- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Query on morph command in Chimera
by Elaine Meng 22 Mar '15

22 Mar '15

On Mar 22, 2015, at 9:38 AM, vinothkumar <vkumar(a)mrc-lmb.cam.ac.uk> wrote: > Dear Elaine, > I have three different volumes/maps of the same protein but differing in conformation. I am able to use the command line - ‘vop morph #0,1,2 constantVolume True model #3 frames 200’ which then interpolates and I could produce a movie. However, by default the threshold for the volumes and level goes to 4. Is there a way to insert in the command line to tell that all the volumes be set to level (1) and a certain threshold. > Thank you > Regards > Vinoth Dear Vinoth, You should adjust the threshold of the maps before the morphing. This could be done with the “volume” command if you are not using GUIs, e.g. command: volume all level 1 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general> Actually, my own experiments suggest it is only the threshold of the first input map that matters in setting the starting level of the morph. If you use the “constantVolume” morphing option, however, the threshold will be adjusted to keep the enclosed volume constant. If you really wanted to keep it exactly at 1 through the whole morph, you would not use that option. I hope this helps! For future questions, we recommend you send them to chimera-users(a)cgl.ucsf.edu (CC’d here) instead of to me or other individuals directly, unless you are including private data. Thanks, 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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problem related to open the chimera file by Coot
by Smith Liu 21 Mar '15

21 Mar '15

Dear All, I have fit a PDB file with a MRC by the Chimera. I saved both the fitted PDB file and the fitted MRC file by coot. When I open the fitted PDB file and the fitted MRC file by Chimera at the same time, they still fit perfectly. However when I open the Chimera fitted PDB file and the Chimera fitted MRC file by coot, the protein backbone (and the sidechains) does not fit the MRC file anymore. Will you please tell me what should I do in order to have the Chimera fitted PDB file and the Chimera fitted MRC file still fit in Coot? I am looking forward to getting your reply. Smith

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Constraining map-to-map fitting based on symmetry?
by Oliver Clarke 20 Mar '15

20 Mar '15

Hi, If I have two maps of the same symmetry (say C4), and I align them using fit in map, is there any way to force chimera to keep the rotation axes of the two maps aligned, and to only search rotation around (and translation along) that axis, rather than arbitrary rotations? Cheers, Oliver.

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Contour levels
by Nicholas Michelarakis 20 Mar '15

20 Mar '15

Hello all, Forgive me if this is a silly question but I was under the impression that when you opened two density maps in volume viewer and used the Fit in Map tool, with the Use only data above contour level option ticked, the correlation would change according to the contour level you selected in the volume viewer. In my case this does not happen. If this is indeed a bug, I would be happy to provide further information. Atm, I'm using Chimera 1.10. Thank you very much in advance. Best, Nick

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Total number of atoms in all submodels
by Cruz, Phil (NIH/NIAID) [C] 19 Mar '15

19 Mar '15

Dear Chimera users, When I fetch a biological unit into Chimera from PDB, the symmetry related units are placed into separate submodels. I would like to find the total number of atoms in all submodels that make up the biological unit within a python script. Constructs (and variations that I've tried) such as the following only give the number of atoms in each sub model: numAtoms = len(openModels.list(modelTypes=[Molecule])[0].atoms) Is there some way to get the grand total of atoms? Alternatively, if the script could find the total number (or list) of the submodels, I could probably still handle it. My example is the virus capsid 1ej6. Thanks for any suggestions. -- Phillip Cruz, Ph.D. Contractor, Medical Science & Computing Computational Structural Biologist Computational Biology Section Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Dr., Room 3B62 Bethesda, MD 20892-0485 Office: 301-451-1089 http://bioinformatics.niaid.nih.gov<http://bioinformatics.niaid.nih.gov/> (Within NIH) http://exon.niaid.nih.gov<http://exon.niaid.nih.gov/> (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Interaction interface between two residues and measure buriedArea
by ms 19 Mar '15

19 Mar '15

Dear all, I am trying to understand what is the area buried between two residues (or between one residue and two other ones) in several structures. It seemed to me the best way to do this was to use the command "measure buriedArea :res1 :res2" on the full structure (once all non-protein components have been cleaned out of it). The overall trend of these measures seems consistent with visual inspection. However I have a couple of questions about it: 1) I am unsure about what value is best to use/compare, buriedSAS and buriedSES. It seems to me that the difference between the two is essentially in the geometrical protocol used. Is there any general wisdom about what do they physically mean and how should I approach each value? 2) In some cases I receive *negative* values for buriedSAS and/or buriedSES. Looking on the ML it seems that it is a symptom of a buggy or failed area calculation (e.g. http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-April/005119.html ). However it also says that I should see a "fallback" warning on the Reply Log -I see nothing of the sort. How do I troubleshoot this? Also in cases where the calculated value is positive, how can I be sure that the values are indeed meaningful? Any other feedback on the kind of measurement I am trying to do is more than welcome. Thanks a lot, Massimo

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how to convert mtz file to a file which can be openne by Chimera
by Smith Liu 19 Mar '15

19 Mar '15

Dear All, Will you please tell me how to convert mtz file to a file which can be openne by Chimera? Smith

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Chimera service unavailable
by SA 18 Mar '15

18 Mar '15

Dear developer, I am using Chimera PDB2PQR module. However, it is failed. The error message is below: self.backend = Backend(service, url) File "/soft/chimera/Chimera64-1.10.1/share/WebServices/opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Service 'opal:pdb2pqr_1.8' is unavailable. See Reply Log for more details. For your indormation, I am using the latest linux version of Chimera. Thank you. Siti Postdocs UCSD

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How to get prmtop file corresponding to a pdb file
by Mahendra B Thapa 18 Mar '15

18 Mar '15

Dear Chimera users, To get *Amber prmtop file* corresponding to a *pdb file using Chimera*, I did the following steps: 1] tools -> Amber -> write prmtop 2] In a pop-up window 'save file in chimera', I gave file name, say, aa.prmtop, then clicked save. 3] No charges message appeared, then I clicked 'Assign charges'. 4] In a pop-up window 'Add charge', I selected 'AM1-BCC' in other residues, then clicked ok. 5] In a pop up window 'specify net charge', I selected 'AMI-BCC' in charge method 6] I got 'chimera error' - failure running ANTECHEMBER for residue HIS. Check reply log for details. 7] In reply log, '*Failure running ANTECHEMBER for residue HIS*' seen. Any help in this issue will be a good help for me. Thank you. Mahendra Thapa University of Cincinnati,OH

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visualization of electrostatic potential
by Christos Deligkaris 18 Mar '15

18 Mar '15

Dear Chimera Users, I am interested in visualizing the electrostatic potential calculated by the APBS tool Chimera provides and I have several questions regarding this. 1) We have been having troubles running the PDB2PQR/APBS tools (I am not sure if we had trouble with both, it has been a few weeks) that Chimera provides, and I believe we fixed this by changing the version number at the very end of the web server address. Is there anything else we could have done to fix this? 2) I noticed that the numbers that are displayed when I visualize the APBS-calculated potential on the MSMS are very different from the numbers shown when I use the volume viewer (I mapped the values to atoms and then displayed those as labels). Why are those numbers not the same? Is it because the volume data will map the potential near the atoms and display that, whereas the potential on the surface (or actually 1.4 Angstroms from the surface) will display the potential value on the surface? Should I assume that the units are the same? 3) I am interested in finding the "patches" of the molecular surface the have fairly positive potential. I am familiar with the PatchFinderPlus server but I am interested in finding several patches, not just the largest one. I have not found any tool related to this in Chimera, please let me know if I am wrong. So,I found the redarea.py script avalaible from Chimera's website and I am thinking about modifying it in order to do this. The script iterates over all surface pieces. Is it possible to calculate the distance between vertices and atoms? Is it possible to obtain the potential value at a vortex? I think this would help me get started... Thank you very much, Christos Deligkaris, PhD Assistant Professor of Physics, Drury University 900 N Benton Ave, Springfield MO, 65802 Office Phone: (417) 873-7234 www2.drury.edu/christos <http://www2.drury.edu/christos/index.html> @DeligkarisGroup <https://twitter.com/DeligkarisGroup> +ChristosDeligkaris <http://google.com/+ChristosDeligkaris>

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Re: [Chimera-users] FW: How to get prmtop file corresponding to a pdb file
by Mahendra B Thapa 18 Mar '15

18 Mar '15

Dear Dr. Victor, Thank you for reminding me about the protonation state of HIS. As a trial, I changed all HIS to HID and again repeated my previous steps. This time, I got some python track back errors. I suspect the source of error could be the initial pdb file which I used in chimera ; the pdb file was obtained from other software (like online server), so some atom names were different from that of AMBER. My goal was to get AMBER prmtop corresponding to pdb files which were generated by programs other than AMBER so that I could use ambertools. So, may I need to convert all such pdb files compatible with amber pdb format ? Thank you for help, Mahendra Thapa On Wed, Mar 18, 2015 at 5:08 AM, Thapa, Mahendra (thapamb) < thapamb(a)mail.uc.edu> wrote: > > ------------------------------ > *From:* Victor Muñoz > *Sent:* Wednesday, March 18, 2015 3:08:18 AM (UTC-06:00) Central America > *To:* Thapa, Mahendra (thapamb) > *Cc:* chimera-users(a)cgl.ucsf.edu > *Subject:* Re: [Chimera-users] How to get prmtop file corresponding to a > pdb file > > Dear Mahendra, > > The error is due to HIS not being the standard residue name for Histidine > in the Amber force field. In Amber, histidine residues are named either > HIE, HID or HIP depending on their protonation state ( > http://ambermd.org/Questions/HIS.html) Change the name of the histidines > on the PDB file accordingly to their protonation state and it should work > fine. > > Kind regards, > > Victor > > 2015-03-18 6:39 GMT+01:00 Mahendra B Thapa <thapamb(a)mail.uc.edu>: > >> Dear Chimera users, >> >> To get *Amber prmtop file* corresponding to a *pdb file using Chimera*, >> I did the following steps: >> 1] tools -> Amber -> write prmtop >> 2] In a pop-up window 'save file in chimera', I gave file name, say, >> aa.prmtop, then clicked save. >> 3] No charges message appeared, then I clicked 'Assign charges'. >> 4] In a pop-up window 'Add charge', I selected 'AM1-BCC' in other >> residues, then clicked ok. >> 5] In a pop up window 'specify net charge', I selected 'AMI-BCC' in >> charge method >> 6] I got 'chimera error' - failure running ANTECHEMBER for residue HIS. >> Check reply log for details. >> 7] In reply log, '*Failure running ANTECHEMBER for residue HIS*' seen. >> >> Any help in this issue will be a good help for me. >> >> Thank you. >> Mahendra Thapa >> University of Cincinnati,OH >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >

