- Chimera-users - RBVI Mailing Lists

Electrostatic Potential based on Poisson-Boltzmann using APBS
by leila karami 18 Jul '15

18 Jul '15

Dear chimera users, I am using chimera 1.10.1. I did following steps to obtain Electrostatic Potential based on Poisson-Boltzmann using APBS: open... pr.pdb action... surface... show to obtain *.dx file, I typed APBS in command line, after minutes, *.dx file was created and surface color window was opened, I pressed color tab. Please see the figure in following link: https://www.dropbox.com/s/99gjecypqu910hu/apbs.png?dl=0 Why are the colors black and white in the surface, instead of blue and red? Any help will highly appreciated.

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RMSD
by Valerio Chiarini 17 Jul '15

17 Jul '15

Hi everyone, I am dealing with an NMR structure and I noticed in literature that among the parameters required for presentation is included "RMSD from the ideal geometry". Does anyone know if is possible to calculate such value from chimera and how? Currently I just know how to calculate RMSD to the mean coordinate... thank you all in advance Val

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question
by leila karami 16 Jul '15

16 Jul '15

Dear chimera users, 1) I want to have electrostatic surface of my protein in chimera. To this, I used *Tools... Surface/Binding Analysis... Coulombic surface coloring* A new window is opened, but apply bottom is inactive. 2) There are ray command in pymol to obtain better image of molecular structures. Is there a similar command or utility in chimera? Any help will highly appreciated. Best wishes, Leila

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adjusting threshold values on volume rendering
by Dougherty, Matthew T 15 Jul '15

15 Jul '15

Hi, I can access threshold values from solid/volume rendering. eg: from VolumeViewer import active_volume v = active_volume() if v==None: return levels = getattr(v, "solid_levels") t,a=levels[0] How can I change a threshold value? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Error opening file
by Sneha Poondru 10 Jul '15

10 Jul '15

Hello! I’m trying to prepare a receptor for dock6, so I downloaded a file (1tvb_.all.sph) from our cluster onto my desktop. However, when I click to open it, I keep getting this error message from Chimera: non-standard sph header Error while processing /Users/SnehaPoondru/Desktop/Project/1tvb_.all.sph: cannot open file "/Users/SnehaPoondru/Desktop/Project/1tvb_.all.sph": syntax error, line 1832 Any help is appreciated! Thanks! ~Sneha

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Structureviz Cytoscope plugin problem
by Ahmed Ezat 10 Jul '15

10 Jul '15

Dear Sir, I am trying to use structureviz Cytoscope plugin to launch Chimera, but it does not work. I installed Chimera and Cytoscope properly and set the path to Chimera in structureviz settings but it is not working. What can I do? I am using windows 7. I have also a problem to install chimera on Linux. if possible,c Can you send me detailed procedure for the installation process. Best Ahmed A Ezat

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swapaa: choosing rotamers
by roz orchidea 09 Jul '15

09 Jul '15

Dear all, I would like to use swapaa and choose which rotamer I want. Foe example I want from library dynameomics the second rotamer that appears in the pop-up menu of Arg. is it possible? Thank you for your time, Alex

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How to display two EM map and a PBD simultaneously
by 师扬 08 Jul '15

08 Jul '15

Dear all, Recently, I have a task to display two EM density map ('A' and 'B') and one PDB ('C') at the same time. B and C fit in map to A. So, I need to make A and B transparent to observe them simultaneously. However, one strange thing happened when I made A and B transparent. I can only see the density which A is lager than B or B is larger than A, and I could not see the buried density. In another words, when I make both A and B transparent, the map can be changed in to the 'A+B' map, and I could not see any 'A-B' or 'B-A' information. Have anyone met this problem? Do change something in setting can solve this problem? Best regards Yang

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on the movie command “turn y 3 120”
by Smith Liu 07 Jul '15

07 Jul '15

Dear All, For movie command "turn y 3 120", the molecule will turn counter-clockwise. Will you lease tell me the movie command which makes the molecule turn clockwise？ Best regards. Smith

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Measure translation of two domains?
by Oliver Clarke 07 Jul '15

07 Jul '15

Hi all, I’m puzzling how to measure the translation of two domains in Chimera, in a situation where there is small but non-zero translation. I expected I could do this by first using match to superimpose the two selections, then using measure rotation to obtain the rotation (if any) and translation. This has worked fine for me in measuring rotation of domains. However, on a purely translational test case, this gives confusing results. I have attached two structures of 1bl8, one of which has been displaced from the other manually by 20 Å. If I match one to the other, it successfully superimposes the two structures. If I then use measure rotation to try to recover the translation, I get a message telling me that the rotation angle is near zero (which is not surprising), but when I check the reply log, the listed translation along the axis is only 1.7Å (see screenshot attached), rather than the 20Å I expect. What am I doing wrong here? Is there another command I ought to be using? Or am I misinterpreting the output? Cheers, Oliver.

