berenger/usr/chimera-1.12/lib/libgomp.so.1: version >> `GOMP_4.0' not found (required by /usr/lib/libopenbabel.so.4) >> --- >> >> Thanks a lot, >> F. >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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(1) Autodock Vina executable on windows (2) selection of submodels
by Visvaldas K. 14 Nov '18

14 Nov '18

Dear colleagues, I'd like to report a couple of issues which have cropped up. (1) On Windows, running Autodock Vina in Chimea using local executable fails due to spaces in file path (gives error something like "File "C:\Program" not found). The thing is, the university computer admins do not allow change paths or copy system files around. It should be possible to escape spaces in file names, wouldn't it? (2) The selection of submodels does not work if it is used as a part of the list. For example, "sel #1.1" selects just the submodel 1 (let's say I have a set of 20 molecules in sdf file), which is fine, while "sel #1.1,#0" selects ALL submodels in #1 in addition to #0, and that does not seem to be right. Best regards, Visvaldas

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Secondary structure recognition issue in homology model
by Monika Tokmina-Lukaszewska 14 Nov '18

14 Nov '18

Dear Chimera Team, In my homology model (see attachment) it looks like there has been some issue with secondary structure recognition in one of the domains (highlighted in cyan). In .py file I added one of the protein templates (yellow) based on which the C-terminal domain was constructed. I am not sure what has happened to a final model, since template for that domain looks good. I was wondering if there is an option in Chimera which could fix that issue? Thank you for your time, Sincerely, Monika Lukaszewska -- Monika Lukaszewska, Ph.D. Senior Research Scientist Chemistry & Biochemistry Department Montana State University Bozeman MT, 59717 lab: (406) 994 5418 tokminalukas(a)montana.edu <tokminalukas(a)chemistry.montana.edu>

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Chimera installation
by Gonzalez Fernandez, Cristina 13 Nov '18

13 Nov '18

Hi all, I am new in the molecular docking field and I would like to start using Chimera. I would like to install it in Linux but use a GUI as in Windows. Is it possible? Thank you in advance! Cristina

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Save measured distances
by Dhananjay 13 Nov '18

13 Nov '18

Dear all, I am calculating distance between CA atoms as follows: sel #0:13@CA, #0:129@CA color red selection distance #0:13@CA #0:129@CA I want to save the measured distance between residue 13@CA and 129@CA in a file. I can do it using GUI. How can I do this within the command line ? Any help would be appreciated !! Thank you -- Joshi

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Editing mol2
by Francesco Pietra 13 Nov '18

13 Nov '18

Hi all: Is it possible editing .mol2 files with chimera? thanks francesco pietrta

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Drawing vectors depicting the movement of one conformer to another
by Beth Stroupe 12 Nov '18

12 Nov '18

Hi, I would like to make a figure depicting the movement of an RNA molecule from one conformation to another. It is not a simple rigid body rotation or translation but a rolling motion where some parts of the molecule move more than others. I would like to show vectors to show the rotation that are colored coded by the distance of the move. Is there a straightforward way to do this in Chimera? Thank you, Beth

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how to create using Chimera?
by Paris Tzou 10 Nov '18

10 Nov '18

Dear Sir, I am studying PDB id: 5MCT (p53-dna) complex. There is a "BIOMT TRANSFORMATIONS" required to generate the biological unit. Would you please guide me how to do this? Thanks a lot, Paris

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Re: [Chimera-users] 1up opt
by Elaine Meng 09 Nov '18