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on color zone
by Smith Liu 17 Mar '15

17 Mar '15

Dear All, I have a mrc file for a protein complex with a 3-fragment sheets (from A to B, from B to C, from C to D, and they were connected by H-bonds). Will you please introduce to me on how to use color zone to split to get the mrc file for each fragment of the sheets? I have tried to do it by myself, however I find the splitting was not done based on fragment, i.e., I cannot get the mrc file for each fragment of the sheets. I am looking forward to getting your reply. Smith

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Chimera tutorial at VIZBI conference in Boston on Tuesday, March 24
by Samuel Hertig 16 Mar '15

16 Mar '15

Dear Chimera users, In case you are interested in learning the basics of Chimera and if you can make it to Boston on March 24, the RBVI will be teaching a small Chimera tutorial as part of the Visualizing Biological Data (VIZBI) conference. Details and registration: http://www.vizbi.org/2015/Program/#Tuesday Best regards, Sam Hertig, PhD Postdoctoral researcher Resource for Biocomputing, Visualization, and Informatics University of California, San Francisco

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UCSF Chimera error: X Error of failed request: BadDrawable (invalid Pixmap or Window parameter)
by Muhammad Sufian 16 Mar '15

16 Mar '15

Dear all Chimera users, I tried to install following version of Chimera; chimera-1.10.1-linux_x86_64.bin but after installation, following error appeared after its execution; sufian@system01:/usr/local/chimera/bin> ./chimera X Error of failed request: BadDrawable (invalid Pixmap or Window parameter) Major opcode of failed request: 72 (X_PutImage) Resource id in failed request: 0x2200064 Serial number of failed request: 1357 Current serial number in output stream: 1363 I also tried to install Chimera 1.9, but got same error. My system specifications are; Processor: x86_64 Operating-system: GNU/Linux (OpenSUSE 12.1) Kernel: Linux 3.4.63-2.44-desktop Kindly guide me how to resolve this issue. Regards. Muhammad SufianM.Phil. scholar (Molecular Medicine),Computational Biology Laboratory,Lab no. P-103, PCMD-Extension,Dr. Panjwani Center for Molecular Medicine and Drug ResearchInternational Center for Chemical and Biological SciencesUniversity of Karachi, Karachi, Pakistan

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a question related to segment map
by Smith Liu 16 Mar '15

16 Mar '15

Dear All, After I segment a map into diffrent color, will you please tell me in detail how can I erase some specific parts of the map which I do not nee for some purpose? Smith

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Selecting just 1 carbohydrate chain
by Tein Leong (PG Research) 12 Mar '15

12 Mar '15

Hello, Thank you for the amazing programme. I’m using it for the first time and I can do most of the things I needed to do. I am writing to ask if it is possible to “color” just one carbohydrate chain ? I’m coloring an antibody crystal structure which is made up of two heavy chains. Each chain has a carbohydrate attached. I wanted to color both carbohydrate in different colors but I’m unable to do so. When I go to “Select” > “Residue” , the programme can only select all carbohydrate residues. Please advice. Thanks ! Best wishes, Tein Foong Leong PhD Student Jacqui Wood Cancer Centre, Level 7 Ninewells Hospital University of Dundee DD1 9SY The University of Dundee is a registered Scottish Charity, No: SC015096

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binned color ranges for scolor?
by Oliver Clarke 11 Mar '15

11 Mar '15

Hi all, I was wondering whether it is possible to use binned ranges for scolor? Specifically, I would like to color one volume by the density values of a second volume, but rather than using a continuous color palette, I would like to highlight several discrete bins with particular colors - e.g coloring all values between 2 and 4 red, and all values between 6 and 8 green, while leaving other voxels uncolored (or colored gray, for example). Is this currently possible? I couldn’t figure it out - both cmap and map range seem to give continuous coloring. Best, Oliver.

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How to lower the map size
by 李智海 09 Mar '15

09 Mar '15

Hi, Now I have a density map with a dimension of 820*820*820, it is too large for me to perform image processes with Chimera. So I was wondering whether there is a way to decrease the map size rather than re-reconstruct the map with bined particle image. please help me out! Thank you in advance! Zhihai Li

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Re: [Chimera-users] Request for support - UCSF Chimera
by Eric Pettersen 04 Mar '15

04 Mar '15

On Mar 4, 2015, at 10:14 AM, Nishant Ray Velagapudi <nishray(a)uw.edu> wrote: > Hello Mr. Petterson, > > I was looking for some help with using UCSF chimera and I was wondering if I can directly email you my question. If this is not the appropriate address, my apologies, and could you point me in the appropriate direction for support? Hi Nishant, You should probably send questions like these to the chimera-users mailing list. That way other people can benefit from the answer, and it also allows others to answer in the cases where I'm not really the best person for the question. > My issue is that I want to automate the process of creating and saving structure based sequence alignments. It has been simple to open the file and align them, but I am not sure how to save the .fasta alignment file out. Here is what I have so far: > > for fn in file_names: > replyobj.status("Processing: " + fn) > rc("open " + fn) > rc(mm #0 #1 show true) > rc("close " + fn) > > The bold line is the problematic one - is there any way to write out the resulting alignment file in a programmatic fashion? Yes. You can locate the MultAlign Viewer (MAV) instance using the code in this previous chimera-users mail: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010017.html That message also describes how to save the alignment to a file, in conjunction with the info in this message: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010015.html You can search the chimera-users list from this page to see if your question has been asked previously: http://www.cgl.ucsf.edu/chimera/docs/feedback.html I hope this helps. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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concatenate
by sunyeping 04 Mar '15

04 Mar '15

Dear all,I am dealing with a EM map which is a double helical filament and composed of two protein chains winding each other. Each of the two chains is composed of multiple same protein subunits. Now I am trying to color one chain of the map with one color, and the other chain with another color. How should I do that?Besides, it is known that multiple such double helixes can constitute a longer helix by a head-to-tail way. I can open several helixes in chimera, but how to concatenate they correctly into a long helix?Could you help me with these questions?With many thanks! Yeping Sun Institute of Microbiology, Chinese Academy of Sciences

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Command for zooming in
by Anindito Sen 04 Mar '15

04 Mar '15

Dear All, What is the command for zooming into a portion of a density map ? This will be just using the command line for the zoom-in instead of using the middle mouse button. Thanks Andy

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Select residue by array index, not residue id
by Thomas Hrabe 03 Mar '15

03 Mar '15

Hi everyone, is there a way to select a residue by it’s array index, starting at 0 -> sequence length rather than using the residue id? Thank you in advance for your help, Thomas

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Re: [Chimera-users] rmsd calculation for pre aligned structures
by Elaine Meng 02 Mar '15

02 Mar '15

Hi Oliver, In that case, you can just show the sequence of one protein, then use the sequence window menu: Structure… Associations to associate both structures with that one sequence, then sequence window Headers menu to show the RMSD of interest, etc. This would work even if the sequences of the structures were slightly different, as long as they were both similar enough to the sequence in Multalign Viewer that Chimera could figure out the association accurately. Elaine On Mar 2, 2015, at 3:12 PM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > Hi Elaine, thanks for the reply! This sounds like exactly the right solution. However, when I try to add a sequence in the sequence dialog, Chimera hangs on “running Needleman-Wunsch”. > > I suspect this is because my sequences are so long (~5000 residues). > > But I don’t actually need to align them - they are already aligned as they are actually the same sequence, because I am looking at different conformations of the same protein. > > I guess I can create a dummy sequence alignment, with two identical sequences, but it would be nice to have some way of telling chimera not to align the sequences, or to allow for manual alignment in cases such as these - perhaps a “Do not align” or “align manually” checkbox in the add sequence dialog would do the trick. > > Thanks again, > Oliver.

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rmsd calculation for pre aligned structures
by Oliver Clarke 02 Mar '15

02 Mar '15

Hi, I have two structures that are pre-aligned in another program, and I would like to calculate a per-residue rmsd between the two structures and assign this to an attribute that I can use to color one of the structures. Is there any way to do this at present? The mavRMSD attribute only seems to be calculated after matchmaker, not after using the regular “rmsd” command. Perhaps there is a way to do a dummy run of matchmaker, somehow forcing both structures to remain fixed? Best, Oliver.

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explicit parentheses in atom selections
by Oliver Clarke 02 Mar '15

02 Mar '15

Hi all, Would it be possible at some point to allow the use of explicit parentheses when grouping selections on the command line? It would make it much easier/clearer when using multiple boolean operations (e.g "ligand z<5 &~ ligand &~ solvent” could be “ligand z<5 &~(ligand | solvent)”). Is there a reason why this kind of syntax is not used at the moment? Also, just a random thought for a future version - it would be really handy to have something like the “Macro recorder” function of ImageJ or similar programs. This records whatever the user does using the GUI (while the recorder is active) and spits out the equivalent scripting commands to a dialog, where they can be saved and reused, or turned into a script. This can be a very powerful tool for learning the command line functionality of a complex application in an interactive manner. Cheers, Oliver.