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question
by A G Szabo 07 Jul '15

07 Jul '15

I am pleased to inform you that I have been using aspects of Chimera that permit me to prepare images of proteins deposited in the pdb. It was a pleasant surprise to find that the learning curve was not as steep as I thought it might be. Mind you, there are many aspects of Chimera that I have not yet attempted to use. Now I wish to do something that may not be possible to do with Chimera. And I am not sure where to look in the tutorials. I have a ribbon diagram of a protein-RNA complex, PDB 4p3e, two proteins, SRP 19 and SRP68, bound to a segment of 7SL RNA. I can also obtain the structure of another protein SRP54 which also bind to this complex. However, the structure of pdb 4p3e with SRP54 is not available. I know where SRP54 should bind to the RNA, and I know which domain of SRP54 binds to the RNA. How can I somehow combine the two files, one for SRP54 and the other 4p3e and locate SRP54 onto the 4p3e structure? (not sure it is possible) Of course crystallographers know how to achieve this structural combination. I don't have a clue. I checked the tutorial list and the closest I seemed to come was the Merge command. However, the tutorial did not seem to deal with what I wanted to do. Thank you in advance for your assistance. Arthur G. Szabo Ph.D. Professor Emeritus, Chemistry Wilfrid Laurier University Waterloo, Canada.

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Question
by Damjanovic Marko 07 Jul '15

07 Jul '15

To whom it may concern, I am trying to solve a problem that is more of mathematical nature, and I would be very grateful if I could get any advice or pointers on how it may be possible to do this (in Chimera or some other program I am not aware of). I have a molecule that is more or less of cylindrical shape (quite simple shape). I would need a way to surround this molecule with a certain number of layers of solvent molecules that fit around the surface of a cylinder (preferably 1 layer and then going up gradually). The solvent molecules should be packed around the central molecule efficiently (closest packing). An alternative way to approach this would be to take a sphere made out of solvent molecules, put in the centre of the sphere the one cylindrical molecule what is of interest, and let the big sphere accommodate the new molecule. Also, for the sake of simplicity, the solvent molecules can be approximated as small spheres as well (their exact shape is not that relevant). When this is done, all I would need is to get this file in a format like cif, mol or gjf. I underline here that I am looking for a relatively crude model. Could anyone please advise me on how to do something like this? Thanks in advance and best wishes, Damjanovic Marko

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chimera extensions & dialog location
by Dougherty, Matthew T 06 Jul '15

06 Jul '15

1) How can I reload an extension when chimera is running? At the present, after I modify python code I restart chimera for the s/w changes to take effect. Is there a way through idle, etc, that I can cause user code modifications to load without restarting chimera? 2) How can I position the location of IDLE using python? I have IDLE on autostart. In a user extension I have a button, when pressed it organizes the various dialogs, placing them in specific locations. When I try to do something with IDLE, running dialogs.activeDialogs() does not show IDLE in the list. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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change B factor
by McCafferty, Caitlyn (NIH/NEI) [F] 06 Jul '15

06 Jul '15

Hi, Is there a feature in Chimera that allows you to change the B-factor of the Amino Acids. I have a txt file with the values that I would like to replace the current B-factors with. Thank you, Caitie

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Undisplay pseudo bonds (missing segments) in pipes-and-planks representation?
by Oliver Clarke 03 Jul '15