09 Nov '18

Hi Zhengzheng The format of your PDB file is not standard because all the H atoms are all at the end instead of with their their residues. Also they are all in a different chain (chain A) than the other atoms (chain B). Whatever program wrote this file wrote it incorrectly. You can easily see all atoms, e.g. commands: ~ribbon display (or use Actions menu to do the same things) but if you use Chimera features requiring chemical knowledge (findhbond etc.) it will not work correctly if the H and the other atoms are not recognized as being in the same residue. I tried editing so that all atoms were chain B, but it did not fix the problem, which is apparently instead caused by placing all the H atoms at the end instead of with their individual residues. You could fix it be removing and re-adding hydrogens in Chimera, but then the H atom positions wouldn’t be exactly the same. Commands: delete H addh It is recommended to send questions to chimera-users(a)cgl.ucsf.edu (CC’ed here) in case I’m not available to answer. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 7, 2018, at 8:02 AM, zheng l <zhengsfriend(a)hotmail.com> wrote: > > Dear Dr. Meng > > I used Chimera software for analyzing many protein crystal structures and then modified them and it has so faithfully doing job for me. However, this structure that I attached below is very difficult to modify. > > The problem is that the hydrogens in structure are hidden. Usually when I need to, for example, replaces a carbon to a nitrogen in a Phe the nitrogen will attached with a hydrogen if I set to have 3 bond for the nitrogen. But this structure is not showing hydrogens at all > > Would you please help me find a way of show all hydrogens need for modifying the protein structure? > > Thank you! > > Best regards! > >> Zhengzheng > > <1tup chain b opt 2.pdb>

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(no subject)
by rekha pydala 09 Nov '18

09 Nov '18

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FW: Chimera [viewer] for iOS in the future?
by Williams, Joanne 05 Nov '18

05 Nov '18

From: Bryan Crawford <bryanc(a)unb.ca> Date: Wednesday, October 31, 2018 at 3:53 PM To: "chimera(a)cgl.ucsf.edu" <chimera(a)cgl.ucsf.edu> Subject: Chimera [viewer] for iOS in the future? Hello, I use Chimera occasionally in my research, and extensively for teaching (biochemistry, cell biology, developmental biology). It is now the only remaining piece of software I use that requires me to bring a laptop computer to class. For everything else (PDFs, animations, Keynote presentations, etc.) I can use my iPad which connects by AirPlay to the projector, and screencast everything using Doceri. Furthermore, the touch-screen interface of the iPad seems ideally suited for many of the analyses and/or molecular renderings people use Chimera for. So I’m wondering if there are any plans to produce either a full or partial version (perhaps with only viewing capabilities) of Chimera that runs on iOS? If there is, I would be very happy to help with beta testing. If not, can I ask if you can recommend any software that runs on iOS that I might consider? Cheers -- Dr. B.D.Crawford Professor Matrix Dynamics Lab Department of Biology University of New Brunswick Fredericton, NB, Canada

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Automating H bond distance retrieval
by Samuel FreemanFox 01 Nov '18

01 Nov '18

Hi, I was wondering about the possibility of writing a setup.com file which is capable of opening a receptor.pdb and ligand.pdb file, locating the H-bonds between these two structures and then reporting back the lengths of the bonds? Currently I am able to open both files, execute addh, addcharge, and hbonds with my setup.com file. However I am unsure of how to proceed from there. Many thanks and I look forward to your response. Samuel Freeman-Fox ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Porton Biopharma Ltd, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. *******************************************

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Batch Processing of Molecular Attributes
by Benjamin Feinsilver 01 Nov '18

01 Nov '18

Hello, Is it possible to pass a CSV file to Chimera containing a list of SMILEs, then output their molecular attributes in a new CSV file? For example, volume, surface area, the number of surface points with positive electrostatic potential, and the energy of the molecule's current 3D conformation. If so, would you please let me know how I would accomplish this? Thanks, Ben

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Chimera use
by Hui Min 31 Oct '18

31 Oct '18

Hi there, Sorry to disturb you. I have a question of how to use the Chimera software. If I've already got a .pdb file and use SMART to predict the domains, how can I mark the 3D structure with user defined color？ Thank you in advance for your help -- *Hui Min* Postdoctoral Scholar Research, Department of Internal Medicine, College of Medicine, University of South Florida, Tampa, FL 33612 minh8(a)health.usf.edu

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How can I load a list of residues of protein?
by Paris Tzou 31 Oct '18