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Embed chimera into my gui code
by hy liao 26 Feb '15

26 Feb '15

Hi, I am creating a GUI using tkinter, and I would like to embed chimera into it. Specifically, I would like to display a 3D molecule density map using chimera and inside my GUI. Chimera would be activated while the GUI is on. Is there documentation to accomplish this? Thanks! Stu

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Inverse volume-erasing
by kzhang＠mrc-lmb.cam.ac.uk 25 Feb '15

25 Feb '15

Dear Chimera users, Dose anyone know how to do inverse volume-erasing? Normally we use the eraser to erase density we don't want to keep. However, what shall I do if I want to keep the density within the eraser while getting rid of other parts? Many thanks Kai

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Re: [Chimera-users] Inverse volume-erasing
by kzhang＠mrc-lmb.cam.ac.uk 25 Feb '15

25 Feb '15

Thanks! This is a good solution. But I wonder if there's an interactive way just like the eraser, but doing the opposite thing. It might help on difficult cases when you want a real time feedback what you are erasing and keeping just in Chimera without external command. Kai > difference ma p > <kzhang(a)mrc-lmb.cam.ac.uk>于2015年2月25日星期三写道： >> Dear Chimera users, >> Dose anyone know how to do inverse volume-erasing? Normally we use the eraser to erase density we don't want to keep. However, what shall I do if >> I want to keep the density within the eraser while getting rid of other parts? >> Many thanks >> Kai >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu <javascript:;> >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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about model coordinates
by Tat Cheung Cheng 20 Feb '15

20 Feb '15

Hi, I recently got a ~4.4A EM map and built a improved model using MDFF. The map and model is well aligned when loaded in Chimera. But it is off when I hit "center" in the volume viewer, as the origin is shifted. As I try to improve the model in Coot, the map and model isn't aligned at all in Coot, seemingly by the same offset when "center" button was hit. And also the values in the original index in the volume viewer is different from the values in the header in the density map. So I wonder what determines the origin index? and is it possible to find the shift and transform the coordinates in the model so as to align the model with the map in coot? Thanks a lot. Tc

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problem installation on linux 64 bit
by Chiara Parravicini 20 Feb '15

20 Feb '15

<chimera-users(a)cgl.ucsf.edu>Dear Chimera Users, After installing Chimera from the precompiled version chimera-1.10.1-linux_x86_64.bin (the installation completed without any error), I get the following error when I run the binary: libGL error: unable to load driver: nouveau_dri.so libGL error: driver pointer missing libGL error: failed to load driver: nouveau libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: GLXBadContextTag Major opcode of failed request: 156 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1455 Current serial number in output stream: 1455 I would appreciate any help or suggestion! Many Thanks in advance Chiara

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Restricting "select by conservation" to a subset of sequences in a multiple alignment
by Oliver Clarke 18 Feb '15

18 Feb '15

Hi, I very much like the sequence tools within Chimera - I find the capacity to load in multiple alignments and select by conservation particularly handy. I have two suggestions that I would love to see in a future version of chimera (or maybe they are already in there and I don’t know about them!): 1. Selection of sub-groups of sequences within a multiple alignment for selecting residues by conservation. This would enable the easy selection/identification of residues that are specifically conserved within individual families with different functions or substrates - for example, a position that is an arginine, and always an arginine, in one subgroup of proteins that we know have a particular function, and always a glutamate in another group of proteins that we know possess a different but related function. It is possible to do this currently by loading in multiple different sequence alignments and saving and intersecting selections, but having a popup menu in the select/render by attribute tab where you could select or deselect sequences that contribute to the analysis of conservation would make it much easier. 2. Optional addition of sequence similarity, as well as identity, to the analysis of sequence conservation would make analysis of alignments including quite divergent sequences much more meaningful. Even better would be if the definition of similar groups for this purpose was user-adjustable and had allowance for overlapping groups of similar residues. Cheers, Oliver Clarke.

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MD movie export from per frame script
by Ankit Agrawal 18 Feb '15

18 Feb '15

Hi all I want to write a script which can create movie (.mp4) from per frame script. Because I want to show all models in movie. Please help Thanks Ankit Agrawal Department of Chemical Science IISER Mohali, India

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showing shapes in only selected Chimera animation scenes
by Michael Oldham 17 Feb '15

17 Feb '15

Chimera users, I am making an animation that needs to include either a box generated with an opened .bild file using a .box command or a rectangle generated by "shape rectangle” I wish the box or rectangle to appear in some scenes but not in others. My problem is, if I choose to show the box or rectangle in the first scene then it is shown in all subsequent scenes even if they were created in which the box or rectangle were not shown. Any suggestions on how to show the box or rectangle in only selected scenes of the animation. Thanks Mike Oldham Rockefeller University

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Fwd: Problem running chimera through a command script
by Christos Deligkaris 17 Feb '15

17 Feb '15

Dear all, I have a python script that creates a .com command script for chimera and then attempts to run the chimera script. Here is the python script: ************** #!/usr/bin/env python import re,os,sys,math, decimal, subprocess from copy import deepcopy from openeye.oechem import * from decimal import * script_file=open("chimera_script_for_" + "ligand" +".com", 'w') script_file.write("open "+ "127D" +"\n") script_file.write("open " + "127D" +"\n") script_file.write("open "+ "ligand.pdb" +"\n") script_file.write("match #0:"+ "6" + " " + "#1:"+ "18" +"\n") script_file.write("write format pdb 2 "+ "flipped_" + "ligand" + "\n") script_file.write("stop") script_file.close print script_file.name chimera=subprocess.call(["chimera", " --nogui ", " chimera_script_for_ligand.com"]) print chimera #delete the script, leaving just the flipped ligand #os.remove(script_file.name) ******************* When I run the script, it successfully generates the .com chimera script. However, I get the following error message: ******************* [christos@biophysics Desktop]$ ./script.py chimera_script_for_ligand.com Traceback (most recent call last): File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/chimeraInit.py", line 638, in init splash.create() File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/chimera/splash.py", line 25, in create sync=chimera.debug) File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/lib/python2.7/lib-tk/Tkinter.py", line 1747, in __init__ self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use) _tkinter.TclError: no display name and no $DISPLAY environment variable 1 ********************** The python script successfully creates the .com script: ****************************** [christos@biophysics Desktop]$ more chimera_script_for_ligand.com open 127D open 127D open ligand.pdb match #0:6 #1:18 write format pdb 2 flipped_ligand stop *************************** and if I manually execute this chimera script, everything works out well: ************************** [christos@biophysics Desktop]$ chimera --nogui chimera_script_for_ligand.com Fetching 127D from web site www.rcsb.org 0 Kbytes received Fetch 127D: finished Done fetching 127D; verifying... Opening 127D... #0, chain A: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') #0, chain B: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') Opening VRML model in 127D - Nucleotides... 127D opened Opened VRML model in 127D - Nucleotides Opened 127D containing 1 model, 639 atoms, and 146 residues Fetching 127D from web site www.rcsb.org 88 Kbytes received 80 Kbytes received Fetch 127D: finished Done fetching 127D; verifying... Opening 127D... #1, chain A: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') #1, chain B: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') Opening VRML model in 127D - Nucleotides... 127D opened Opened VRML model in 127D - Nucleotides Opened 127D containing 1 model, 639 atoms, and 146 residues Opening ligand.pdb... ligand.pdb opened Opened ligand.pdb containing 1 model, 32 atoms, and 1 residues Executing match ['#0:6', '#1:18'], no iteration RMSD between 21 atom pairs is 0.630 angstroms Wrote flipped_ligand into /home/christos/Desktop ***************************** Why do I get the error message when I attempt to run chimera through script.py? Is this a python issue or a chimera issue? I appreciate any thoughts on solving this problem....thank you, Christos Deligkaris, PhD Assistant Professor of Physics, Drury University 900 N Benton Ave, Springfield MO, 65802 Office Phone: (417) 873-7234 www2.drury.edu/christos <http://www2.drury.edu/christos/index.html> @DeligkarisGroup <https://twitter.com/DeligkarisGroup> +ChristosDeligkaris <http://google.com/+ChristosDeligkaris>

2 5

Announcement: Release of DOCK 6.7
by Scott Brozell 12 Feb '15

12 Feb '15

We are pleased to announce the release of DOCK 6.7. DOCK is a suite of programs for molecular docking. The source code for DOCK 6.7 is available for download and free for academic users at http://dock.compbio.ucsf.edu/. In version 6.7 the default values for several input parameters were updated based mainly on a performance assessment using large data sets and employing multiple metrics including pose reproduction, cross-docking, and database enrichment For full information on what is new in DOCK 6.7, please visit: http://dock.compbio.ucsf.edu/DOCK_6/new_in_6.7.txt Sincerely, The DOCK Team Please visit us at the DOCK Web site. http://dock.compbio.ucsf.edu

1 0

UnitCell.molecule_center(): Attribute does not exist
by Alejandro Virrueta 11 Feb '15

11 Feb '15

Hello all, I'm trying to execute the script to fill out the crystal unit cell found here: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q13 However, I get the error that UnitCell does not have the 'molecule_center' attribute (code line ~12). I checked with dir(), and yeah, it's not there: ['ModelessDialog', 'Unit_Cell_Dialog', '__builtins__', '__doc__', '__file__', '__name__', '__package__', '__path__', 'chimera', 'dialogs', 'find_model_by_name', 'outline_box', 'place_molecule_copies', 'remove_extra_copies', 'show_unit_cell_dialog'] Where did the attribute go? Is there some other module I could use? Could someone explain (or direct me to some webpage that explains) the process of expanding the ASU and I can write my own script. Any help is greatly appreciated! Thanks! Alex

2 1

Re: [Chimera-users] Problem using structureViz plugin for Cytoscape - Chimera
by Scooter Morris 11 Feb '15

11 Feb '15

Hi Juan, I've uploaded a new version of structureViz (1.0.1) that should fix your problem. Don't hesitate to let us know if there are other issues/enhancements you would like to see. -- scooter On Feb 9, 2015, at 6:39 AM, Juan Eiros Zamora <j.eiros-zamora14(a)imperial.ac.uk <mailto:j.eiros-zamora14@imperial.ac.uk>> wrote: > Hi all, > > I am using Chimera 1.10.1 and Cytoscape 3.2.0, and have installed the > structureViz2 plugin. > > I use structureviz to open chimera through cytoscape and load an MD > trajectory of a protein to create a RIN through Analysis --> Residue > interaction network... > > What I am trying to do is colour the nodes in cytoscape based on which > chain they belong to. My protein has three chains, and in chimera I > color each differently. In cytoscape, I go to apps --> structureviz--> > synchronize residue colors. Here I am given two options. The first one > is “Apply colors from current network view to associated Chimera > models”: This one works fine, but it is not what I want. What I want > to do is the second option: “Apply colors from associated Chimera > models to current network view”, but when I clik on OK it does nothing. > > Anybody having the same problem or some suggestions on how I might > solve this? > > Much appreciated, > > Juan Eiros >