03 Jul '15

Hi all, just wondering if there is an option I am missing to undisplay pseudobonds when using pipes-and-planks? At present chimera seems to represent missing segments in pipes-and-planks as a continuation of the chain rather than a break, which is a little confusing, e.g. check the following pair of snapshots (chain break in green section corresponds to missing 10aa loop): https://www.dropbox.com/s/cbwar1i197kt3ep/Screenshot%202015-07-03%2010.09.5… <https://www.dropbox.com/s/cbwar1i197kt3ep/Screenshot%202015-07-03%2010.09.5…> https://www.dropbox.com/s/we058qjv3ibwjmn/Screenshot%202015-07-03%2010.10.0… <https://www.dropbox.com/s/we058qjv3ibwjmn/Screenshot%202015-07-03%2010.10.0…> Also in general it would be nice if cylindrical representations of helices were more integrated into chimera, perhaps with their own style adjustments (e.g. allowing for curved cylinders), as for large structures they provide much less visual clutter, but I guess that is probably something for Chimera 2. Cheers, Oliver.

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Cross eyed stereo pair generated by default
by Oliver Clarke 02 Jul '15

02 Jul '15

Hi all, I’ve noticed that when I save a stereo pair (using File/Save Image/Image Type/stereo pair), the resultant stereo pair is suitable for cross-eyed viewing. This is great for me, as I can’t do wall eyed stereo, but the default for many journals is to provide a wall-eyed stereo pair. Of course it is easy enough to convert by swapping the two halves of the pair, but for the sake of convenience, would it be possible to list stereo pair (cross eye) and stereo pair (wall eye) as two separate options in this dialogue? Cheers, Oliver.

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Re: [Chimera-users] Chimera-users Digest, Vol 147, Issue 4
by Oliver Clarke 02 Jul '15

02 Jul '15

Thanks Greg! To clarify, I wasn't actually intending these for use with a viewer of any sort - just to provide in a paper for use as a stereo pair, viewed by either diverging or crossing one's eyes to superimpose the two halves of the pair. Some people can easily view wall-eyed pairs, while others (myself included) can only view cross-eyed pairs, so it would be nice to have the option of generating either. Cheers, Oliver. On Thu, Jul 2, 2015 at 3:00 PM, <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: on beta strand assignmet by chimera (Elaine Meng) > 2. Cross eyed stereo pair generated by default (Oliver Clarke) > 3. Re: Cross eyed stereo pair generated by default (Greg Couch) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 2 Jul 2015 09:55:55 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > To: Smith Liu <smith_liu123(a)163.com> > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] on beta strand assignmet by chimera > Message-ID: <E1E1B5D3-B0A5-4849-88D2-237944AFFA48(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=utf-8 > > Dear Smith, > If the PDB files came from the Protein Data Bank repository, generally the > proteins already have secondary structure assigned in HELIX and SHEET > records. If so, Chimera just uses those assignments. > < > http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#se… > > > > If the PDB file of a peptide/protein doesn?t have HELIX and SHEET records > in it, then it runs a method ?ksdssp? described here: > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html> > > If you don?t like the results for some reason, you could try re-running > the ?ksdssp? command (or the ?compute SS? function in the Model Panel) with > different (nondefault) parameters, or just manually assign residues as > helix or strand however you like with the ?setattr? command, as shown in > the lower part of this previous post: > < > http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-January/009574.html > > > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Jul 2, 2015, at 6:09 AM, Smith Liu <smith_liu123(a)163.com> wrote: > > > > Dear All, > > > > I have a protein, which contains fragment aa 239-251. The protein has > been fitted its map with 2 different (minor difference) resolution, and > thus I have 2 PDB. For PDB 1 (the first resolution), the H-bonds inside aa > 239-251 include: > > #2 Gly 245.A N-Asn 242.A O 2.708A > > #2 Asn 242.A N-Tyr 246.A O 3.120 A > > #2 Val 248.A N-Val 240.A O 3.120 A > > #2 GLN 251.A N-Ser 238.A 0 3.033 A > > > > For PDB 2 (the second resolution), the H-bonds inside aa 239-251 include: > > #0 Gly 245.A N-Asn 242.A O 2.715A > > #0 Asn 242.A N-Tyr 246.A O 3.1206 A > > #o Val 248.A N-Val 240.A O 2.858 A > > #0 GLN 251.A N-Ser 238.A 0 3.074 A > > > > Naked eye check found the H-bonds in PDB 1 were almost the same H-bonds > in PDB 2. > > > > However for PDB 2, aa23-242 and aa 247-251 form 2 strands, but for PDB > 1, it was a un-disconnected loop for aa 239-251. > > > > Will you please explain how chimer assign beta strand? > > > > Best regards. > > > > Smith > > > > > > ------------------------------ > > Message: 2 > Date: Thu, 2 Jul 2015 14:20:01 -0400 > From: Oliver Clarke <olibclarke(a)gmail.com> > To: Mailing List <chimera-users(a)cgl.ucsf.edu> > Subject: [Chimera-users] Cross eyed stereo pair generated by default > Message-ID: <B5D941AF-2692-4E71-8D5A-2A9C8D1610E2(a)gmail.com> > Content-Type: text/plain; charset=utf-8 > > Hi all, > > I?ve noticed that when I save a stereo pair (using File/Save Image/Image > Type/stereo pair), the resultant stereo pair is suitable for cross-eyed > viewing. > > This is great for me, as I can?t do wall eyed stereo, but the default for > many journals is to provide a wall-eyed stereo pair. > > Of course it is easy enough to convert by swapping the two halves of the > pair, but for the sake of convenience, would it be possible to list stereo > pair (cross eye) and stereo pair (wall eye) as two separate options in this > dialogue? > > Cheers, > Oliver. > > > ------------------------------ > > Message: 3 > Date: Thu, 02 Jul 2015 11:39:26 -0700 > From: Greg Couch <gregc(a)cgl.ucsf.edu> > To: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] Cross eyed stereo pair generated by > default > Message-ID: <5595855E.4020903(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > I'll look into it. > > FYI, cross-eyed stereo is the standard for stereo PNG and stereo JPEG > files. There is a buglet in stereo image saving -- the .png files > should be renamed to have a .pns suffix, and the stereo JPEG images > should have a .jps suffix. However there aren't many viewers other than > the one that comes with NVIDIA's 3D Vision setup. > > -- Greg > > On 07/02/2015 11:20 AM, Oliver Clarke wrote: > > Hi all, > > > > I?ve noticed that when I save a stereo pair (using File/Save Image/Image > Type/stereo pair), the resultant stereo pair is suitable for cross-eyed > viewing. > > > > This is great for me, as I can?t do wall eyed stereo, but the default > for many journals is to provide a wall-eyed stereo pair. > > > > Of course it is easy enough to convert by swapping the two halves of the > pair, but for the sake of convenience, would it be possible to list stereo > pair (cross eye) and stereo pair (wall eye) as two separate options in this > dialogue? > > > > Cheers, > > Oliver. > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 147, Issue 4 > ********************************************* >