31 Oct '18

Dear all, I want to load a file containing a lit of residues of protein which is already shown in Chimera. I don't want to manually select the residues under investigation through "Favorite -- Sequence". Is there a way of doing this ? I know I can do it using command line like:select #0:15-17.C,263-265, 300-310.A. Instead, I can have a text file with content like: 15,C 16,C 17,C 263,A 264,A 265,A Thank you very much. Paris Tzou

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Split map from command line
by armoelle 30 Oct '18

30 Oct '18

Dear Chimera Team, I am trying to call the split map command directly from a script but somehow I don’t seem to be able to get it to run - maybe you can help me? I am calling scolorzone (which works perfectly) and then ( as suggested in the mailing list) use the accelerator command ac sm to split the map. However, generally nothing happens - sometimes though (I don’t know what triggers it - and I am not doing anything different) it runs perfectly fine. I am a bit puzzled as the same is the case no matter if I run form command line or I use the keyboard shortcuts gui. Many thanks for your help! cheers Arne ________________________________ Dr. Arne Moeller Independent Research Group Leader Department of Structural Biology Max-Planck-Institute of Biophysics Affiliated Researcher DANDRITE, Aarhus University, DK www.moeller-lab.com www.biophys.mpg.de/en/moeller.html Arne.Moeller(a)biophys.mpg.de 0049 69 63033057 Max-von-Laue-Strasse 3 D-60438 Frankfurt am Main Office L.1.015

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CUDA on Mac OSX 10.14 Mojave
by David Bhella 26 Oct '18

26 Oct '18

Dear All I just learned (after updating) that nVidia CUDA support is not in place for the latest Mac OS X release. I have a 2010 Mac Pro with a Quadro 4000 card in - which is still fine as a desktop. Chimera throws an error now - complaining about the graphics settings being incorrect: "Display misconfiguration. Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera installation instructions." Presumably because the graphics driver is not working correctly. Has anyone succeeded in resolving this? Or do I need to roll back to 10.13? A quick scan of the Mac/nVidia Forums suggests that CUDA support may not be forthcoming anytime soon, but I thought I would check if anyone has resolved this before going through the hassle of downgrading. Thanks, D Dr David Bhella Director - Scottish Centre for Macromolecular Imaging MRC-University of Glasgow Centre for Virus Research Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella

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Dynamic Protein
by Alex Nazlidis 26 Oct '18

26 Oct '18

Dear Elaine, is there any way in chimera to produce a clip similiar to this ( https://www.youtube.com/watch?v=zm-3kovWpNQ at 5:44)? You know animating the dynamic nature of a protein and its folding process. Thank you very much in advance, Alex

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defining planes and axes based on existing ones
by ChuHui Fu 25 Oct '18

25 Oct '18

Hello, I am trying to define planes and axes that are orthogonal to the planes and axes that I have previously defined. I have an alpha helix, and I only managed to define one plane and two orthogonal axes around the helix. Is it possible to define the rest of the axes and planes? Thanks! -- ChuHui Fu B.S.Candidate in Chemistry Haverford College, Class of 2019 cfu(a)haverford.edu

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Saving a moved PDB only moved in a new session
by Marta Perez Illana 25 Oct '18

25 Oct '18

Hi all I am working with chimera, and I have a map and a pdb. 1) I have split the pdb into several fragments in order to fit them into the map 2) I have successfully moved the PDBs and fitted them into the map 3) I have "write each PDB" "relative to the map, which seems to make sense :) 4) In the current session I keep the map and the moved PDB open ...plus I open the just saved "wrote PDB" (intended to be on the same position I moved it). To me both, the opened PDB (which I have moved) and the just saved PDB, might be in the same position, fitting into the map... But... the just save-written PDB is clearly somewhere else... :( 5) But... If I make a NEW session, opening the map and the "wrote PDB", everything make sense, and the PDB is where I in fact moved to keep it fitted... Why is that that in the current session the written-PDB is not where it was "moved"; but when a new session is opened it is displayed where it was moved? It seems that everything works fine, it is just a bit confusing to me. Thanks in advanced! Marta