1 0

Manipulate individual hexagons/pentagons in cage builder
by vamsee 10 Feb '15

10 Feb '15

Hello Elaine, I am trying to build a cage but with incorrectly attached pentagons and hexagons to represent mis-assembly. Though I don't believe it is possible using the cage builder, I was wondering if the wonderfully brilliant chimera team would know of any other ways of doing this or even with the cage builder. Thank you yet again, Vamsee

3 2

pymol get_view and set_view in Chimera?
by Jan Kosinski 10 Feb '15

10 Feb '15

Is there an equivalent of pymol get_view and set_view in Chimera? I am aware of savepos command, but I am looking for a feature like Pymol get_view command (http://www.pymolwiki.org/index.php/Get_View) which allows to copy the current view to a script as text and restore it using set_view (http://www.pymolwiki.org/index.php/Set_View) Thanks in advance, Jan

2 4

adding morphs to scene animation in Chimera
by Michael Oldham 10 Feb '15

10 Feb '15

Chimera users, I want to use a combination of various scene selections and morphs in a Chimera animation. Can someone tell me how morphs and scenes be combined to make one movie. Thanks Mike Oldham Rockefeller University

2 2

Problem using structureViz plugin for Cytoscape - Chimera
by Juan Eiros Zamora 09 Feb '15

09 Feb '15

Hi all, I am using Chimera 1.10.1 and Cytoscape 3.2.0, and have installed the structureViz2 plugin. I use structureviz to open chimera through cytoscape and load an MD trajectory of a protein to create a RIN through Analysis --> Residue interaction network... What I am trying to do is colour the nodes in cytoscape based on which chain they belong to. My protein has three chains, and in chimera I color each differently. In cytoscape, I go to apps --> structureviz--> synchronize residue colors. Here I am given two options. The first one is “Apply colors from current network view to associated Chimera models”: This one works fine, but it is not what I want. What I want to do is the second option: “Apply colors from associated Chimera models to current network view”, but when I clik on OK it does nothing. Anybody having the same problem or some suggestions on how I might solve this? Much appreciated, Juan Eiros

2 1

radial density map
by Jian Guan 09 Feb '15

09 Feb '15

Hi all, I have a mrc map of virus, T=7 icosahedron. Does anyone know how to make radial density map (averaged radial density VS radius of virion)? I tried chimera method of shortcut rd. It took long time but return one result. For the rd result, is it make along x, y or z axis? Or along assigned axis, like 5 fold symmetric axis? I have asymmetric extra density around 5-fold axis. What will happen in my case if use rd? Are there any other ways to make the plot besides of rd? Thank you so much. Sincerely yours, Jian

2 1

CHIMERA movie with parm7/dcd
by Francesco Pietra 09 Feb '15

09 Feb '15

Hello: In the recent past, issues in running movie with parm7 files were solved. Now, with ambertools14 problems come out again, unless I dropped into a silly mistake. That is, parm7/dcd was refused because no top file was found. Renaming the prm7 extension prmtop led to File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 354, in SetupFrame raise IOError, "Trajectory/Restart header line is greater than 80 characters -- invalid!!" Thanks for your kind attention francesco pietra

2 1

command line
by Dieter Blaas 09 Feb '15

09 Feb '15

Hi, sorry for asking again an old question but I lost the solution: how do I show single solid planes of several volumes? I tried: 'vol all style solid plane one axis z' and many combinations thereof but it always tells me: 'volume invalid planes argument "one": Value must be one of x,y,z, got "one" when I try ' vol all style solid plane z' it tells me: 'volume invalid planes argument "z"' and so on.... Thanks a lot for your patience, best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

2 2

Re: [Chimera-users] Ramachandran plot statistics
by Nadia Raboana 08 Feb '15

08 Feb '15

Hi, It works perfectly, thank you for helping me. Best regards, Nadia Sent from Windows Mail From: Elaine Meng Sent: ‎February‎ ‎8‎, ‎2015 ‎12‎:‎52‎ ‎AM To: Nadia Raboana CC: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Ramachandran plot statistics Hi Nadia, You would have to decide for yourself what probability cutoff you want to use as the boundary between allowed and disallowed. First assign the probabilities to the residues: in the Ramachandran Plot dialog, click the button at the bottom to “Assign Residue Probabilities” (or use the ramachandran command option “assign”): <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ramachandran/rama…> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ramachandran.html> Then in Select by Attribute (Chimera menu: Select… By Attribute Value) choose attributes of “residues” with Attribute: ramaProb … that will show a histogram of the probability values. Then you can move the green bars to enclose the range of probabilities you want to select. After you use that dialog to select everything above your cutoff probability, then you can get a count of the selected residues by clicking the green magnifying glass at the bottom right corner of the Chimera window to show the Selection Inspector. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.htm…> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html> Then you would divide by the total number of amino acid residues to get the percentage. You could count the total number of amino acid residues, for example, by using command “select protein” and then clicking the green magnifying glass. 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 On Feb 7, 2015, at 4:49 AM, Nadia Raboana <nadia_raboana(a)hotmail.fr> wrote: > Hello, > I am using UCSF Chimera to generate Ramachandran plot related to my protein structure. I would like to know how to get the statistics about the analysis. I would precisely know the percentage values of residues in most favored regions, allowed regions and disallowed regions. > Thank you for answering me. > Best regards, > Nadia Raboanatahiry

1 0

Change selection mode programatically
by Mario J. Borgnia 07 Feb '15

07 Feb '15

Hi, I am trying to find a way to split a complex selection pattern among a number of lines in a script. I was expecting that this would be an option to the select command, but apparently it is not. I know that I can combine "select" commands by changing the selection mode to "append" in the GUI, but I am struggling to find the way of doing this from command line or from a script. Is there a way to change the selection mode to "append" without using the GUI? Thanks Mario -- +---------------------------------+ | Mario J. Borgnia, Ph. D. | | | | Lab of Cell Biology | | NIH NCI/CCR | | 50 South Drive Rm 4306 MSC 8008 | | Bethesda MD 20892-8008 | | | | Tel: (301) 594 0563 | | mborgnia(a)nih.gov | +---------------------------------+

2 2

Ramachandran plot statistics
by Nadia Raboana 07 Feb '15

07 Feb '15

Hello,I am using UCSF Chimera to generate Ramachandran plot related to my protein structure. I would like to know how to get the statistics about the analysis. I would precisely know the percentage values of residues in most favored regions, allowed regions and disallowed regions.Thank you for answering me.Best regards, Nadia RaboanatahirySchool of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan, CHINA

2 1

Help in writing python code
by Ankit Agrawal 06 Feb '15

06 Feb '15

Hi I am doing trajectory analysis which has 40000 frames. So for all frames I wanted to calculate the all three inertia axes. That I did. But problem is that when I run the python code it starts making all the three axes for each frames that becomes messy. So I want a little change in my code so that during trajectory analysis it should create axes but should delete or hide the previous axes also. So during run I will see only the axes which are related to that frame. Here is the python code in per-frame analysis. from chimera import runCommand frame = mdInfo['frame'] runCommand("measure inertia #1:0-120 color yellow") runCommand("measure inertia #1:120-237 color green") Thanks. Ankit

2 2

Help in executing python script in per-frame analysis
by Ankit Agrawal 05 Feb '15

05 Feb '15

Hi I am analysing a protein molecule (MD simulations). I wrote a python script to calculate inertia for the protein and ran it over 40000 frames. I got a data in log file but it is creating a ellipsoid around the molecule. I want 3 axes of the ellipsoid to be shown in that protein molecule not the ellipsoid as it covers the whole protein molecule. So that I can easily visualize the movement of all 3 axes of ellipsoid over the 40000 frames (means how the axes are changing during trajectory run). Thanks Ankit Department of Chemical Science IISER-Mohali, India

2 1

multiple Chimera sessions on Mac
by Vladimir Yarov-Yarovoy 03 Feb '15

03 Feb '15

Hello, Is it possible to open multiple Chimera sessions on Mac OS X Yosemite? I tried to start multiple chimera sessions from different terminal windows that was recommended in this thread - http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003231.html - but it doesn't work. Thank you, Vladimir

2 3

Command line problem
by Luca Pellegrini 03 Feb '15

03 Feb '15

Hi, I am having the following problem when I try to use the command line. When I select ‘Command line’ from the ‘Favorites’ menu, the command line window appears, but I can’t type anything in it. Or rather, I can type in it, because if I hit return the command gets executed, but I can’t see what I type. Any idea of what’s going on? I suspect that it might be something to do with Yosemite 10.10.2, since this problem arose after upgrading the MacOSX operating system. I am using Chimera 1.10.1, build 40415. Thanks for any advice. Kind regards, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

2 2

Error: UnboundLocalError: local variable 'i' referenced before assignment
by Letizia Meregalli 03 Feb '15

03 Feb '15

Hi, I have a tRNA molecule and I would like to measure the angles between two nitrogenous bases. I created two planes, each for each base. When I select both planes, in order to measure the angles between them (Structure Measurements Axes/Planes/Centroids) I get following message: <type 'exceptions.UnboundLocalError'> Exception in Tk callback Function: <bound method SortableTable._browseCmd of <CGLtk.Table.SortableTable instance at 0x117990638>> (type: <type 'instancemethod'>) Args: ('1',) Traceback (innermost last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/Applications/Chimera.app/Contents/Resources/share/CGLtk/Table.py", line 1043, in _browseCmd self.userBrowseCmd(self.selected()) File "/Applications/Chimera.app/Contents/Resources/share/StructMeasure/Geometry.py", line 268, in _tableCB self.feedback(sels) File "/Applications/Chimera.app/Contents/Resources/share/StructMeasure/Geometry.py", line 113, in feedback diff = " ".join(words2[i:]) <type 'exceptions.UnboundLocalError'>: local variable 'i' referenced before assignment UnboundLocalError: local variable 'i' referenced before assignment File "/Applications/Chimera.app/Contents/Resources/share/StructMeasure/Geometry.py", line 113, in feedback diff = " ".join(words2[i:]) See reply log for Python traceback. I really don’t know how can I solve this problem.. I’d be really grateful if you could help me or give me some hints! thank you a lot Letizia

