- Chimera-users - RBVI Mailing Lists

On the fly map sharpening?
by Oliver Clarke 21 Jul '15

21 Jul '15

Hi, just a request for a future chimera version (probably Chimera 2 I guess) - would it be possible to integrate on the fly map sharpening into chimera, perhaps as an option for vop? It would be great to be able to play with different negative B-factors within chimera and thereby get instant feedback on map contrast and detail in different regions. Alternatively, would it be possible to call an external program that does the same thing from within chimera, perhaps bfactor from the Grigorieff lab or similar? Cheers, Oliver,

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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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on chimera saved PDB file
by Smith Liu 29 Jun '15

29 Jun '15

Dear All, By chimera I have saved a PDB file, but at the end of the saved PDB there are following sentences which I do not understand: CONECT 3 2 4 17 CONECT14560145591456114574 CONECT29117291162911829131 Will you please explain it to me the meaning of "CONECT 3 2 4 17" and the other 2 sentences? And why there is no space in "CONECT14560145591456114574"? Smith

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Morph volumes after alignment
by Haselbach, David 28 Jun '15

28 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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ViewDock
by leila karami 27 Jun '15

27 Jun '15

Dear all Now, I want to save 1 pdb file containing target + one of poses of ligand for example, number 3. For this aim, what to do? I did following steps, but I did not succeed: file ---> save pdb ... In save models section, I selected both of target.pdb (#0) and (#1.3) In file name section, I wrote complex.pdb and then save. I encountered with error (see the below link): https://www.dropbox.com/s/bdkq1x1db96amhi/chimera%20error.png?dl=0 I tested other names such as $target.pdb and $1.3.pdb. Unfortunately, I encountered with the same error. Best regards,

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drawing shapes
by Bala subramanian 25 Jun '15

25 Jun '15

Friends, I have used HOLE program ( http://www.sciencedirect.com/science/article/pii/S026378559700009X) to find the pore radius of a channel as a function of z-axis. As output, the program gives the location of capsules (that were filled inside the channel), capsule length and radius etc, as a function of z-axis. Capsule graph option***** Data: cenxyz.cvec eff.rad area CAP.LEN cap.rad angle.X-axi cen.line.di integ.s/(ar point sourc *-14.00000* *2.23465* 15.68804 *1.72142* 1.39301 73.21487 0.00000 0.03187 (sampled) -14.50000 2.40709 18.20262 1.96609 1.46141 58.41143 -0.54015 0.05934 (sampled) -15.00000 2.51292 19.83844 1.37866 1.78410 73.19154 -1.11224 0.08454 (sampled) -15.50000 2.69525 22.82171 1.34834 1.97026 87.40431 -1.71545 0.10645 (sampled) I was wondering if i can use the shape command to draw the capsules in Chimera. I thought to create 'tube' with 'shape' command but i was not lucky. For instance, the following command didnt work (i opened channel as model #0) shape tube #0 radius *2.23* bandLength *1.72* center 0, 0, *-14.00 * Pls help to know some way to do this. Thanks, Bala -- C. Balasubramanian

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Windows 8.1 and nVidia Quadro drivers.. grrr
by Kenward Vaughan 24 Jun '15

24 Jun '15

Hello! I have Chimera working wonderfully with sequential stereo under Linux with our Quadro card (a K4200), but am getting terribly frustrated with trying to have it work at all under Win 8.1. The latest non-beta driver is installed. It took me a while to find where the nVidia control panel is located after finding that Chimera didn't recognize any stereo-capable hardware (including some references to togl and pixels). Blah. I started up the "wizard" of 3D, which gave me a nice slide show, but Chimera didn't see anything. Interestingly, rebooting directly into Linux gave the same problem, which had me fuming and frothing all over the place. A shutdown followed by fresh start into Linux reset the card. So the Windows driver touches something inside the card which has to be reset hard. There are multiple things installed when this driver is put on the system. Is it possible that there are things I don't want, which are slyly strengthening my thoughts about Windoze? Some searching of the archives was inconclusive for this system. I have played with the settings in the control panel but have found no combination that gets sequential stereo working. Does anyone know what settings should be changed from the defaults to get this working? Many thanks for any help! Kenward -- In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca

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savepos
by Dougherty, Matthew T 24 Jun '15

24 Jun '15

in defining the text string view_name, spaces are disallowed, eg "rotate 30". Although the position will be created, the reset command will not properly access the position key. What are the allowable characters? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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ViewDock
by leila karami 24 Jun '15