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Help SASA
by Andrea Yimena Cardona Barreto 25 Oct '18

25 Oct '18

Good afternoon, my name is Andrea Cardona and I´m a student of a magister in Human Genetics at Universidad Nacional de Colombia. In my thesis I´m interested in obtain the surface accessible solvent area of a homotetrameric protein (fumarate hydratase) but I have some troubles with Chimera. Can you give some help? -- Andrea Yimena Cardona Barreto Maestría en Genética Humana Universidad Nacional de Colombia

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Accessible surface area and ASA per residue
by anastasia＠campus.technion.ac.il 25 Oct '18

25 Oct '18

Dear User, I'll appreciate your help. I've worked with Chimera previously, but have not used it recently. Now I try to repeat some of the analysis I've done, but I don't see the option ,solvent accessible surface, in the software (I guess I've installed a newer version). I would like to color all the exposed (to the solvent) residues like in the image below and export a table with these values per atom and residue. [cid:7c648fa9-c7cf-4dab-bf40-f0b4a95b8f47] What I tried to do this time is : 1. Show a molecular surface.. 2. Depiction --> render by attr , when attr is set to areaSAS on residues [cid:f46b071c-36ab-4792-bfc2-31eb50fc2be3] The result I got was: [cid:6b44e796-b2c2-42f8-aac8-1ab725121d38] Am I doing it right? how can export the calculated areaSAS per atom and residue from chimera? How the SAS values calculated in Chimera? Does the higher value means that this residue is more exposed? Thank you for your help, Anastasia

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Chimera bug report submission
by Anas 23 Oct '18

23 Oct '18

The following bug report has been submitted: Platform: osx_x11 Chimera Version: (None given) Description Hello, I am trying to superpose a .pdb file on a density map (.mrc), and save it as .pdb. Chimera saves the file, but when I open it it doesn’t display any density map. Just the pub file which was superposed. I am doing it to start model building, but I am stuck at this. Kindly help.

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MacOS Mojave
by Eric Pettersen 22 Oct '18

22 Oct '18

Hi all, A fix for the non-showing buttons problem on MacOS Mojave (10.14) is now in the Chimera daily build and the 1.13.1 release candidate. If you encounter any problems with the new version please use Chimera’s Help→Report A Bug to let us know about them. Note that the fixed version only runs on Mac OS 10.10 or later, whereas the previous version also ran on 10.8 and 10.9. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Re: [Chimera-users] Chimera problems
by Elaine Meng 20 Oct '18

20 Oct '18

> On Oct 19, 2018, at 8:41 PM, Shriwas, Pratik <ps774614(a)ohio.edu> wrote: > > Hi, > I am trying to use USCF chimera for studying docking between my compound and the receptor called GLUT1 (PDB - 4pyp or 1SUK). My concerns are: > > • I find different scores everytime I use the same compound and receptor Hi Pratik, Sounds like you are using the Autodock Vina interface of Chimera. Chimera does not calculate the docking, it just sends/receives data from an outside web service that is running the Autodock Vina program. It may be that the docking process uses some random numbers, and because the web service does not allow a high amount of sampling, it cannot always find the same top score(s). However, I do not know the details of Autodock Vina and you would have to look at its website <http://vina.scripps.edu/> and/or paper to learn about that. I’m guessing you are using Chimera’s Autodock Vina GUI to enter inputs, not the “vina” command. However, if you are using the command make sure you get a recent version of Chimera, because some problems with the command were fixed. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> > • I am not able to show my hydorgen bonds between compound snd receptor in GUI. Although I can see them in the list box. Maybe the atoms are not shown (for example, if the sidechain is not shown, the H-bond to the sidechain won’t be shown). To make sure the H-bonding atoms are shown, in the H-bond parameters dialog turn on the option “If endpoint atom hidden, show endpoint residue.” However, if that is not the problem, then maybe the graphics on your computer has trouble showing lines. You could try updating your graphics driver, or try showing the H-bonds as sticks instead of lines with command: setattr p drawMode 1. Or maybe it can draw lines but they are too thin for you to see. In that case, in the H-bond parameters dialog increase the “Line width” value. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbo…> > • I am not able to find exact binding energy. This is the central problem of docking! Firstly docking scores are not binding energies, only approximations, and secondly, one has to do a lot of conformational and positional sampling to find the most accurate position. The Autodock Vina website does not allow a high amount of sampling, as it is a shared resource provided for free. If you want to do more intensive docking you can download Autodock Vina (or some other docking progam like DOCK, Gold, ...) and run it directly. > • My ligand is not on pubchem/NIH servers. What is best way to find its smiles string. Different websites have different smiles string and I get different interactions. Usually there are multiple ways of writing the SMILES string for the same compound. As long as the compound looks right to you (has the correct covalent structure, the right elements connected in the right way) then the results should be equally valid even though the coordinates might be slightly different (e.g. rotated or translated or different conformation). Any slight change in inputs will change docking outputs, since sampling is not exhaustive, but the change does not mean one answer is “wrong” and the other is “right". > > Regards, > Pratik Shriwas > Phd Candidate, > Molecular and Cellular Biology program, > Edison Biotechnology Institute, > Ohio University. For future reference, Chimera questions should be sent to chimera-users(a)cgl.ucsf.edu (CC’d here). For Autodock Vina questions, see <http://vina.scripps.edu/questions.html> 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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Finding files my session is showing
by David Sáez 19 Oct '18