2 1

Help Needed
by angshu＠klyuniv.ac.in 03 Feb '15

03 Feb '15

Hi, I need a small help. I need to find out the amino acid residues from one chain of a protein which are within 5A of a specific amino acid residue of some another chain of the same protein. For example: Say I have a protein 1XYZ.pdb containing A, B, C chains. I want to find which amino acids from chain B and C are within 5A distance from ALA 78 belonging to chain A. Please let me know. Thanks. Angshuman

2 1

Using Chimera to measure voxel densities
by Noble, Alex 30 Jan '15

30 Jan '15

Hi all, I have a pdb fit into an EM density in Chimera and I would like to be able to see what the nearest voxel densities are at specific atomic coordinates. Is there any way to do this in Chimera? Best, -Alex Noble

3 4

Question
by Monete Rajão Gomes 28 Jan '15

28 Jan '15

Hi, I have some problem these days about superimpose templates with matchmaker. I followed this tutorial http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-August/006686.html. There are regions on aminoacids sequences which are identical. So, when I superimpose them, they stay separated. I am sending a screenshot attached. It would be great if you could help me. Best, Monete

2 2

Morph conformations - estimated time to completion in status bar?
by Oliver Clarke 26 Jan '15

26 Jan '15

Hi all - silly little feature suggestion, but I was wondering if it would be possible to add an live-updating “x % complete” or “estimated time to completion” entry in the status bar when running Morph Conformations? When morphing two structures with very large numbers of atoms, morph conformations can take a long time (hours) to complete, and it would be handy to know whether it is nearly done or not (currently it just shows “computing interpolation 1” until it is finished). On a related note, is there any way to speed up morph conformations for large structures? E.g calculating transformations using C-alpha atoms only? Best, Oliver.

2 1

modelling a dimer
by David Norman (Staff) 23 Jan '15

23 Jan '15

I am trying to model a symmetrical dimer using modeller within Chimera. I cannot work out how to present the alignment and pdb. files in oder to do this. Any hints please. Thanks David David Norman Ph.D Nucleic Acids Research Group School of Life Sciences MSI/WTB Complex Dow St. Dundee, DD1 5EH, Scotland, UK. phone +44(0)1382 384798 mobile +44(0)7808572788 E.mail d.g.norman(a)dundee.ac.uk Web site: http://www.lifesci.dundee.ac.uk/people/david-norman The University of Dundee is a Scottish Registered Charity, No. SC015096 The University of Dundee is a registered Scottish Charity, No: SC015096

2 1

how to find non-bonded interactions between a protein and a ligand?
by Sam Paul D. 22 Jan '15

22 Jan '15

Hi, I need to find non-bonded interactions between a protein and a ligand through command line. Could anyone please suggest which chimera command to use with the syntax? With regards, Sam

3 4

Find subsequence programatically
by Thomas Hrabe 22 Jan '15

22 Jan '15

Hi Chimera Team, How can I automate the Sequence View -> Edit -> Find Subsequence Tool programmatically with the Chimera shell or better within python? Thank you, Thomas

2 2

Coot capabilities in Chimera
by Mario J. Borgnia 22 Jan '15

22 Jan '15

Dear all, WIth the advent of atomic resolution maps in Cryo-EM, we find ourselves refining structures. The blunt question is, should I move to Coot and leave behind Chimera for that or are there overlapping functions and what will I be missing if I choose to stay with Chimera. I have some ideas about the answers but would like to read what the developers and power users have to say on the issue. Thanks!!!

2 1

How to predict/model the structure of two known structure proteins
by Phan Trong Hoang 22 Jan '15

22 Jan '15

Dear UCSF developers, I am Hoang, working in IPK in Germany. I am following your series online tutorials about how to use UCSF Chimera. This program is very useful for me. However, I did not see your video showing how to predict/model the structure of a fusion protein that is made by combination of two known structure proteins in PDB (for example gi|534286646|pdb|4KRN| and gi|390136394|pdb|4DDF|A). Is this function available in your software? If yes can you show me how to manipulate with it. I would like appreciate it very much Thank you for your attention and I am looking forward to hearing from you. Best regards Hoang Phan

2 3

SDF file
by Hernando J Sosa 22 Jan '15

22 Jan '15

I have an sdf file with a small ligand molecule in 2D (it looks flat when opened in chimera). What would be the best way to make it 3D (i.e. assign/minimize the proper bond angles & distances). Is it possible to do it in chimera? Thanks

3 3

How can one create a sculpted view of a cellular assembly?
by Kenward Vaughan 21 Jan '15

21 Jan '15

As I slowly approach the operational realization of my computational/visualization lab, I received your lovely holiday card. This seriously elevated my dreams of larger scale possibilities for chemistry and biology students through the cellPack resources. In playing with it, I found myself wanting a more robust version of a clipping plane which would have several characteristics: 3 dimensional - take a cell and hack out 1 or 2 adjoining octants relative to its center to give a sliced view similar to what is found in some texts (also often used in geology books to depict the earth's internal structure--see http://www.the-science-site.com/earths-interior.html for an example). Being able to leave the nucleus alone while the surface strips away the cytoplasm would be cool, much like the referenced image above showing the core of the earth. Likely a difficult one to actually implement? Have the clipped surface not be flat, but rather allow a component to stay visible as the surface is moved past it until some determined relationship at which point it vanishes (perhaps when it has passed entirely through the clipping surface?). The clipped surface would thus show structure of a sort. Have the choice of the clipping surface being static with the assembly (it could rotate with the assembly, keeping the same internal view), or separately static (how a clipping plane behaves now--as I know it--where rotating the structure causes things to move through the unmoving plane. One approach I can imagine would be the use of a spherical or ellipsoidal (?) surface of specific size at a specific distance from the center of the cellular assembly. Is this already implemented in a way that can be manipulated to achieve at least the major aspects of this effect (e.g. logical ANDing of clipping by 3 intersecting planes)? Sorry for the long question... ;-/ Kenward -- In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca

3 3

Ringer/Chimera/IDLE
by Alejandro Virrueta 21 Jan '15

21 Jan '15

Hello, I am modifying some Ringer files for my own needs, but I am running into a weird issue. If I run Ringer via typical means: $RINGER/ringer/ringer -i ringer_in_${pdb_ID}.txt -o ringer_out_${pdb_ID}.txt it works fine. However, when I step through it in what I think is my version of IDLE ("$CHIMERA_HOME/bin/chimera --nogui --nostatus --script `which idle2.7` /usr/bin/idle2.7", with `which idle2.7` returning "/usr/bin/idle2.7"), I run into this error: Traceback (most recent call last): File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 233, in <module> main() File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 161, in main move_set, pdb = structureFile(parameters, path) File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 65, in structureFile pdb = chimera.openModels.open(parameters.pdbfileName) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1817, in open checkForChanges=False, noprefs=noprefs) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1644, in add makePseudoBondsToMetals(realMolecules) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1961, in makePseudoBondsToMetals cmPBG = mol.metalComplexGroup(issueHint=True) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 119, in _getMetalPbg am.color = preferences.get(MOLECULE_DEFAULT, MOL_COMPLEX_COLOR) File "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 608, in get forPrefSave=forPrefSave) File "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 179, in get return self._options[name].get(forPrefSave=forPrefSave) File "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 80, in get return self.prefToVal(self.value) File "/Applications/Chimera.app/Contents/Resources/share/chimera/tkoptions.py", line 1229, in _prefToColor return getColorByName(pref) File "/Applications/Chimera.app/Contents/Resources/share/chimera/colorTable.py", line 87, in getColorByName color = chimera.MaterialColor(r/255.0, g/255.0, b/255.0) ValueError: missing default material Any suggestions? Cheers, Alex

2 1

Alternate conformations in residues
by Alejandro Virrueta 21 Jan '15

21 Jan '15

Hello all, Is there a way to get the all the information for an alternate conformation from a residue object? I have res.altLocs resulting in set([a,b]), but how can I get chi1-4 for conformation b for example? Thanks! Alex

2 1

Alternate conformations in residues
by Alejandro Virrueta 21 Jan '15

21 Jan '15

Hello all, Is there a way to get the all the information for an alternate conformation from a residue object? I have res.altLocs resulting in set([a,b]), but how can I get chi1-4 for conformation b for example? Thanks! Alex

1 0

Mesh defined by distance to selection
by R. Michael Sivley 21 Jan '15

21 Jan '15

I have a set of residues in a protein structure that each mark the center of a sphere over which a value has been calculated. I can select a subset of residues by value, but the values actually correspond to the sphere around that residue. I would like to visualize this by creating a mesh defined by being within 10A of any selected residue. If a selected residue isn't within 10A of any other selected residue, I would like this to produce two meshes, but if they are within 10A, I would like a single continuous mesh whose boundaries are defined as being 10A from either residue. Zone-selecting residues within 10A of the selection and then showing their surface as a mesh is a close approximation of what I'm trying to convey, but doesn't give me exactly what I'm looking for. I found this in the Chimera help pages, and it seems to be exactly what I need: http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#z… I think I'm missing a first step, though, because I don't understand how to actually create the mesh. I select my residues, open the Volume Viewer, and define the zone radius, but then I'm stuck. How do I actually instantiate the mesh given those values? I've tried showing the surface for the selected residues, but the changes I make in the Volume Viewer don't appear to have any effect on the surface, so I'm assuming these are two separate features. There is no "apply" button in the Volume Viewer, and closing the window does not create a mesh. I've included a screenshot of where I'm stuck, should it be helpful. Could you help me identify the missing step in this process? Thanks! Mike Sivley PhD Student in Biomedical Informatics Center for Human Genetics Research Vanderbilt University

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UHBD map, generated with APBS
by Feldman-Salit, Anna 20 Jan '15

20 Jan '15

My current "strange" problem: I use APBS stand-alone to generate electrostatic potential for a protein in PQR format. What I do is to ask for output in UHBD (GRD not DX) format. Unfortunately, the generated GRD file is not read by CHIMERA, which upsets me... Strange, but VMD seems to be less sensitive to the GRD generated with APBS to visualize the map. Another point: I am very glad that CHIMERA computes potential. Do you think one could save it not only in DX format? Maybe you could suggest me a way to convert DX to UHBD format? Thank you! Have a lovely working day! Greetings, Anna --- Dr. Anna Feldman-Salit Molecular and Cellular Modeling (MCM) Group HITS gGmbH, Schloß-Wolfsbrunnenweg 35 69118 Heidelberg, Germany phone: +49-6221-533-260 fax: +49 6221 533298

