- Chimera-users - RBVI Mailing Lists

Fitmap in batch mode
by ingvar 22 May '13

22 May '13

Hello, I am trying to run fitmap on a set of volumes on a server without a display. I would like to collect the results of the top hits to store in a database – correlation coefficients, inclusion scores, and the transforms. The only way I found to collect the fitting results is to save the session after displaying the listFits dialog. The listFits dialog cannot be displayed when running Chimera in –nogui mode, otherwise this would have been a solution. I tried to use a virtual display, with Xvfb. I have used Xvfb with some java applications in the past. When I use Xvfb with Chimera, it appears that Chimera do not want to start up properly, the process just hangs, i.e. no cpu usage. Is there a way around this, or am I asking for an enhancement, e.g. a “writeListFile toFile” option. I am on RHEL 6.2/6.3 if that matter. Noticed that there is a local correlation option in the pipeline for Chimera 1.8, looking forward to try it out. Kind Regards, Ingvar Typical python script: from chimera import runCommand as rc rc("open emd_5500.map") rc("volume #0 level 1.34 transparency 0.5") rc("open emd_2017.map") rc("volume #1 level 0.58 transparency 0.5") rc("fitmap #1 #0 search 200 metric overlap envelope true inside 0.2 listFits false") #rc("fitmap #1 #0 search 200 metric overlap envelope true inside 0.2") rc("save session5500_2017") rc("stop now") Setup to run with Xvfb (in bash): i=0 while [ -f /tmp/.X$i-lock ] do i=$[$i+1] done Xvfb :$i & pid=$! export DISPLAY=:$i chimera fit5500_2017.py kill $pid

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Pipes and planks representation
by Ernesto Arias Palomo 21 May '13

21 May '13

Dear chimera developers, I have noticed that in the last Chimera releases you have significantly improved the 'pipes and planks' representation. I find it particularly useful because, in my opinion, it makes the structures look simpler and clearer, especially when you are displaying large PDBs. I would like to suggest an improvement. It would be really useful if you could make that representation an attribute of the structure (like the 'ribbons' one) instead of a separate object. That way one could easily show, hide or color different regions of the structure without having to modify the actual PDB file. Thank you very much for your help, and congratulations for your great work. Cheers, Ernesto.

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Re: [Chimera-users] RMSD i.b and RMSD u.b
by Elaine Meng 20 May '13

20 May '13

Please send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of just my address. The RMSD lb (lower bound) and RMSD ub (upper bound) of a docked ligand are calculated by AutoDock Vina and are described in the manual for that program: <http://vina.scripps.edu/manual.html> (go to that page and search for "RMSD") I believe they just indicate how similar each position is to the best-scoring position found. 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 May 20, 2013, at 6:10 AM, Muhammad ALi <muh.ali741(a)yahoo.com> wrote: > AOA > > sir > when I check my result with ViewDock their are two RMSD values i.e RMSD i.b and RMSD u.b plz tell me about them.....

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3D Printing our protein
by Bart Janssen 19 May '13

19 May '13

Hi My apologies for what are likely to be stupid questions. We are plant developmental biologists and we just obtained our first X-ray crystal structure for a new hormone receptor in plants. We'd really like to make a 3D model of the protein using one of the 3D printers at our institute. I've been trying to use and understand Chimera for the last week and I'm a bit out of my depth :). I can import our protein 4DNP.pdb and display it using solid surface or using the sphere representations of atoms. I can also display it with the "lid" domain hidden and vice versa. My problem has been getting files that our 3D printer can read. The solid surface model of the whole protein can be exported as a scene in .stl format and that can be printed just fine. Although I can't figure out how to adjust resolution or the smoothness of the exported file. But I'd really like to print the two domains of the protein separately. If I use Solid surface model with the lid hidden what I get is an eggshell like model which has no internal detail. If I use atoms shown as spheres instead I get the internal detail I want BUT when I try and export the scene I get a 2 Gb+ file that is unreadable by the printer. If I export .obj format instead the colleague who runs the printer says the file won't load and appears to have errors. I have a horrible feeling I am going about this entirely the wrong way but I can't find a tutorial that describes what I'm trying to achieve. I do realise chimera is not really written for the somewhat trivial use that I am attempting but it really would be helpful if we had a physical model of the protein to look at. Is there a tutorial I should follow or another part of Chimera (or another program) that I should be using instead? Any advice would be much appreciated. Cheers Bart Bart Janssen Scientist Plant Development team Breeding and genomics Plant and Food Research Private Bag 92169 Auckland 1142 New Zealand Ph +64 09 9257179 bart.janssen(a)plantandfood.co.nz The contents of this e-mail are confidential and may be subject to legal privilege. If you are not the intended recipient you must not use, disseminate, distribute or reproduce all or any part of this e-mail or attachments. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. Any opinion or views expressed in this e-mail are those of the individual sender and may not represent those of The New Zealand Institute for Plant and Food Research Limited.