19 Oct '18

Hello everyone. I saved some sessions time ago. Now I found the .py files, and they work fine, but I do not remember what files I am opening when I restore the session. In the .py file I could not find any information about loaded topologies or pdb files. Can these data be recovered from a session? Thanks in advance

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Saving PDBs
by Elliott, Jabari 17 Oct '18

17 Oct '18

When attempting to save PDBs of multiple models into one file, I end up with a pdb file with no data (0-600 bytes). When attempting to open files in pymol, they are blank. Please advise. Thank you.

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Alias commands for volume pieces
by Benjamin Looker 17 Oct '18

17 Oct '18

Hello! I have recently received emails from Tom Goddard and Elaine Meng on this subject, but I believe it can be further clarified. The research group I am a part of routinely generates Gaussian cube files for molecular orbitals using the DFT program ORCA, we then manually use Chimera to change the level and color of the two phases of the resulting wave function, *which appear in Chimera as two **surface pieces* belonging to the same surface. In the volume viewer menu Data, *and* in the Model Panel, there is no way to see a #0.1 #0.2 model subnumber, and Group/Ungroup returns the error "Cannot group a single molecule." Is there a way to refer to volume pieces in the command line? Such that an alias can be written to do this formatting in a more efficient manner? Best, -- Benjamin G. Looker Graduate Student Lancaster Group

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Re: [Chimera-users] [chimera-dev] Chimera orbitals alias question
by Elaine Meng 16 Oct '18