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Simply, keep up the good work
by Kevin D. Walker 20 Jan '15

20 Jan '15

I really enjoy using the Chimera program, and I am trying to convince my lab members to make the switch. I hope you get these types of emails all of the time. Your program is duly acknowledged during my seminars. ---------------------------------- Kevin D Walker Associate Professor Michigan State University Department of Chemistry and Department of Biochemistry & Molecular Biology 578 S Shaw Lane; Room 208 East Lansing, MI 48824 Phone: 517 355 9715 x 257 Fax: 517 353 1793 websites: 1) http://bmb.natsci.msu.edu/about/directory/faculty/kevin-d-walker/current-re…

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Creating a cubic box for a density map
by Juan Luis Loredo Varela 18 Jan '15

18 Jan '15

Dear Chimera users When I use the Segment map option to save a specific fragment as .mrc file, Chimera uses the minimal box containing the segment. Does anyone know how to modify the dimensions of a density map to have it in a cubic box that can be used in Flex-EM? Thanks Juan -- Juan Luis Loredo Varela PhD Student Antson Group York Structural Biology Laboratory L0 Department of Chemistry University of York

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Scripting image writing in Mac OSX
by Mike Sivley 16 Jan '15

16 Jan '15

I have a Chimera script that takes a set of attribute files and generates a collection of scenes images. This script is usually run on Scientific Linux using the Headless Linux 64-bit distribution of Chimera. I'm now trying to run this script on Mac OSX Mavericks and hitting issues with the GUI. If I pass the --nogui flag to Chimera, then the script fails, stating that the GUI is necessary to save images. If I remove the flag, the GUI starts up correctly, but scripted control stops once the new attributes are defined. The user is prompted by the Render by Attribute window, and the script will not progress until the user confirms the changes and closes the GUI. How can I get the script to run start-to-finish without stalling for user-interaction, the way it does in linux? Thanks! Mike Sivley PhD Student in Biomedical Informatics Center for Human Genetics Research Vanderbilt University

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Re: [Chimera-users] dotted lines
by Elaine Meng 16 Jan '15

16 Jan '15

On Jan 16, 2015, at 8:46 AM, Thomas Evangelidis <tevang3(a)gmail.com> wrote: > Hi Elaine, > I don't know why, but none of the 3 approached works, even with the latest Chimera version. > […] Hi Thomas, Your pseudobonds are in stick style. You would have to change the stick to wire before doing those other things; in Chimera there are no “dotted or dashed” sticks, only wires (lines). E.g. in Selection Inspector, inspect: Pseudobond, change bond style to wire. That only changes the specific pseudobond(s) you have selected; if you first select one distance pseudobond, you can press keyboard up arrow to expand the selection to all the distance pseudobonds. Can also be done with setattr command, e.g.: setattr p drawMode 0 Hard to see on white background. Can change color with setattr too: setattr p color black When you first create distances they are normally already in wire style, which is why I didn’t mention the stick/wire issue before. 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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vop add
by Fco Javier Chichón 16 Jan '15

16 Jan '15

Dear all I would like to merge several volumes. Not all the voxels of the two volumes fit, so when I used vop add command, Chimera add the densities instead of average them. Anyone know how to do that? Thanks -- ======================================================= Francisco Javier Chichón García Centro.: Centro Nacional de Biotecnología Dept.: Macromolecular Structure Lab.: S1-S0.1 Tel.: (+34) 91585-5497:4690 =======================================================

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dotted lines
by Thomas Evangelidis 15 Jan '15

15 Jan '15

Greetings, I have created a figure with manually added Hbonds (Tools->Structure Analysis->Distances). Is there any way to make these lines dotted/dashed? thanks, Thomas -- ====================================================================== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tevang(a)pharm.uoa.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ =============================================================== *Physics is the only real science. The rest are just stamp collecting.* *- Ernest Rutherford*

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Distance measurement in density map
by Maarten Schledorn 14 Jan '15

14 Jan '15

Dear reader, I'm looking at EM tomography data summarised in *.mrc density files. Since there are no atoms defined in these files, the usual distance measurement tool is inappropriate (I suppose). Is there another way to assess the dimensions of the oligomerised protein I'm looking at? With my sincere thanks in advance, Maarten

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shown/hidden state of axes/planes not saved with scene
by Oliver Clarke 14 Jan '15

14 Jan '15

Hi all, Planes seem to be shown by default when I load a scene, regardless of whether they were displayed when I saved the scene. This is not normally an issue, but it is a little problematic when preparing animations using many different scenes - I will often have a plane defined at the start so I can use it to align the x/y/z axes to the normal of that plane (e.g. aligning the fourfold axis of an ion channel), but I do not want the plane displayed during the animation, and I don’t want to have to delete it from each scene and re-arrange the animation timeline if I can avoid doing so. Would it be possible to alter this behavior such that chimera knows the displayed/undisplayed states of axes/planes/centroids when saving a scene or session? Best, Oliver Clarke.

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New to Chimera
by Mike 12 Jan '15

12 Jan '15

This is my first day with Chimera. I'm trying to find how to draw a small molecule, minimize the structure of the small molecule and then have it interact with my protein of interest. However, I don't see any way for me to draw a small molecule (potential drug). Can you provide any direction ? Thanks, Mike

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need guidence
by Maria Saqib 08 Jan '15

08 Jan '15

Dear user i am using chimera for some images of protien .I have a problem while labelling i want to change font colors , How can i label it with different font colors? Waiting for your reply Maria

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VR in Chimera?
by Andrey Malyutin 07 Jan '15

07 Jan '15

Good morning, With recent resurgence in virtual reality technology, such as Oculus Rift and Samsung Gear VR, is it possible that we'll see support for VR headsets in future releases of Chimera? Thank you, Andrey

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Distance Grid SES calculation available?
by Hurt, Darrell (NIH/NIAID) [E] 06 Jan '15

06 Jan '15

Hi Chimera friends, This question is probably for Tom Goddard, but I'm happy to hear from anyone. I'm really interested in using Tom's code for "distance grid SES" calculations as described here: http://www.cgl.ucsf.edu/chimera/data/surface-oct2013/surface.html The above page suggests that this code will be part of Chimera 2, but I'm wondering if it is available now for surface calculations. Too many of my surface calculations are failing for our production server using Chimera. This would help immensely. Molmap is a decent alternative in some instances, but for my purposes, distance grid calculations are going to be more MSMS-like, which will be a better solution (cf. the description on the page comparing the internal pockets formed by molmap vs MSMS surfaces). Is there some way to call the routine, especially in a script? Python maybe? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 5601 Fishers Lane, 4A31 North Bethesda, MD 20852 Office: 240-669-2741 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> , @NIH3Dprint<https://twitter.com/nih3dprint> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Parsing a new 3D file format
by ros 05 Jan '15

05 Jan '15

Hello! I would like to ask for advice and starting directions to be able to parse a new file format in Chimera so I can use Chimera's tools and generate images. The file format that I want to be able to open is generated from the Atoms in Molecules program AIMAll ( http://aim.tkgristmill.com/ ) The AIMAll program of course can also do visualization and is very good at it. I am attaching an example of how a molecule looks. The problem is that if you want to work with big biomolecules (like DNA), the program is not very good to cloak/hide/select atoms so you have to click atom by atom to hide it and make some sense of the visualization. So, I will try to make a parser (or something that you would recommend) to open the file in Chimera and use Chimera's masking rules to select/deselect, hide/show atoms, which is very powerful. The text output generated by AIMAll has an XYZ list for each atom like this: Nuclear Charges and Cartesian Coordinates: ------------------------------------------------------------------------------- Atom Charge X Y Z ------------------------------------------------------------------------------- C1 6.0 0.0000000000E+00 2.3265459100E+00 0.0000000000E+00 C2 6.0 0.0000000000E+00 0.0000000000E+00 1.7647056500E+00 C3 6.0 0.0000000000E+00 0.0000000000E+00 -1.7647056500E+00 H4 1.0 1.6866221200E+00 3.4814514700E+00 0.0000000000E+00 H5 1.0 -1.6866221200E+00 3.4814514700E+00 0.0000000000E+00 C6 6.0 -2.0148478600E+00 -1.1632729600E+00 0.0000000000E+00 H7 1.0 -2.1717143500E+00 -3.2013833400E+00 0.0000000000E+00 H8 1.0 -3.8583364700E+00 -2.8006813000E-01 0.0000000000E+00 C9 6.0 2.0148478600E+00 -1.1632729600E+00 0.0000000000E+00 H10 1.0 2.1717143500E+00 -3.2013833400E+00 0.0000000000E+00 H11 1.0 3.8583364700E+00 -2.8006813000E-01 0.0000000000E+00 H12 1.0 0.0000000000E+00 0.0000000000E+00 3.8040484300E+00 H13 1.0 0.0000000000E+00 0.0000000000E+00 -3.8040484300E+00 That is easy, I think. But as you can see from the attached image, I want to be able to visualize the green spheres (which are called critical points and represents special properties of the electron density, extracted from quantum mechanical calculations). Those points are represented in the output file as: CP# 16 Coords = 5.97894312844235E-20 1.21974356425640E+00 -9.60854463947958E-01 Type = (3,-1) BCP C1 C3 Rho = 2.4067790431E-01 GradRho = 3.5016504866E-18 -2.7948129921E-14 1.7716730860E-14 HessRho_EigVals = -4.4278076226E-01 -4.3836581782E-01 3.5682199801E-01 HessRho_EigVec1 = 1.0000000000E+00 0.0000000000E+00 0.0000000000E+00 HessRho_EigVec2 = 0.0000000000E+00 -6.1321358320E-01 7.8991714842E-01 HessRho_EigVec3 = 0.0000000000E+00 7.8991714842E-01 6.1321358320E-01 DelSqRho = -5.2432458207E-01 Bond Ellipticity = 1.0071370222E-02 V = -2.5219393995E-01 G = 6.0556397216E-02 CP# 18 Coords = 1.05289204670721E+00 3.04112062239339E+00 1.96757752864282E-18 Type = (3,-1) BCP H4 C1 Rho = 2.9524693796E-01 GradRho = 1.0061396161E-16 -1.6479873022E-16 1.6660693347E-18 HessRho_EigVals = -7.9444808957E-01 -7.8708168641E-01 4.1039750300E-01 HessRho_EigVec1 = -5.7017191910E-01 8.2152539989E-01 0.0000000000E+00 HessRho_EigVec2 = 0.0000000000E+00 0.0000000000E+00 1.0000000000E+00 HessRho_EigVec3 = 8.2152539989E-01 5.7017191910E-01 0.0000000000E+00 DelSqRho = -1.1711322730E+00 Bond Ellipticity = 9.3591342377E-03 V = -3.7782718105E-01 G = 4.2522056404E-02 etc etc etc First line indicates the critical point number followed by the XYZ coordinate of the point, and the second line shows which atoms are involved between that critical point. The rest is the electronic properties of the critical point (nothing to visualize there) So, I am guessing that the critical points can be represented as dummy atoms in Chimera following the XYZ coordinates? The idea is that first the molecule coordinates are parsed and the molecule is displayed and then display the critical points of each atom. If possible, show lines joining atoms that have a critical point between them... I know it is a difficult task, but maybe you can provide some starting directions? Anything will help because right now is double clicking 1000+ atoms! Thank you so much and have a good day, Rodrigo. ------------------------- Rodrigo Galindo-Murillo, PhD Department of Medicinal Chemistry University of Utah 30 South 2000 East, Room 307 Salt Lake City, UT 84112-5820 http://home.chpc.utah.edu/~cheatham/ (801) 587-9652 (801) 585-6208 (Fax)