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showing salt bridges in pdb trajectory movie
by Albert Lyons 18 May '13

18 May '13

Hi all, I am having a problem trying to show salt bridges between selected atoms in a movie of my pdb format trajectory. I am using the following commands in the Per-Frame script, to display H-bonds between the residues but with a less strong distance criterion (to bring the distance of interaction to 6 A) and angle criterion (to make the angle 0deg and so make all angles available): select :1,6,7,10,16,18 findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145 When I apply this script I get a Chimera error saying: Error while sourcing select :1,6,7,10,16,18 findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145 ,line 1: "findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145" Non-alphanumeric character in keyword ':6@2HH2,2HH1,HE,2HH1,1HH1' I have tried tweaking it different ways but just get other error messages, I can't seem to write it in the correct format. Can anyone see a problem with this script and how I might fix it? Cheers Albie

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showing salt bridges in pdb trajectory movie
by Albert Lyons 18 May '13

18 May '13

Hi all, I am having a problem trying to show salt bridges between selected atoms in a movie of my pdb format trajectory. I am using the following commands in the Per-Frame script, to display H-bonds between the residues but with a less strong distance criterion (to bring the distance of interaction to 6 A) and angle criterion (to make the angle 0deg and so make all angles available): select :1,6,7,10,16,18 findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145 When I apply this script I get a Chimera error saying: Error while sourcing select :1,6,7,10,16,18 findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145 ,line 1: "findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145" Non-alphanumeric character in keyword ':6@2HH2,2HH1,HE,2HH1,1HH1' I have tried tweaking it different ways but just get other error messages, I can't seem to write it in the correct format. Can anyone see a problem with this script and how I might fix it? Cheers Albie

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Re: [Chimera-users] Conserved amino acids
by Rebecca Swett 17 May '13

17 May '13

Use match-> align to get a structural superposition and sequence alignment, then set your alignment type to AL2CO. Go to render by attribute and then hit the select by attribute tab. Select the range from 0-whatever your maximum is. Should be around 4 if you've got any conserved tryptophans. That will select all invariant residues. Jean-Paul Boissel <boissel(a)uni-mainz.de> wrote: >Hi, > >By homology modelling, I got putative structures for five closely related >amino acid transporters. Is there any script that will allow the quick >selection and visualisation of the invariant residues on the structures? >Thanks, > >Jean-Paul > > > > > >_______________________________________________ >Chimera-users mailing list >Chimera-users(a)cgl.ucsf.edu >http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Conserved amino acids
by Jean-Paul Boissel 17 May '13

17 May '13

Hi, By homology modelling, I got putative structures for five closely related amino acid transporters. Is there any script that will allow the quick selection and visualisation of the invariant residues on the structures? Thanks, Jean-Paul

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Carbon color of 1 chain
by Markus Heller 16 May '13

16 May '13

Hello, I don't seem to be able to figure out how to color a scene by element, but with different carbon colors for different chains. I can't figure out how to get an expression like "color green, chain C C" Or something like that ... How to go about this? Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller(a)cdrd.ca<mailto:kessabar@cdrd.ca> | www.cdrd.ca

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Re: [Chimera-users] energy optimization of the modle from homology modeling
by Elaine Meng 16 May '13

