- Chimera-users - RBVI Mailing Lists

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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