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WebGL viewer
by Thomas Hrabe 05 Jan '15

05 Jan '15

Hi everyone, I am trying to implement a EM density viewer in a HTML page based on the chimera webgl & html export feature. The original page chimera exports when you save a webgl / html scene has been modified to load multiple JSON objects with densities as they come from chimera. The bar at the bottom of the page essentially performs a coarse density sliding similar to chimera. Almost all works great but what I am missing is how to connect the rotation that was applied to one model and to propagate it to all other models. What is happening now is that when one rotates one model and slides the bar, the next model will not be rotated but will be in it’s original position. Here’s my page I am currently working on http://localize.pytom.org/php/displayWebGL.php?jobID=tutorial I tried catching the mouse event with a loop, but it seems it fails to propagate the rotation to the other models. Check the block at line 916 in the code try { var rotMat = vsphere(mouse_position, new_position); var camera = this.camera; var matrix = new Mat4; matrix.$translate(camera.target[0], camera.target[1], camera.target[2]); matrix.$mulMat4(rotMat); matrix.$translate(-camera.target[0], -camera.target[1], -camera.target[2]); for (var i = 0, models = this.scene.models, l = models.length; i < l; ++i) { var elem = models[i]; elem.matrix = matrix.mulMat4(elem.matrix); } } Thank you in advance for your help, Thomas

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mmaker usage with md-movie perframe
by Bala subramanian 02 Jan '15

02 Jan '15

Friends, I have a crystal structure of a protein (370aa). I have a trajectory of a similar protein (not same) with (210aa). I opened the crystal structure and the trajectory via md-movie tool. In the perframe analysis, i gave the following command (#1 my traj, #0 crystal.pdb) *mmaker #1 #0 computeSS false* mmaker uses different number of atom pairs for rmsd calculation. If there are say 150aa that match between my target and crystal, then mmaker should make the rmsd firt for 150 atom pairs in every frame. Why does it use different no. of atom pairs. Do i need to give some extra options ? Thanks, Bala -- C. Balasubramanian

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Add reasonable bonds from command line
by Enrico Ronca 29 Dec '14

29 Dec '14

Dear Sir. I'm Enrico Ronca a post-doc researcher at the National Research Council of Italy in Perugia. I'm contacting you because I often work with metal atoms and not always chimera show me bonds. I solved the problem removing all bonds and pseudo bonds and adding "reasonable bond between selected atoms" in the adjust bonds menu of chimera. Is there a way to run the same procedure from the command line so that I could automate it by a script? Thank you in advance for your reply. I'm looking forward to hearing from you Enrico

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Re: [Chimera-users] Customizing Chimera
by Eric Pettersen 25 Dec '14

25 Dec '14

On Dec 22, 2014, at 1:08 AM, Michał Kadlof wrote: > Hello, > > I'm currently work on proteins with disulfide bonds. I'm very often do the same sequence of tasks in Chimera: > > 1. open structure > 2. Select -> chemistry -> functional group -> disulfide > 3. extend selection to have selected all atoms of Cys-Cys bridge > 4. Show selected atoms > > Is there any way to wrap it into one-click button on toolbar? Hi Michał, While it is literally possible to put what you want on the toolbar, it's a bit easier to make a menu item instead. To do that, you create a command alias for the actions, and put that in a file that Chimera reads at startup so that it is always available. Details: The alias would be alias ^showbridge sel disulfide; sel up; disp sel This creates an alias named "showbridge" which is only expanded if typed at the beginning of a line -- that's what the ^ indicates. Such beginning-of-line aliases are also placed in an Aliases menu that appears after the Favorites menu (if you have any such aliases). To get the alias read by Chimera at startup you would put it in any of the files listed in the "Files to read at startup" section of the Command Line preferences (Favorites->Preferences). This is also described in more detail here: Command Line. Finally, if you really want it on the toolbar instead, that will involve making your own (simple) plug-in in Python. I can provide more detail about that if you like. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Can't open the CASTp site
by Lei Jinmin 18 Dec '14

18 Dec '14

Hi, I have to use CASTp tool for research sake, but I can't open the site anymore( http://sts-fw.bioengr.uic.edu/castp/index.php ). I remember it worked a couple of weeks ago. Does anyboday know when it begins working again? Thank you in advance! Best, Jinmin Lei Researh assitant Aalto University, Finland

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constrain measurement of rotation to a particular axis?
by Elaine Meng 18 Dec '14

18 Dec '14

Begin forwarded message: > From: Tom Goddard <goddard(a)sonic.net> > Subject: Re: [Chimera-users] constrain measurement of rotation to a particular axis? > Date: December 18, 2014 11:07:57 AM PST > > I think the sensible thing is to report the hinge angles without trying to use a common rotation axis. I can think of different ways to define the common rotation axis (you have to align all the structure in some way, then say how much the observed rotation about the axis for a particular structure translates into a rotation about a slightly different common axis), all of them arbitrary and hard to explain, and even harder to compute, so I wouldn’t go that way. > > Tom > >> From: Oliver Clarke <olibclarke(a)gmail.com> >> Subject: [Chimera-users] constrain measurement of rotation to a particular axis? >> Date: December 17, 2014 2:36:45 PM PST >> To: Mailing List <chimera-users(a)cgl.ucsf.edu> >> >> Hi all, >> >> When using the “measure rotation” command, is there any way to constrain the rotation to be measured about a particular axis? >> >> I am thinking specifically of a case where I have multiple structures of a protein with different inter domain hinge angles - I can use chimera to measure the hinge angle, but for each pair of structures it chooses a slightly different rotation axis, whereas I would like to keep the same axis so I can directly compare the rotation observed between pairs of structures. >> >> Or perhaps there is there another way to do this that would make more sense? Suggestions are welcome... >> >> Best, >> Oliver. >>

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How to change colour of H-bond between atoms
by Mahendra B Thapa 18 Dec '14

18 Dec '14

Dear Chimera Users, There is a hydrogen bond between, say, H20 of a ligand (LIG,res no: 240; this H-atom is attached with N atom of LIG) and O atom of GLU 120 residue. There are other hydrogen bonds too, but I am interested to change the color of that H-bond only to, say, red. I tried some like bondcolor red :240@H20 But, it is not working. Any suggestion might help me. Also, is there any way to change width of the H-bond? Thank you, Mahendra Thapa University of Cincinnati,OH

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constrain measurement of rotation to a particular axis?
by Oliver Clarke 17 Dec '14

17 Dec '14

Hi all, When using the “measure rotation” command, is there any way to constrain the rotation to be measured about a particular axis? I am thinking specifically of a case where I have multiple structures of a protein with different inter domain hinge angles - I can use chimera to measure the hinge angle, but for each pair of structures it chooses a slightly different rotation axis, whereas I would like to keep the same axis so I can directly compare the rotation observed between pairs of structures. Or perhaps there is there another way to do this that would make more sense? Suggestions are welcome... Best, Oliver.

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Re: [Chimera-users] Request for Source code
by Elaine Meng 16 Dec '14

16 Dec '14

Dear Jayaraman T, You can turn off helical correction and mass weighting using command options, for example with this command: define axis perHelix true helicalCorrection false massWeighting false See: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> I’m just trying to convince you this is the easy way! However, you already also have the source code in your download, as Eric described in his reply: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-December/010574.html> Best, Elaine On Dec 15, 2014, at 6:57 PM, Jayaraman T <jaai.nasa(a)gmail.com> wrote: > Yes Elaine, > > We can use Chimera but there are helical correction and mass weighting options exist. And am trying to get it done for all these helices without these options. > > Anyway let me follow up and write you back if there is a need of further assistance. > > I think it would help us more and thanks again for your kindness. > > Good day. > > On Tue, Dec 16, 2014 at 6:51 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Dear Jayaraman T, > Chimera download already includes the Python code, but why not just use Chimera? It seems like that would be much, much easier than trying to find and understand all the parts of the code to do it. You can script it with Chimera commands “define” to create helix axes cylinders and “angle” to measure the angle between any pair of those. > > See: > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html> > > …and information on looping through structures: > <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 > > On Dec 14, 2014, at 6:25 PM, Jayaraman T <jaai.nasa(a)gmail.com> wrote: > > > Dear, > > I'm Jayaraman T pursuing PhD here in Pusan National University. Since we are interested to calculate the interhelical angle and axes for a set of proteins, we found Chimera is really helpful for getting us the results. And i would like to do certain analysis on the basis of these interhelical angles, so i kindly request you to provide me the source code and other requirements for calculating the angle between helices. It would be grateful to you and please help me out at your earliest convenience. > > Thanks > > > > -- > Regards > > > Jram | 201493155 > PhD Student > Bio molecular Engineering Lab > School of Chemical Engineering > Pusan National University. > 30 Jangjeon-dong, Geumjeong-gu, > Busan, South Korea - 609-735. > +8210 9906 3680 > jram(a)pusan.ac.kr >