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on beta strand assignmet by chimera
by Smith Liu 02 Jul '15

02 Jul '15

Dear All, I have a protein, which contains fragment aa 239-251. The protein has been fitted its map with 2 different (minor difference) resolution, and thus I have 2 PDB. For PDB 1 (the first resolution), the H-bonds inside aa 239-251 include: #2 Gly 245.A N-Asn 242.A O 2.708A #2 Asn 242.A N-Tyr 246.A O 3.120 A #2 Val 248.A N-Val 240.A O 3.120 A #2 GLN 251.A N-Ser 238.A 0 3.033 A For PDB 2 (the second resolution), the H-bonds inside aa 239-251 include: #0 Gly 245.A N-Asn 242.A O 2.715A #0 Asn 242.A N-Tyr 246.A O 3.1206 A #o Val 248.A N-Val 240.A O 2.858 A #0 GLN 251.A N-Ser 238.A 0 3.074 A Naked eye check found the H-bonds in PDB 1 were almost the same H-bonds in PDB 2. However for PDB 2, aa23-242 and aa 247-251 form 2 strands, but for PDB 1, it was a un-disconnected loop for aa 239-251. Will you please explain how chimer assign beta strand? Best regards. Smith

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gzip error while starting REST server on Windows
by Mungo Carstairs (Staff) 02 Jul '15

02 Jul '15

I'm testing Jalview starting Chimera (1.10.1) with RESTServer on a Windows 7 machine without gzip installed. On starting the Chimera process: new ProcessBuilder().start("chimera.exe", "--start", "RESTServer") I get two lines of response: Cannot execute 'gzip': no automatic decompression of .Z files REST server on host 127.0.0.1 port nnnnn which is ok - I can get the REST port number I need and carry on. Am I safe to ignore the other message? I can't see what file (I assume part of the Chimera installation) it is arising from. Thanks, Mungo Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology College of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> The University of Dundee is a registered Scottish Charity, No: SC015096

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Worm representation / command line
by Xavier ROBERT 01 Jul '15

01 Jul '15

Dear all, I am wondering if there is a way to call "Render by Attribute" at the command line in order to render a worm representation? If not, is this feature planned for the near future and is there any workaround for this? Thank you very much in advance. Kind regards, Xavier R.