16 May '13

Hello, I agree with what Tom Goddard said: "How to make a suitable homology model for docking and what force fields to use are not questions specific to Chimera, they are questions about how to do good quality science, and they depend a great deal on the details of your system. So you aren't likely to get the answers you want on this list." Instead, you have to use your scientific judgement and your knowledge of this protein, how similar it is to the template protein, etc. The procheck statistics are only one thing to consider. One reason is that they are for the whole protein, whereas you mostly care about the binding site. Another is that they focus on stereochemical quality, mainly torsion angles, but not other descriptors such as whether the protein is well packed. You could see what others have done in published papers, and/or ask on the Computational Chemistry List (see <http://ccl.net/cgi-bin/ccl/send_ccl_message>) and the Modeller discussion forum (see <http://salilab.org/modeller/discussion_forum.html>) if it is recommended to minimize homology-modeled structures before docking. In complicated structures like proteins, atoms may "feel" multiple conflicting forces, and minimization will usually relieve some strains (for example, move atoms apart if they are too close together) but increase others (for example, distort the angles of the sidechains containing those atoms). That is why the statistics from procheck got worse. It is important to realize that minimization has very little ability to fix a complicated structure with a rugged energy landscape. It is good for cleaning up small molecules, and sometimes for cleaning up a localized area (leaving the rest of the protein unchanged) where you have made some change such as manually rotating some bonds or mutating a residue. It will not predict any significant conformational change to find the global optimum. If you don't have any specific reason to minimize the structure, it might be better not to minimize it. That is only my guess, and you could probably get more expert opinions by asking your question on the other discussion lists mentioned above. If your docking doesn't take too long, you could try docking to more than conformation of the protein (more than one model). Chimera does not do molecular dynamics, although it can show MD results from other programs. However, Modeller itself does sampling to generate multiple models. Also, you could consider using Modeller to further refine parts of the model(s) from the first Modeller calculation. The Modeller scores should provide some indication of which models and refinements are better. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo…> 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 May 14, 2013, at 9:39 AM, Conrad Huang wrote: > Unfortunately, that is getting well beyond my understanding of molecular mechanics. I will have to defer this to our expert when she returns. > > Conrad > > On 5/13/2013 7:56 PM, aixintiankong wrote: >> Dear, >> Thank you for your patience to answer my questions in detail. >> Before /minimizating/ the model, i use the procheck to check the >> quality of the model. the residues in most favoured regions is 95.6% and >> the disallowed regions is 0.0%, the the residues had an averaged 3D-1D >> score>0.2 is 92.02% and the errat is 90.55. >> if i use the chimera to minimizate the model after 200 steps, the >> most favoured regions is 85.5% and the disallowed regions is 0.4%, the >> the residues had an averaged 3D-1D score>0.2 is 99.2% and the errat is >> 95.968. >> if i use the chimera to minimizate the model after 250 using the >> ff99sb! force filed, the most favoured regions is 92.1% and the >> disallowed regions is 0.4%, the the residues had an averaged 3D-1D >> score>0.2 is 96.96% and the errat is 98.000. >> if i use the chimera to minimizate the model after 500ns the most >> favoured regions is 90.8% and the disallowed regions is 0.4%, the the >> residues had an averaged 3D-1D score>0.2 is 96.58% and the errat is 96.047. >> which one model should i select to make docking . >> thank you very much! >> >> At 2013-05-14 00:24:03,"Conrad Huang" <conrad(a)cgl.ucsf.edu> wrote: >>> Unfortunately, our local expert on this is on vacation and will be back >>> at the end of the week, so a more definitive answer should come then. >>> In the mean time, I'll try to answer as best as I can. >>> >>> First, Homology Modeling uses Modeller and that does a bit of >>> optimization already. If the model structure looks reasonable, further >>> energy optimization might be helpful. On the other hand, if the model >>> has extended chains because Modeller does not have appropriate templates >>> or just looks unreasonable because the model is not well packed or has >>> large dangling loops, then energy minimization probably will not help. >>> >>> Second, I do not know the answer, but have you tried using the default >>> paramters? >>> >>> Third, conjugate gradient is much much slower than steepest descent, so >>> it probably pays to use steepest descent to get near the minimum before >>> starting conjugate gradient. You can look at the reported energy values >>> reported to decide whether the minimization is proceeding as expected. >>> Chimera energy minimization is not highly optimized, so it may take a >>> while to run for a large system. If only one portion of the model is >>> "interesting", e.g., an active site, it might be faster to select just >>> the region of interest (plus a buffer around it) and only optimize that >>> part. >>> >>> Hope this helps a bit. Better answers should come later in the week. >>> >>> Conrad >>> >>> On 5/11/2013 6:50 PM, aixintiankong wrote: >>>> Dear, >>>> i am a newer use the chimea, i have some question to consult to you, >>>> please help me. >>>> Frist, after Homology modeling using the chimera modeller, should i >>>> optimizate the modle by energy optimization or Molecular dynamic >>>> simulations? The next step i will use the model to make docking. >>>> Second, i want to use chimera to minimize the structrue of my modle. >>>> i select Tools>Structure Editing>Minimize Structure to perform my >>>> work, but my modle include protein and a organic molecule NAD+, so i >>>> don't know how to select the force fileds for the minimiztion of the >>>> modle. please help me. >>>> Third, if i olny want to use the conjugate gradient to perform the >>>> minimiztion, should i only need to set the steepest descent steps to 0? >>>> in general, how many conjugate gradient s! teps and size should be ? >>>> Thank you very much!

