June 2016 - Chimera-users - RBVI Mailing Lists

query regarding volume viewer
by Nidhi Batra 09 Jun '16

09 Jun '16

Dear Sir/Madam I have carried out MD simulations on a set of proteins belonging to a protein family. Further, I computed the water density around the protein and have the output in .dx format. I want to use Chimera to visualize the water density around the protein within 4 A. For this, I loaded the protein and the .dx file in volume viewer, selecting the protein and changing the zone to 4 and generating results. I want to have a comparison of water density across all proteins. I am unable to understand how to normalise the settings so that the results are comparable. What I understand is to keep the step same. Additionally, all the .dx files have different ranges which is obvious, what should be the value of level so that I can compare the water density across different proteins? Should it be kept at a median value of the range or something else? Please help. If I keep everything default, the results are misleading. Thanking you Yours sincerely -- Nidhi Batra DBT-Research Associate Institute of Genomics and Integrative Biology (IGIB), Mathura Road, Sukhdev Vihar New Delhi, INDIA 110020

2 4

renumbering missing residues
by Charles, Fiorella 08 Jun '16

08 Jun '16

Dear sir or madam, I am working with structure 1p22 and want to renumber the residues of chain A so they match Uniprot Q9Y297, but when I tried to it does not work for the 2 missing structures on the pdb file, and it continues the numbering as if they were not there. Is there a way to number this part correctly? with kind regards Fiorella

2 2

deleting entries from rapid access list (plain text format)
by Oliver Clarke 07 Jun '16

07 Jun '16

Sort of related to this - would be great to have a way to filter the rapid access list by filetype or pattern match - maybe have a box one could type in up the top of the list to filter what is displayed? Oli. > Very useful for clearing the Rapid Access list entirely. FYI, since that original message an “Edit” button has been added below the list so that you can selectively delete items. > > —Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > >* On Jun 2, 2016, at 6:53 AM, Jaime Rodríguez-Guerra Pedregal <Jaime.RodriguezGuerra at uab.cat <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>> wrote: > *> >* Hi, > *> >* I was searching for a Chimera function that did this very same thing, but found nothing, so I created a little script to do that from the terminal. I know this is old, but maybe somebody finds it useful after all! > *> >* Get it here https://gist.github.com/jaimergp/8c2efd34fb2c7eba8054eeec791bf768 <https://gist.github.com/jaimergp/8c2efd34fb2c7eba8054eeec791bf768> <https://gist.github.com/jaimergp/8c2efd34fb2c7eba8054eeec791bf768 <https://gist.github.com/jaimergp/8c2efd34fb2c7eba8054eeec791bf768>> > *> >* Jaime Rodríguez-Guerra Pedregal > *>* Molecular modeling of transition metal systems group > *>* Department of Chemistry, Faculty of Sciences > *> >* Edif. C · C7/153 > *>* Campus de la UAB · 08193 Bellaterra > *>* (Cerdanyola del Vallès) · Barcelona · Spain > *> >* +34 93 581 28 57 > *>* www.uab.cat <http://www.uab.cat> <http://www.uab.cat/ <http://www.uab.cat/>> > *> >* <http://orcid.org/0000-0001-8974-1566 <http://orcid.org/0000-0001-8974-1566>> <https://www.linkedin.com/in/jaimergp <https://www.linkedin.com/in/jaimergp>> > *>* This message may contain private or confidential information, and is addressed exclusively to its intended recipient. If you have received it in error, please notify the sender and delete it. Please bear in mind that you are not authorized to use it for any purposes. > *> >* Please consider the environment before printing this email. > *>* _______________________________________________ > *>* Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> <mailto:Chimera-users at cgl.ucsf.edu <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>> > *>* Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>> > *

2 1

Trouble starting Chimera
by Janet Iwasa 07 Jun '16

07 Jun '16

Hello, I recently upgraded to a new workstation, and am running into trouble with installing Chimera. The error (with an exit code of 2) I'm getting is: Error initializing OpenGL: couldn't set pixel format Couldn't configure togl widget My workstation is 64 bit, running Windows 7, with a NVIDIA Quadro M4000 graphics card. I've tried installing the latest NVIDIA driver, which didn't seem to help. I've reinstalled Chimera several times, trying both 32 and 64 bit. My tech support also tried changing permissions on various files, to no avail. The weird thing is that my tech support folks got Chimera to open a few times successfully when they were logged in, which makes me wonder whether it might be a permissions issue, but they aren't able to get it to open consistently, either. Any ideas/advice would be welcome! thank you! Janet Iwasa

2 1

mtz file of an mrc map and its model open correctly in coot but not in chimera
by Oliver Clarke 07 Jun '16

07 Jun '16

Dear Shabih, I haven't used mrc2mtz.sh, but have had no problems with Coot/chimera compatibility using phenix.map_to_structure_factors for the same purpose, ( http://www.phenix-online.org/documentation/reference/map_to_structure_facto…) perhaps you might try that? Cheers, Oliver, > Dear All, > > > I converted an mrc map to mtz (using mrc2mtz.sh from CCP4EM) in order to do model building and model refinement in coot. However when I open the model in chimera along with its corresponding mrc map they do not open in same place. How can I rectify it? > > > Any help will be appreciate. > > > Regards, > > Shabih > >