16 Oct '18

> On Oct 13, 2018, at 2:34 PM, Benjamin Looker <bgl44(a)cornell.edu> wrote: > > Hello! > My name is Benjamin Looker, I am a chemistry graduate student at Cornell University, and our group often uses Chimera to visualize the orbitals output from the DFT software ORCA. > > When these .cube files are opened in Chimera, the two phases of the wavefunction surface are given different colors and bars in the volume viewer. > > My question is, when using an alias command, how would one set the level and color of only one of these phases, ie: to perform actions on only one of the bars and colors, instead of homogenizing the whole function? > > An alias such as: > alias ^orbitals volume all level 0.05 color #2d2d00000b0b style surface > > Is great, but that pesky "all" undermines the point of the operation. I have tried referencing model numbers, such as #0, #1, and #2 instead of "all," but Chimera returns an error. I do not know the label of the object that I am trying to affect. > > Any help would be greatly appreciated! > Best, > -- > Benjamin G. Looker > Graduate Student > Lancaster Group Hi Benjamin, I don't have an example cube file to test with, but from your description I'm guessing it has signed data and that is why Chimera automatically shows two isosurfaces when you open a single file. The levels are the same magnitude, just the opposite signs. How the initial display values are set is described in the “surface and mesh display” section of the Volume Viewer documentation: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/fram…> "For unsigned data types, an initial threshold is set so that 1% of voxels (1% of the volume encompassed by the data region) lie above it; for signed data types, positive and negative thresholds are placed symmetrically about zero." In that case, there is no way to specify in the command line changing only one isosurface and not the other. You can see in the Model Panel (open from Favorites) that the entire dataset is listed as one model. Although you could open the data twice and use your volume command on only one copy (specified by the model number as shown in the Model Panel) that would still leave both the isosurfaces on the other copy as initially shown. However, there is nothing magical about the initial display setting other than it is meant to be easily viewable. There is no knowledge used about the type of data (i.e. it doesn’t care or know that orbitals are what you’re showing) so you may want to go ahead and set all the isosurfaces using your values rather than relying on initial display. You can specify level and color multiple times in the volume command for multiple isosurfaces, e.g. volume #0 style mesh level 0.8 color red level 1.2 color 0,.5,.8 This is one of the examples in the “volume” command manpage <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. for future reference, the chimera-dev list is mainly for programming questions. General usage questions are better sent to chimera-users(a)cgl.ucsf.edu CC’d here

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Visualize 3-10 helix
by BuddySphinx 15 Oct '18

15 Oct '18

Dear Chimera users, I am wondering if there is a quick way in Chimera to visualize 3-10 helix? Or showing the dihedral angle of the peptide bonds? Best, Yangqi Sent from Mail for Windows 10

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problem with autodock vina page
by ammad aslam 13 Oct '18

13 Oct '18

I wonder, is there any problem with autodock vina website vina.scripps.edu/download.html ? I and my friends here cannot open it. Can anyone update me about the real problem. Regards, Ammad

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Morphing code
by Minh Le 12 Oct '18

12 Oct '18

Hello there, I'm currently having trouble with the morphing code in chimera and I don't know how to use Python to make the morph.py. Is there any way you can help me with this? Thank you, Minh

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MD movie metafile
by Matthias Fellner 12 Oct '18

12 Oct '18

Good day I successfully loaded NAMD psf/dcd files into chimera (version 1.13.1) using the tools MD movie interface. As I have many runs and each has multiple dcd files I wanted to use a script to load the different runs, instead of manually picking all the files through the interface each time. I tried to follow the limited instructions of the MD Movie homepage but failed to get anywhere. I tried some versions of this command: md: D:\script.txt or movie: D:\script.txt The command md appears to try to start MDA (MultiDomain Assembler), the command movie wants some other unrelated inputs. I am also not sure if the script command would even work like this: namd(psf/dcd) D:\structure.psf structure_MD001.dcd - D:\ Any advice is appreciated Thank you Matthias Fellner

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Generating symmetry mates
by Vani Pande 10 Oct '18

10 Oct '18

Hello, I wanted to generate symmetry mates for the protein, I am not finding a way to do so in chimera.The protein is a monomer in an asymmetric unit. Thanks Vani Pande Int PhD Biological sciences IISER Pune 20162013

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C-N peptide bond within one peptide
by Emily Xu 08 Oct '18

08 Oct '18

Hello, Is there a way to join two ends of a peptide in Chimera? I am trying the create a peptide bond linking the C and N termini in a singular peptide to form a cyclotide. Is this possible in Chimera?

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error opening .cif file
by Francesco Pietra 07 Oct '18

07 Oct '18

Hi With my /opt/UCSF/Chimera64-1.11.2/bin/chimera, I notice a mistake in opening 4i4t.cif.gz (as 4i4t.cif), i.e., residue 43 and 44 in chain D are mis-numbered 44 and 45, giving the wrong impression that residues 43 and 44 are missing. I have not checked anything else. cheers francesco pietra

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Recording movie at 720p
by Ahmad Khalifa 05 Oct '18

05 Oct '18

I'm recording a movie in the command line using: movie record movie stop movie encode output ~/ I tried to include the option preset dvd for movie encode, I recieved the following error: "Error reading paper_movie.txt: AttributeError: 'module' object has no attribute 'standard_formats' File "/opt/UCSF/Chimera64-1.12/share/MovieRecorder/moviecmd.py", line 124, in encode_op settings = RG.standard_formats.get(preset) See reply log for Python traceback." What am I doing wrong and how can I record my movie at 720p? Regards.