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Request for Source code
by Jayaraman T 15 Dec '14

15 Dec '14

Dear, I'm Jayaraman T pursuing PhD here in Pusan National University. Since we are interested to calculate the interhelical angle and axes for a set of proteins, we found Chimera is really helpful for getting us the results. And i would like to do certain analysis on the basis of these interhelical angles, so i kindly request you to provide me the source code and other requirements for calculating the angle between helices. It would be grateful to you and please help me out at your earliest convenience. Thanks -- Regards Jram | 201493155 PhD Student Bio molecular Engineering Lab School of Chemical Engineering Pusan National University. 30 Jangjeon-dong, Geumjeong-gu, Busan, South Korea - 609-735. +8210 9906 3680 jram(a)pusan.ac.kr

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different behavior of the Win and OS-X version seen in case of surface calculations
by Marek Maly 15 Dec '14

15 Dec '14

Hello, I found already several times the differences between OS-X and Win version of Chimera (1.10.). Problem is regarding the ability to calculate molecular surface. There are some cases when Win version of Chimera 1.10 is not able to calculate molecular surface of some more complicated molecular structure (e.g. protein) but on the other hand the OS-X version of Chimera (again 1.10) is able to do it (although writes warning that there was some partial problems). Moreover when I create PY session of such molecule with surface calculated/visualized under OS-X and then I want to open this session under Win version it is opened but without the surface and writes many errors into the log - see below. In both versions I am using default settings (no special changes in parameters important for the surface calc.). How is this different behavior of the same program under Win and OS-X possible ? Do you have any recommendation how to eliminate this problem ? Thank you in advance, Best wishes, Marek Here is the err list after the attempt to load into Win Chimera 1.10 session containing "problematic" molecule with surface calculated under OS-X version of the Chimera 1.10 ***** C:\Program Files\Chimera 1.10\bin\mscalc.exe 1.400000 2.000000 0 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags Surface calculation failed, mscalc returned code 5. 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 Traceback (most recent call last): File "gB_2G_S16_A.py", line 2669, in <module> restoreCoreModels() File "gB_2G_S16_A.py", line 2654, in restoreCoreModels restoreSurfaces(surfInfo) File "C:\Program Files\Chimera 1.10\share\SimpleSession\versions\v40.py", line 55, in restoreSurfaces elif len(customColors) != len(s.triangleData()[0]): TypeError: 'NoneType' object has no attribute '__getitem__' Error restoring core models: TypeError: 'NoneType' object has no attribute '__getitem__' File "C:\Program Files\Chimera 1.10\share\SimpleSession\versions\v40.py", line 55, in restoreSurfaces elif len(customColors) != len(s.triangleData()[0]): See reply log for Python traceback. Traceback (most recent call last): File "gB_2G_S16_A.py", line 3025, in <module> restoreRemainder() File "gB_2G_S16_A.py", line 3020, in restoreRemainder restoreSilhouettes(silhouettes) File "C:\Program Files\Chimera 1.10\share\SimpleSession\versions\v62.py", line 265, in restoreSilhouettes model = idLookup(modelID) File "C:\Program Files\Chimera 1.10\share\SimpleSession\versions\v23.py", line 162, in idLookup return globals.sessionMap[sesID] KeyError: 27136 Error restoring post-model state: KeyError: 27136 File "C:\Program Files\Chimera 1.10\share\SimpleSession\versions\v23.py", line 162, in idLookup return globals.sessionMap[sesID] See reply log for Python traceback. Warning: Could not restore surface color on surface model with id 0.0 because that surface was not restored. C:\Program Files\Chimera 1.10\bin\lib\site-packages\matplotlib\axes.py:2369: UserWarning: Attempting to set identical left==right results in singular transformations; automatically expanding. left=1, right=1 + 'left=%s, right=%s') % (left, right)) -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Chimera Published Paper
by Kurt Degabriele 08 Dec '14

08 Dec '14

Dear sir/madame, I am a pharmacy student currently undergoing my 4th year pharmacy project at the University of Malta as part of my 5 year study course; I am currently doing research within the Med. Chem. field and would like to ask if you can send me a copy of the following paper so I can include it in my study: UCSF Chimera—A visualization system for exploratory research and analysisEric F. Pettersen, Thomas D. Goddard,Conrad C. Huang, Gregory S. Couch,Daniel M. Greenblatt, Elaine C. Meng andThomas E. Ferrin* Article first published online: 1 JUL 2004DOI: 10.1002/jcc.20084 Regards Kurt

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Re: [Chimera-users] How to use a colour-valued attribute?
by Elaine Meng 04 Dec '14

04 Dec '14

On Dec 3, 2014, at 1:30 AM, Mungo Carstairs (Staff) <g.m.carstairs(a)dundee.ac.uk> wrote: > Thanks all. > Tom, your suggestion of comma- instead or or-delimiter improves speed several times! > Elaine, your point about specifying the chain is noted. > > Conrad, I didn't explain too clearly: my 'real' command is the 'non-contiguous' example (think Zappo colouring with some custom features colours on top). The 'contiguous' example was just what I was using to explore behaviour of setattr / defattr / rangecolor. > (Also by the way the REST API is working fine for me.) > > Instead of 'color' I am now using 'setattr' followed by 'rangecolor'. > I tried both 'setattr' and 'defattr' (passing a temporary file) and didn't see any significant performance difference between them, at the scales I am testing so far (up to 3 models of 1600 residues). > > So I have what I need for now. But I'm still curious to know if / how you get Chimera to 'act on' (display) a colour-valued attribute. > > Best regards, > Mungo Hi Mungo, Setting the color attribute with setattr or defattr does change the color immediately. The problem in what you sent earlier: setattr r color green #0:1-84.B … is that there is no residue attribute named “color". There are atom and molecule-model attributes by that name (setattr a color …) but the only per-residue color setting is ribbon color, name “ribbonColor” … thus you would want something like: setattr r ribbonColor green #0:54.a,76.a … and that would only color the ribbon, not the atoms/bonds. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#respr…> Actually I am mystified as to why this would be any faster than using the color command with the same atomspec (#0:54.a,76.a in the example above), but maybe the others who know more about the “guts” of Chimera can comment. Best, 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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Commands for multiscale models?
by Hurt, Darrell (NIH/NIAID) [E] 03 Dec '14

03 Dec '14

Hi Chimera friends, I was reading this post from 2009 that indicates that there are no Chimera commands for multiscale models: http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-June/004009.html Is it still the case that there are no Chimera commands for manipulating the multiscale models? I saw the blue-tongue virus example script for doing something similar using Python itself: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/blueto… I want to script the loading of an arbitrary VIPERdb model and then create multiscale model surfaces for every chain (not just the copies). Can it be done with Chimera commands? Or do I need to work up my Python-fu? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Bethesda office: 301-402-0095 Rockville office: 240-669-2741 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> , @NIH3Dprint<https://twitter.com/nih3dprint> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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volume viewer step value
by Ludovic Renault 03 Dec '14

03 Dec '14

Hi, When I load different EM volumes into Chimera, depending on the size of the box the display step value changes from 1 to 4. Is it possible to force chimera to always load the 3d map with a step value of 1? Or at least change some parameters in preferences to have step 1 loaded with my routine volumes (up to 300 pixel boxes for example). Thanks, Ludo

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show surface fails
by Hartzell Jr., Criss 02 Dec '14

02 Dec '14

I am struggling to show an electrostatic surface on the solvent accessible surface for several related proteins. It works fine in Pymol with APBS but with Chimera I continue to get "surface calculation failed, mscalc returned code 5". I have read posts going back at least 5 years about this problem and I have tried all of the various work-arounds (vdwdef, split, probe radius and vertex density). Has this problem been solved? I am using version 1.8.1 on a PC. Is there a way to identify which part of the protein is causing the problem? Criss Hartzell Professor Department of Cell Biology Emory University School of Medicine Atlanta, GA 30322 ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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regarding distance measurement
by abhishek jamwal 02 Dec '14

02 Dec '14

Dear All, I have created a stereoview using chimera where I am showing distance between sidechain atoms of a protein. when I save an image of this stereoview (tiff, 600dpi), the connector lines showing the distances are fading, they are not of same quality in the image as in the original view ! Is there a way to save image without disturbing quality of the connector lines showing distances ? thnx abhishek

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How to use a colour-valued attribute?
by Mungo Carstairs 02 Dec '14

02 Dec '14

Hi, This feels like a basic question but it has stumped me for a day now so here we go... I'm exploring ways of programmatically setting colours to find the most efficient method. This is for the 'custom coloured' case (residue-based colour schemes are not a problem). The simple version is to send as many 'color' commands as there are colours in my (Jalview) sequence: color #ffafaf #0:1.B|#0:5.B|#0:7-8.B|....;color #ffff00 #0:39.B|#0:44.B|#0:47.B|#0:77.B; This works, but doesn't seem to scale up well for large/many structures - I start to see Chimera using 100% CPU for minutes at a time. I'm trying instead to see whether setting a colour-value attribute is faster. I can set the attributes ok with commands like setattr r color green #0:1-84.B etc and confirm they are set with list residues spec #0:1-84.B attribute color but I can't figure out how to get Chimera to use the attribute value as the display colour. 'Render by Attribute' only seems to consider numeric (range-valued) attributes, not colour-valued. I thought perhaps 'my' colour was just hidden in the colour hierarchy, but removing other colours doesn't seem to help. What am I missing? Thanks, Mungo Carstairs Division of Computational Biology University of Dundee http://www.jalview.org The University of Dundee is a registered Scottish Charity, No: SC015096

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Display atoms after multiscale model
by vamsee 02 Dec '14

02 Dec '14

Hello, I am working on a virus capsid and trying to figure out the buried surface area between subunits (similar to what ViperDB has. I have to do this for a few capsids and I am trying to automate this to the maximum possible extent. I have been able to follow the steps in this link Buried surface area calculation <http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-December/001131.html> and manually calculate the information. Are there commands available to do the same? Also, what is the difference between the surfaces created using a multiscale model and surfaces computed from the atom-spec? Would this difference in the surface affect the calculation of the buried surface area? And if it does affect it which one be a more accurate representation? Thank you Vamsee

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