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generating symmetry mates of a surface model created with shape command
by Carmen San Martin 01 Jul '15

01 Jul '15

Dear all, is it possible to generate symmetry-related copies of a surface model created by the shape command? I am interested in masking out certain map regions related by symmetry. I got the right shape at the right place but now cannot figure out how to create the shape symmetry mates. The sym command followed by the model number of my shape complaints that no molecules are specified. Thanks, Carmen ------------------------------------------------------------- Carmen San Martín, Ph. D. Centro Nacional de Biotecnología (CNB-CSIC) Darwin, 3 28049-Madrid (SPAIN) Email: carmen(a)cnb.csic.es Phone: 34-91-5855450 Fax: 34-91-5854506 http://www.cnb.csic.es/ http://tinyurl.com/carmensanmartinlab http://orcid.org/0000-0001-9799-175X ------------------------------------------------------------

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Using Chimera to read Maestro files
by CG Deer 30 Jun '15

30 Jun '15

Hello Chimera Developers and Users, My name is Christopher Deer, and I am trying to use Chimera as part of a workflow for getting a maestro file (.mae) ready for presentation in a CAVE environment. The .mae file contains color references and specifics defined by a researcher. However, these details are not appearing when I open the file in Chimera. So is there any way to open this file type without having to redefine all the specific features the researcher originally made? Here is a screenshot of what I am seeing in Chimera, and I have attached what the researcher originally wanted it to look like (minus white background).[image: Inline image 1] Thank you for your help, --Chris Deer University of Arizona Research Computing, Data Visualization Specialist

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animation error
by Hartzell Jr., Criss 30 Jun '15

30 Jun '15

I am at a meeting making an animation for a talk using my MacAir. When I play it back from the animation panel, about half way through the animation, I receive this error and the animation crashes. Can you help debug? Thanks. File "/Volumes/ChimeraInstaller 1/Chimera.app/Contents/Resources/share/Animate/SceneState.py", line 1031, in _msmsSameColors return false NameError: global name 'false' is not defined Criss Hartzell Professor Department of Cell Biology Emory University School of Medicine Atlanta, GA 30322 404-242-5719 (cell) For Fedex, UPS, other courier: Criss Hartzell 615 Michael St. 535 Whitehead Building Emory University Atlanta, GA 30322 ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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morph volumes after alignment
by Haselbach, David 30 Jun '15

30 Jun '15

Dear all, I have a few volumetric cryo EM Maps of the same protein in different conformations. And I would like to morph between those conformations. However, the volumes are not perfectly aligned in first place. So I align all of them on one of the maps using the "fit in map" functionality. This works great and when I look through the different structures with the volume viewer, they are perfectly aligned. However, if I morph through the maps using the following command: vop morph #0-19 playstep 0.003 constantVolume true frames 1000 the maps are morphed in their original position so the morph is quite jumpy. Is there a way to morph through them in the aligned coordinate system directly? Kind regards David ----------------------------------------------------------------------------------- Dr. David Haselbach Max-Planck-Institut für biophysikalische Chemie AG Stark Am Fassberg 11 D-37077 Goettingen dhaselb(a)gwdg.de<mailto:dhaselb@gwdg.de> +49-551-2011302

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Linux and stereo in the vizvault
by Greg Couch 29 Jun '15

29 Jun '15

So it works with some caveats -- iff the projector is the primary and only display and you use reverse sequential stereo. Getting there was difficult, you have to disable the LCD monitor with the system display settings instead of the amdcccle interface that appears to do the same thing. But you need to use the amdcccle interface to turn on quad-buffered stereo. Once quad-buffered stereo is setup (after several reboots), you can turn on and off the LCD monitor, but the stereo-sync signal is only generated only if the LCD monitor is turned off. The driver also got confused occasionally and wouldn't display a stereo image -- that was fixed by reenabling the LCD monitor and disabling it again. -- Greg

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