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Maps/models display/activate checkboxes? [Feature suggestion]
by Oliver Clarke 04 Oct '18

04 Oct '18

Hi, It would be very helpful to have a way to undisplay all maps, or all models, at once. This would be particularly handy when inspecting the fit of a model in a map, as the residue tooltips don’t work when there is a surface in front of the atoms. Would it be possible to add two checkboxes in addition to the model specific checkboxes and the “all” checkbox that controls whether models, maps, or both are displayed? I would envision both the model and map checkboxes working as toggles, checked by default, but one could uncheck either to temporarily undisplay all maps/models, and then check the box again to return to the previous state. I know most effort is going into ChimeraX, so please disregard if this is difficult to implement. Cheers OIi

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Chimera pdb error
by 김민재 03 Oct '18

03 Oct '18

Hi! Thanks for all of your help, but I got another problem... I uploaded a picture of the Chimera error. The HG hydrogen atoms are not being shown in Chimera. When I extract just the CG and HG pdb lines and input them, Chimera works fine and can even calculate the surface. But, when I run it with the pdb file that I have right now, it keeps returning that error. I thought that maybe Chimera could only calculate the surface for atoms which are connected, and that the program was looking for mandatory bond between the atoms. I was wondering if there was a settings change I could make to fix this, or if there was any other way to go about straightening things out to calculate the solvent excluded area of this pdb file.

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MacOS Mojave
by Eric Pettersen 01 Oct '18

01 Oct '18

Hi all, MacOS Mojave will be released this Monday, Sept. 24. On Mojave, Chimera buttons and popup menus are not shown until the window containing them is resized. Therefore we advise against upgrading to Mojave until we come up with a fix for this issue — which we will announce on this list as soon as it is available. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Hiding models one by one?
by Ahmad Khalifa 01 Oct '18

01 Oct '18

I'm trying to hide a range of models using ~modeldisplay #16-60. For display purposes, I want to to make them disappear one by one or in groups. I can of course write down a bunch of ~modeldisplay #16; wait 5; ~modeldisplay #17; wait 5;...etc. Is there a way to for loop that process in the command line or do it in a better way? Regards.

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Calculating surface area of a single atom
by 김민재 01 Oct '18

01 Oct '18

Hey everyone! I've been trying to calculate the solvent excluded surface area of a single hydrogen atom, but Chimera keeps returning an error "miscalc code 5" message whenever I run the "surface probeRadius" command. I would really appreciate anyone's help.

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FW: Contributing to ChimeraX ?
by Williams, Joanne 01 Oct '18

01 Oct '18

From: Nicholas Yue <yue.nicholas(a)gmail.com> Date: Sunday, September 30, 2018 at 3:40 AM To: "chimerax(a)cgl.ucsf.edu" <chimerax(a)cgl.ucsf.edu> Subject: Contributing to ChimeraX ? Hi, I took ChimeraX for a spin and when I save out to OBJ, the geometries looks connected up wrongly. I was hoping I can take a look at the source code to attempt to fix it myself. I see git being mentioned in the documentation. Is there a git repo I can clone and contribute to? If I need to sign any documents before contributing, let me know :-) I have other geometry format I'd like to write out to and also I am hoping to write out quads rather than triangles for use with OpenSubdiv in rendering software like RenderMan, Arnold, Mantra etc. Cheers -- Nicholas Yue Graphics - Arnold, Alembic, RenderMan, OpenGL, HDF5 Custom Dev - C++ porting, OSX, Linux, Windows http://au.linkedin.com/in/nicholasyue https://vimeo.com/channels/naiadtools

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