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Error reading PubChem3D SDF Files
by Jon Fuller 15 May '13

15 May '13

I tried to read an SDF file directly downloaded from pubchem into Chimera. However, I ran into the following problem (link to example file used, and reply log below). Is this expected behaviour, or a bug? Additionally I tried to import the pubchem CID 71739 (same compound) from the fetch structure by ID tab, and got the error message: Unexpected end of file (parser state: counts) in MOL/SDF file 'FILEPATH HERE!' Many thanks in advance, Jon http://pubchem.ncbi.nlm.nih.gov/vw3d/vw3d.cgi?cmd=crtvw&reqid=2385389770715… You are now running Chimera version 1.8 (build 38642). Your previous version was 1.5 (build 32133). Check the release notes for new features and other info. (To access the release notes, use the Help menu to bring up the User's Guide. Then click the 'Documentation index' link and you will then see a link for the release notes.) Error while processing CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data Error reading CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data Error reading CID_3672_e5800000001_conf.sdf: Non-numeric charge (1 -0.65) in PUBCHEM_MMFF94_PARTIAL_CHARGES data Error reading CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data

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energy optimization of the modle from homology modeling
by aixintiankong 15 May '13

15 May '13

Dear, i am a newer use the chimea, i have some question to consult to you, please help me. Frist, after Homology modeling using the chimera modeller, should i optimizate the modle by energy optimization or Molecular dynamic simulations? The next step i will use the model to make docking. Second, i want to use chimera to minimize the structrue of my modle. i select Tools>Structure Editing>Minimize Structure to perform my work, but my modle include protein and a organic molecule NAD+, so i don't know how to select the force fileds for the minimiztion of the modle. please help me. Third, if i olny want to use the conjugate gradient to perform the minimiztion, should i only need to set the steepest descent steps to 0? in general, how many conjugate gradient steps and size should be ? Thank you very much!

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desmond in chimera
by lecan 15 May '13

15 May '13

Hi to everybody. Can the newest version of Chimera use the .cms files from desmond by schrodinger to analyse trajectories and make movies? Regrads, Luis L.

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surface
by Gesa Volkers 13 May '13

13 May '13

Hi chimera users/developers, I have a problem with a surface calculation from one monomer of a structure that I want to show. As you can see in this image http://imageshack.us/photo/my-images/801/testss.png/ it looks like the surface calculation failed (?) because the surface is missing in the middle (note the chewed up structure of the surface). Most of the surface is smooth but for whatever reason not this part of the structure. I have played around with probeRadius, vertex density and zone and they all increase quality but do not add the missing surface part (I'm not even sure if zone is applicable to surfaces at all or only to electron density maps). Any suggestions which parameter I am missing? Thanks for suggestions, Gesa

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Contour maps or step-gradient of volume map?
by Bullitt Esther 13 May '13

13 May '13

Hi, Is it possible to choose n levels of gray for a volume map? I'd like to make a known-thickness slice using clip, and then see that slice as a defined number of colors. I can kluge it by displaying the map 4 times at 4 contour levels, but is there a better way? thanks, Esther --- Esther Bullitt, Ph.D. Dept. of Physiology & Biophysics Boston University School of Medicine 700 Albany Street, Room W302 Boston, MA 02118-2526 Email: bullitt(a)bu.edu Telephone: 617-638-5037 Facsimile: 617-638-4041 http://www.bumc.bu.edu/phys-biophys/faculty/bullitt