24 Jun '15

Dear Elaine, Thanks for your guidance. It was very good. Now, I want to know there is this possibility to have these separate 252 pdb files as 1 pdb file? Thanks for your time and consideration. Best

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How to crop a map
by Tom Goddard 24 Jun '15

24 Jun '15

You can crop a map using volume dialog menu Features / Region Bounds, then save it with volume dialog File / Save Map As…. Other Chimera map capabilities are described in the Guide to Volume Data Display in Chimera: http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html <http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html> Tom > On Jun 23, 2015, at 7:52 PM, 李智海 wrote: > > Adding to the previous one. > the map I want to convert has a same pixel size with the data set. So maybe the question could be that how can I cutting the boundaries of the map to fit the size of reconstruction images. > > Thanks! > > Zhihai Li > > >> On Jun 24, 2015, at 10:44 AM, 李智海 wrote: >> >> Hi, Tom >> An another question, >> I want to make a reference map for reconstruction, here I have a map but with different map size from my raw image, how can I scale the map dimensions into a specific value without changing the centre coordinates. >> Thanks! >> >> Zhihai Li >> >> >>> On Jun 24, 2015, at 2:00 AM, Tom Goddard wrote: >>> >>> If you used the Chimera Segment Map dialog (volume dialog menu Tools / Segment Map) then you select a segment (ctrl click on it) and use Segment Map menu entry Regions / Mean and SD. If you segmented the map by some other means and have the pieces as separate maps use volume dialog menu Tools / Measure Mean, SD, RMS. >>> >>> Tom >>> >>> >>>> On Jun 23, 2015, at 6:42 AM, 李智海 wrote: >>>> >>>> Hi, >>>> Here I want to evaluate the flexibility of variable domains of a density map. How can I quantify the mean intensity of segmented parts by Chimera? Thanks! >>>> >>>> Best wishes! >>>> >>>> Zhihai Li >>>> >>>> Ph.D student in State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics. >>>> School of Life Sciences, Xiamen University. >>>> Xiang'an Road(South), Xiang'an District, Xiamen City, >>>> Fujian Province, China. >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list >>>> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >>> >> >

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PDB not opening
by YAikhombA Mutum 24 Jun '15

24 Jun '15

Hi 1. I'm not able to fetch pdb's from Chimera by the command 'open 121p'. It just says 'opened 121p' in the reply log while it display a blank black screen. There are no active models displayed too (in the active models panel, there are no active tabs for models (0,1,2...)) despite the status in the reply log. The internet connections are ok (my browser is working fine). On checking the preferences (Favorites ---> preferences), everything seems fine (for instance in Category: Fetch (save fetched flie: True and use local files:True/False (I've tried both cases))). Even the category of web access seems ok. A day before I'd been able to fetch pdb's by just the command (open 1zik (say)). Now, the only way to retrieve it is to go to the rcsb website, download the pdb from a browser and then run it in chimera. Moreover, even if it (the pdb file) is already downloaded it doesn't run by entering the command (again the preferences are fine). How can I sort out this? 2. Is there a way to color the capped surface (the flat surface when you cut a protein virtually) based on sequence conservation color range. I tried the same way B factor surface capping is done as in the tutorials but the one for conservation doesn't work. It instead colors the 'whole' surface something else (Automatically uses default 'color by heteroatom' (red, tan and blue) not the colors I used for the sequence conservation). The same when I try to cap a surface based on hydrophobicity. Thanks in advance! Yaikhomba

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Issue with cytoscape plugin
by Juan Eiros Zamora 23 Jun '15

23 Jun '15

Hi Chimera users, I'm using cytoscape and structureviz to visualize interaction networks of my MD simulations. I've been using it for quite awhile now on the normal structure of my protein. Now I am simulating it with two adjacent phosphorylated serines (all is done with AMBER), and I think there are some issues with this because: 1) If I select a region of the protein that does not contain this "special" aminoacids, the RIN visualization works just fine 2) When I select the region that contains these two phosphorylated Serines (about +-10 aminoacids from them), when the RIN is set up on cytoscape I get the following error: RINLayout Fetching coordinates from Chimera... null Which is pretty generic. What is more confusing is that if I select all the system (which is not interesting for me, but I've done it anyway to try) it seems to work as well. My cytoscape version is 3.2.0 and all the apps in it are up to date: structureViz2 1.0.1 RINalyzer 2.0.0 I think the RIN is being calculated just fine, but it's having problems recognising the 3D shape in Chimera. Also, it fails to synchronize the colours, I don't know if this is related to what I'm reporting here, but I suspect it is. Does anyone know how can I proceed? It would be very useful for me to compare the RINS of the non-phosphorylated version of my system to the phosphorylated version. Thanks for any help, Juan Eiros

