- 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>

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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

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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

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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 >

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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

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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

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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

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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

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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

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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

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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 ------------------------------------------------------------------------

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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

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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 | +---------------------------------+

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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

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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

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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

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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

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