1 0

mtz file of an mrc map and its model open correctly in coot but not in chimera
by Shakeel, Shabih 07 Jun '16

07 Jun '16

Dear All, I converted an mrc map to mtz (using mrc2mtz.sh from CCP4EM) in order to do model building and model refinement in coot. However when I open the model in chimera along with its corresponding mrc map they do not open in same place. How can I rectify it? Any help will be appreciate. Regards, Shabih

2 1

box size limit
by Franken, L.E. 07 Jun '16

07 Jun '16

Dear chimera users, I am running into troubles displaying a map of a 650x650x650 volume and I was wondering if there is a box size limit to chimera or what else could be the problem. The way it displays the 3D .mrc file is as a single slice rather than a volume. It will also go straight to solid display rather than surface, did anyone encounter such a problem before? I can open the map in coot and relion (slices), so I do not think that the map is corrupt. Thank you for your time. Best wishes, Linda On Mon, Jun 6, 2016 at 11:14 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: coloring by RMSD (conformational variability) (Elaine Meng) > 2. Re: Chimera-win10-install (Greg Couch) > 3. Re: coloring by RMSD (conformational variability) (George Tzotzos) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 6 Jun 2016 12:55:52 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > To: George Tzotzos <gtzotzos(a)me.com> > Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] coloring by RMSD (conformational > variability) > Message-ID: <5242FA3C-E185-453E-93DD-BEF75F495BBC(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=utf-8 > > Hi George, > I?m not really sure how you got those flat ribbons, but I think you can > just use the transparency command. It takes a percentage transparency, so > for 75% transparent, a command something like: > > transp 75,r :1-10,124-125 > > ? where the ?,r? part does NOT have any space before it, and ?r? stands > for ribbons. > > 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 Jun 6, 2016, at 11:36 AM, George Tzotzos <gtzotzos(a)me.com> wrote: > > > > Following PC analysis, I have obtained pseudo trajectories for each of > the first 3 principal components. I used Chimera to colour the regions > exhibiting the largest structural variations as per instructions of Elain > Meng, which I attach for easy reference. > > > > I have placed side by side, say the 1st PC, of two independent pseudo > trajectories (see attached image). As the structure is disordered between > residues 1-10 and 124-125, I?d like to render these ranges of residues > semitransparent. I?ve tried to do this with the transparency command but > this applies to ribbons only (I think). > > > > I?d appreciate any suggestions as to how this can be done. > > > > Thank you in advance > > > > George > > > > <dimer_deet2015_6MH2016.tif> > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > > Subject: coloring by RMSD (conformational variability) > > Date: 25 March 2014 at 19:32:47 GMT+1 > > To: George Tzotzos <gtzotzos(a)me.com> > > Cc: chimera List <chimera-users(a)cgl.ucsf.edu> > > Reply-To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > > > > Hi George, > > Sure, you can do it by having Chimera calculate the CA-RMSD at each > position and then mapping that value to color. The file is a little > strange in that it has only CA atoms and all the residues are ALA, but it > will still work: > > > > (1) show the sequence (menu: Favorites? Sequence). Just choose any one > of the 34 -- it doesn't matter which one, since they all have the same > sequence. > > > > (2) associate all 34 copies of the structure with the one sequence: in > the sequence window menu, choose Structure? Associations. In that dialog, > change all the "none" to the same sequence, then click OK. This is > somewhat tedious, but I just did it, so you can too! Now, all of the > structures will be connected to that one sequence. > > > > (3) tell Chimera to calculate the RMSD at each position: in the sequence > window menu, choose Headers? RMSD. Now the sequence window will have an > RMSD histogram above the sequence. It may almost look like a line because > most of the bars in the histogram (the RMSD values) are very low. > > > > (4) color the structures by the RMSD values with Render by Attribute (in > main Chimera menu under Tools? Depiction). In that tool, choose attributes > of "residues" and attribute name "mavRMSD" (the "mav" part stands for > Multalign Viewer, which is showing the sequence). It will show a histogram > of the values with some vertical colored bars. You use those bars to > define how the values are mapped to color. The bars can be dragged left > and right, and you can delete bars or add more bars with Ctrl-click. You > can change the color of each bar by clicking it and then clicking the > "Color" square below the histogram and using the Color Editor, or you can > just use one of the Palette options below that. You can keep clicking > Apply and then adjusting the coloring until it is how you like it. For > example, I show coloring by RMSD from blue->red->yellow (and then menu: > Presets? Publication 1) in the attached image. > > > > I hope this helps, > > Elaine > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > ------------------------------ > > Message: 2 > Date: Mon, 6 Jun 2016 14:01:18 -0700 > From: Greg Couch <gregc(a)cgl.ucsf.edu> > To: Mitja Ogrizek <ogrizek.mitja(a)gmail.com>, > chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] Chimera-win10-install > Message-ID: <5755E49E.7070006(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="windows-1252"; Format="flowed" > > Hello Mitja, > > I was able to get the Windows installer to fail in one situation -- I > hope this is the same problem you're having. > > If you download the installer as a non-administrative user and then try > to run it, it fails because it can't install Chimera in the default > location even though you've typed in an administrative password. My > workaround was to use the file browser to locate the installer on the > disk, do a right-mouse click on the installer, and then "Run as > Administrator". I expect that it would also work if you installed > Chimera to a non-system directory. > > HTH, > > Greg > > On 06/04/2016 05:46 AM, Mitja Ogrizek wrote: > > Dear all, > > > > I tried to install a new version of chimera on my laptop with win10, > > but it doesn't want to load and start the setup. > > Has anybody else reported or had the same troubles? > > > > Kind regards, > > Mitja Ogrizek > > > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