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ViewDock
by leila karami 23 Jun '15

23 Jun '15

Dear chimera users I have docking outputs from Swissdock (there is 252 binding modes for my ligand relative to the target protein). I used following to view my outputs: 1) File > Open , then load target.pdb 2) Tools > Surface/Binding Analysis > ViewDock, choose clusters.dock4.pdb (Dock 4, 5 or 6 format) Now, I want to have several pdb files in which there is target protein and each of binding modes, that is 252 pdb files. How to do this? Any help will highly appreciated.

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measure a mean intensity of a segmented map
by 李智海 23 Jun '15

23 Jun '15

Hi, Here I want to evaluate the flexibility of variable domains of a density map. How can I quantify the mean intensity of segmented parts by Chimera? Thanks! Best wishes! Zhihai Li Ph.D student in State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics. School of Life Sciences, Xiamen University. Xiang'an Road(South), Xiang'an District, Xiamen City, Fujian Province, China.

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Attribute Error: 'AtomType' object has no attribute 'amber_atom_type'
by Karl Sebby 22 Jun '15

22 Jun '15

Hi I am modifying several ligand/protein complexes; usually with the “Build Structures” tool. I modify ligands by changing and deleting atoms, or by using “Join Models” after building or importing a structure with “Start structure”. Sometimes, minimizing the ligand works fine, but other times I get the error: “Attribute Error: ‘AtomType’ object has no attribute ‘amber_atom_type’”. I cannot figure out what is causing this error or how to fix it. It seems to happen when I begin working from a saved session or a pdb that was written with the ‘write’ command and not when I go through a whole series of steps in one shot. Any ideas on what is going on? Thanks, All the best, Karl -- Dr Karl Sebby Left Side Research LLC 1661 K M Ranch Road Whitefish Montana 59937 Office: 406 623 4773

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Using the findHbond via Python Midas Module
by Ahir Pushpanath 22 Jun '15

22 Jun '15

Dear All, I am confused about what input I need to provide to the findHbond command in the FindHBond midas module. This is the help() on the command. findHBonds(models, intermodel=True, intramodel=True, donors=None, acceptors=None, distSlop=0.0, angleSlop=0.0, interSubmodel=False, cacheDA=False). For example if I want to find all H bonds between a pre-selected group of residues in loop, saved as: loop = chimera.selection.currentAtoms() and the rest of the protein molecule, what command would I have to run? I am assuming the output(such as the one given in the findHbonds runcommand) would be saved into a variable if I provide one? Ahir -- Dr. Ahir Pushpanath* PhD.* Senior Biologist, Johnson Matthey.

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help please
by Sezer Akgöl 22 Jun '15

22 Jun '15

how can I associate 2 protein with each other from their C and N terminals respectively

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Feature request - lock center of rotation to center of view ("pseudo-Coot mode")
by Oliver Clarke 22 Jun '15

22 Jun '15

Hi, I have a request for a future version of Chimera - would it be possible to add a command or menu item that (reversibly) locks the center of rotation to the center of view, such that when the view is translated, the cofr is updated automatically also? This is the way structure navigation works in Coot, and I find it is a much more intuitive and precise way to travel when examining the finer details of a structure (as one would expect given that the main purpose of Coot is model building while Chimera is exceptionally good for structural analysis and visualization). This would make navigation of large structures much easier, particularly when one is just browsing around the structure. In addition, it would be nice to have a dynamically updated pseudoatom to indicate the current center of rotation - this is implemented in Coot as the “pink pointer”, and I find it very helpful for getting my bearings. Cheers, Oliver.