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mask using volume contour surface
by gongpu zhao 13 May '13

13 May '13

Hi All, I have a question about volume contour surface in chimera. I have a density volume of a shell shape. I plan to use the outer contour surface of the volume to mask out all density encased by the outer surface in a tomogram. But instead, I could only mask out the density within the shell. I am wondering if I can make a surface model only using the outer surface. Thanks a lot. Gongpu

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About Morph Conformations
by 吕柯 13 May '13

13 May '13

Dear Sir./Madam, I am a graduate student in Chinese Academy of Sciences. I have two PDB files: one for virus(4 chains, PDB:3VBS), the other for empty particle(3 chains, PDB:3VBU). I would like to use Morph Conformations to make movie for that. However, it turns out "Can not interpolate models: models have different number of chains". Could you please show me what should I do next? Thanks a lot. Yours, Lyu Ke -- Lyu Ke, Ph.D. student Structural Virology Unit Institut Pasteur of Shanghai Chinese Academy of Sciences No.411 Hefei Road Shanghai, 200025, P.R. China Tel: +86-21-54920652

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Re: [Chimera-users] saving sessions
by Tom Goddard 08 May '13

08 May '13

Hi Thomas, There is no session saving option that copies density map files to the same directory as the session file. All other Chimera models including PDB files are included (not linkied) in the session file. The reason maps are not put into the session file is because they are sometimes very large, Gbytes in size. Some day I intend to add an option to include the maps in the session file so you can have a self-contained session if you want. Copying the files could be another approach but it has problems. What if there is already a map with the same file name in the current directory? Could modify the copied file name I guess. Maybe better put all the map files in a new subdirectory. But are you really going to make copies of all the map files on every session save? If you only do it sometimes it doesn't solve the problem of moving data to a new computer. It will be slow to copy the files and it makes many redundant copies which then can become confusing as to whether two files with the same name really are identical. Hard links could be used to avoid copying the file, but that won't work when a session is on one file system and data on another. I think the way to handle moving data files to a new computer is to keep all your data including sessions under one directory tree so the whole thing can be easily copied. If instead the goal is to occassionally make a self-contained session then copying the map files and session file to a new directory would be a nice option similar to embedding all files in the session. I've noted this in the feature request for embedding the map files. http://plato.cgl.ucsf.edu/trac/chimera/ticket/9763 The sphere/axes display idea is one way to see the axes of a displayed model. The transparent sphere would cause problems in Chimera some of the time because Chimera can only correctly display one transparent model at a time. The current default is to show a single transparent layer, so any transparent model inside the sphere would disappear. This is a longstanding and hard problem to fix. But a mesh could work. Another idea is simply to depict the x,y,z axes. I've made a feature request for this. http://plato.cgl.ucsf.edu/trac/chimera/ticket/12062 Tom On May 8, 2013, at 12:25 AM, "Marlovits,Thomas" wrote: > Hi Tom, > > I do have a question related to saving sessions, which is a great option btw. > Is there a way that one can save the session - let's say in a new folder but then have all models also saved in there. For now, as I understand, it will only save the path/filename of those models. So, whenever we switch computers, hard-drives etc … this can turn out to be a lengthy process to find those models (we often have many models open at the same time). > Ideally, also fetched files from the pdb would be great to be saved locally in this new folder. > > The second question I have is related to turning molecules around specific x/y/z angles. > I'd love to have an option to display a big sphere that encapsulated the other models displayed. Ideally, this sphere would look like a globe with cordinates in there … if this is displayed at semi-transparency, one can easily go to a specific position but get more of an idea to easier naviagte through the 3D space. Sometimes I only would like to get a rough estimate about the angles to turn molecules. Alternatively a mesh-like grid could do the same job (and if one could display the numbers of the lattidude/longitude or so that would be great too). > > Many tx, > -T. > > > ------------------------------------------------------------------------------- > > Thomas C. Marlovits, PhD, M.A.S. > The MarlovitsLab @ IMP/IMBA > http://thomas.marlovits.myresearchlab.org > > Contact/Address/Directions: > http://thomas.marlovits.myresearchlab.org/lab/Contact.html >