2 2

Re: [Chimera-users] deleting entries from rapid access list (plain text format)
by Jaime Rodríguez-Guerra Pedregal 06 Jun '16

06 Jun '16

Hi, I was searching for a Chimera function that did this very same thing, but found nothing, so I created a little script to do that from the terminal. I know this is old, but maybe somebody finds it useful after all! Get it here https://gist.github.com/jaimergp/8c2efd34fb2c7eba8054eeec791bf768 Jaime Rodríguez-Guerra Pedregal Molecular modeling of transition metal systems group Department of Chemistry, Faculty of Sciences Edif. C · C7/153 Campus de la UAB · 08193 Bellaterra (Cerdanyola del Vallès) · Barcelona · Spain +34 93 581 28 57 www.uab.cat<http://www.uab.cat/> [http://www.uab.cat/vcard/Logo_ORCID_0.png] <http://orcid.org/0000-0001-8974-1566> [http://www.uab.cat/vcard/Logo_LinkedIn_0.png] <https://www.linkedin.com/in/jaimergp> This message may contain private or confidential information, and is addressed exclusively to its intended recipient. If you have received it in error, please notify the sender and delete it. Please bear in mind that you are not authorized to use it for any purposes. Please consider the environment before printing this email.

2 1

coloring by RMSD (conformational variability)
by George Tzotzos 06 Jun '16

06 Jun '16

Following PC analysis, I have obtained pseudo trajectories for each of the first 3 principal components. I used Chimera to colour the regions exhibiting the largest structural variations as per instructions of Elain Meng, which I attach for easy reference. I have placed side by side, say the 1st PC, of two independent pseudo trajectories (see attached image). As the structure is disordered between residues 1-10 and 124-125, I’d like to render these ranges of residues semitransparent. I’ve tried to do this with the transparency command but this applies to ribbons only (I think). I’d appreciate any suggestions as to how this can be done. Thank you in advance George From: Elaine Meng <meng(a)cgl.ucsf.edu> Subject: coloring by RMSD (conformational variability) Date: 25 March 2014 at 19:32:47 GMT+1 To: George Tzotzos <gtzotzos(a)me.com> Cc: chimera List <chimera-users(a)cgl.ucsf.edu> Reply-To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> Hi George, Sure, you can do it by having Chimera calculate the CA-RMSD at each position and then mapping that value to color. The file is a little strange in that it has only CA atoms and all the residues are ALA, but it will still work: (1) show the sequence (menu: Favorites… Sequence). Just choose any one of the 34 -- it doesn't matter which one, since they all have the same sequence. (2) associate all 34 copies of the structure with the one sequence: in the sequence window menu, choose Structure… Associations. In that dialog, change all the "none" to the same sequence, then click OK. This is somewhat tedious, but I just did it, so you can too! Now, all of the structures will be connected to that one sequence. (3) tell Chimera to calculate the RMSD at each position: in the sequence window menu, choose Headers… RMSD. Now the sequence window will have an RMSD histogram above the sequence. It may almost look like a line because most of the bars in the histogram (the RMSD values) are very low. (4) color the structures by the RMSD values with Render by Attribute (in main Chimera menu under Tools… Depiction). In that tool, choose attributes of "residues" and attribute name "mavRMSD" (the "mav" part stands for Multalign Viewer, which is showing the sequence). It will show a histogram of the values with some vertical colored bars. You use those bars to define how the values are mapped to color. The bars can be dragged left and right, and you can delete bars or add more bars with Ctrl-click. You can change the color of each bar by clicking it and then clicking the "Color" square below the histogram and using the Color Editor, or you can just use one of the Palette options below that. You can keep clicking Apply and then adjusting the coloring until it is how you like it. For example, I show coloring by RMSD from blue->red->yellow (and then menu: Presets… Publication 1) in the attached image. I hope this helps, Elaine

2 3

Chimera-win10-install
by Mitja Ogrizek 06 Jun '16

06 Jun '16

Dear all, I tried to install a new version of chimera on my laptop with win10, but it doesn't want to load and start the setup. Has anybody else reported or had the same troubles? Kind regards, Mitja Ogrizek

2 1