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Chimera in Virtual machine
by Milo Westler 18 Jun '15

18 Jun '15

Well I thought I had this figured out, but then my VM broke and I can't get chimera to run in my VM again. I am running Vritualbox with a guest system of ubuntu-mate 15.04. I want to be able to use chimera in the VM for a workshop that we are presenting. I have installed the 64 bit version for linux. I get: ~> chimera pci id for fd 4: 80ee:beef, driver (null) libGL error: core dri or dri2 extension not found libGL error: failed to load driver: vboxvideo libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 154 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 751 Current serial number in output stream: 752 ~> And when I run: /opt/UCSF/Chimera64-1.10.1/share> python __main__.py Chimera is misconfigured. Please reinstall chimera. Thanks, -- -- Milo =================================================== National Magnetic Resonance Facility at Madison An NIH-Supported Resource Center W. Milo Westler, Ph.D. NMRFAM Director Senior Scientist and Adjunct Professor Department of Biochemistry University of Wisconsin-Madison DeLuca Biochemistry Laboratories 433 Babcock Drive Rm B160D Madison, WI USA 53706-1544 EMAIL: milo(a)nmrfam.wisc.edu PHONE: (608)-263-9599 FAX: (608)-263-1722 ======================================================================= ========

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Query on GPI-anchor proteins
by Aditya Padhi 17 Jun '15

17 Jun '15

Dear Chimera Users, I am working on a protein, which is known to cleave few GPI-anchor proteins (Glycosylphosphatidylinisotol). Also, I know that there are several other candidate GPI-anchor proteins which may or may not be cleaved by my protein of interest. I was wondering, if there is any tool/method in Chimera using which I can atleast get some preliminary information on which of the proteins that could be probably cleaved by my protein of interest. The 3D structure of my protein of interest and most of the GPI-anchor proteins is not available. I was therefore wondering if there is any such tools/methods available that I am missing using which I can find out which of the GPI-anchor proteins are being cleaved. Any suggestion/guidance would be highly appreciated. Thank you so much, Aditya

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What happened to my model?
by Sara Cuellar 17 Jun '15

17 Jun '15

So, in my line of work we are focusing on the protein Dihydrofolate Reductase. Using Jmol, I was able to remove all chains except for chain A, and also increased the diameter of the backbone so that it may be printed. When I opened it in Chimera to export it from VRML file to an STL file, it still looked fine. However, when it was opened in my 3d printing program, parts of the protein were missing. All I see is floating fragments. Is there any way I can fix this using chimera? I have included images of the protein.

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Scripted registration of a perframe python script
by Kersey Black 17 Jun '15

17 Jun '15

Hi, I have been 'opening' a python script file from within Chimera to start a session and in that script I open the MovieDialog manager (mdm) and read in a pdb with a series of models to be viewed as a trajectory. That part is working thanks to help from other responses in chimera-users. To modify the molecule (color, etc) it seems like the mdm.ensemble.molecule is giving me the access, though that may not be the right approach for my needs, because it seems to act on all frames. What I would like to do, from within this same initial python script, is to apply/register a perframe (also in python) script to control things like color on a frame by frame basis. I would like to do this as a way of keeping all of the setup in a single script file such that then I just need to record the movie manually, or perhaps there is a way to do this also from the script. Thanks much for any help and/or direction to documentation on the python api to the MovieDialog that allows control of these functions. Kersey

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ImportError: no module named chimera
by 陈雷 16 Jun '15

16 Jun '15

Hello, I got a problem when calling chimera in a python script. ImportError: no module named chimera Here is the line in my script: from chimera import runCommand. Python version is 2.6.6 and chimera is 1.8 in Linux. Would you please help me out with this? Thanks. Best regards, Ryan

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ImportError: no module named chimera
by ryanch＠mail.ecust.edu.cn 15 Jun '15

15 Jun '15

Hello, I got a problem when calling chimera in a python script. ImportError: no module named chimera Here is the line in my script: from chimera import runCommand. Python version is 2.6.6 and chimera is 1.8 in Linux. Would you please help me out with this? Thanks. Best regards, Ryan

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restoring sessions with python & triggers
by Dougherty, Matthew T 15 Jun '15

15 Jun '15

Normally a save session by a python extension is invoked by a trigger SAVE_SESSION. For restoring a session, several related chimera APIs are available that are typically not used. 1) post model restore: SimpleSession.registerAfterModelsCB(afterModelsRestoredCB, arg) 2) BEGIN_RESTORE_SESSION and END_RESTORE_SESSION triggers. I need to reset extension gui values based on midas positions. I presume a normal restore in the session file does not guarantee that these midas positions will be loaded at that time, so I need to delay the gui updates until the restore process has ended or possibly when the models are loaded loaded. What is the distinction between END_RESTORE_SESSION and registerAfterModelsCB? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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setting viewing pref using python
by Dougherty, Matthew T 15 Jun '15

15 Jun '15

the viewing dialog sets the Camera:Stereo parameters:units to inches, and Side View:Side to right. using python how can I reset them to mm & top? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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