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Define centroid issue
by Francesco Pietra 08 May '13

08 May '13

Hello: I was unable to put to work define centroid radius 0.5 color red :ligand_residue_name or define centroid radius 0.5 color red #0&@serialNumber=1972 with a homodimeric protein (I am at CHARMM NAMD/XPLOR, so that the two subunits are only distinguished by either the atom sequential number or the segment name, the latter not being understood by chimera, as far as I know). In the first case, running the movie after the appropriate further steps, the centroid sequence obtained was for the centroid between the two protein ligands, as it was expected. In the second case (as I wanted to refer to the ligand in subunit A only), the command raised the error: AttributeError: 'NoneType' object has no attribute 'openState' File "/opt/UCSF/Chimera64-1.7/share/StructMeasure/Geometry.py", line 293, in _getRefInfo invXForm = lowest.openState.xform Please notice that the line command #0&@serialNumber=1972 correctly selects the ligand on subunit A (a diatomic ligand, where "1972" is the sequential number of one of the two atoms of the ligand. Here "#0" may be redundant, as it deals of a single model. However, using "@serialNumber=1972" raised the same error. I fear I am missing some obvious facet of define centroid, so that I thank you for your patience. francesco pietra

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Question about measuring volume in chimera
by Varun Kumar 07 May '13

07 May '13

Hi, Can we outline a particular area and measure volume in chimera? I wish to measure specifically the purine binding site in the ATP binding pocket of Protein kinase C. Best regards -- Varun Kumar International Graduate Student School of Biomedical Sciences Department of Biological Sciences Kent State University, Kent, Ohio, U.S

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RMSD
by George Tzotzos 04 May '13

04 May '13

Hi everybody, I am trying to measure the RMSD between a docked ligand and the corresponding ligand in an X-ray structure. I've been looking to find a way of doing this in Chimera to no avail. I'd be grateful for any suggestions on how to do this. Best regards George

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save map with the adjusted threshold
by Moumita Dutta 01 May '13

01 May '13

Hello, I'm not sure if I can do this in chimera. Once I open a density map and adjust the threshold and removed dust how can I save the map in this setting so that next time when I open it I don't have to adjust again. Thanks

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Chimera shutsdown when opening sideview
by vamsee 29 Apr '13

29 Apr '13

Hi Elaine, I have recently moved to Linuxmint 14 from Windows 7. I can open virus capsids very easily (much more easier than in Windows 7, which is pretty sweet). But, every time I try to open the Side View option from the menu, Chimera shuts down. I have tried version 1.7 and 1.8rc. Both exhibit the same behavior. The interesting thing is, I can open all the other tabs (Effects, Lighting etc.) on that window from the menu. But when I click on Side View, Chimera crashes immediately with no bug report (Its almost like the process never existed). So, I tried starting chimera from the command line with the Side View option enabled (sudo chimera --start "Side View"). That started the Side View window and that stayed even after I opened my models. I then closed the Side View and re-opened it from the menu bar this time in the same chimera session. That worked again. So, I am kind of at a loss though I seem to have a work around for now. I have used the same features on Windows 7 (I still do using a virtual machine inside Linux) and they work fine. Any reason why this would happen? My computer specifications Processor : Intel® Core™ i7-2630QM CPU @ 2.00GHz × 8 Memory : 8Gb Onboard Video : Intel® Sandybridge Mobile OS : LinuxMint 14 Thank you Vamsee

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morph conformation
by Moumita Dutta 27 Apr '13

27 Apr '13

Hello chimera-users, I'm trying to use the option morph conformations from the command line and cannot specify more than one molecule with the command morph start. How to use the morph start command for more than two molecules ? Thanks for any help. Moumita

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morph map and movie recording
by Moumita Dutta 26 Apr '13

26 Apr '13

Hello, I am trying to morph more than two maps at a time so I am using vop morph instead of Morph map. I am following the mini-video animation example script of vop morph using the recommended chimera 1.7 version 2013. The script actually recorded the movie but in the movie threshold changed from what I set and it turned some maps to x 90 degree not all and it is not showing the morph animation only the superimposed maps. Another problem is though I remove the dust after loading the maps but it came back in the morph and in the movie as well. How can I fix the problems and generate the movie ? Moumita

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