- Chimera-users - RBVI Mailing Lists

Save bond-distance label-position
by Maarten Schledorn 10 Jun '16

10 Jun '16

Dear reader, The distance measurement tool outputs a distance 'label' that by default is on the center of the line connecting the two atoms involved. In my structure I have about twenty of these, and I have manually dragged all distance values to empty spots in the image. However, if I save and re-open the session, the labels are back at their default position. I have tried <savepos>, and also <scene save>, but to no avail. Is there a way to save the bond-distance label-positions? Many thanks in advance, with kind regards, Maarten

2 1

Splitting an pdb with multiple proteins
by Jochen Baßler 09 Jun '16

09 Jun '16

Hi, I´m frequently looking at pdb´s that contain multiple chains, like ribosomes or preribosomes (e.g. Pdb 3JCT). Is there a way to import the information from the pdb database, which tells you the name of the chains? Chain A = rpl2 Chain B = Rpl4 etc. Cool would be to split the pdb into multiple models that have the name from the pdb database. (It is quite annoying to have a pdb with nearly 60 different chains and you have to spend half a day to rename the chains or to create individual models, before analyzing the structure) Thanks for suggestions and solutions Best wishes Jochen

3 2

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

Cap color precedence when global clip planes slice through multiple volumes?
by Oliver Clarke 06 Jun '16

06 Jun '16

Hi, When slicing through multiple superimposed volumes with caps shown, the color of the resulting cap seems to be a bit of a patchwork - sometimes dominated by one volume, sometimes by another, sometimes a mix of the two It would be good if there were a way to control the precedence of the caps, to make a cleaner and more interpretable picture - it is often good to be able to see the outline of both overlayed volumes. I know there is one way to do this, by using per model clipping planes and changing the offsets such that one per model clip plane is just slightly in front of the other, but it might be helpful in ChimeraX to have more granular control over this. Cheers, Oli

2 2

Cut asymmetric unit from volume
by Morris, Kyle 03 Jun '16

03 Jun '16

Hi Chimera team and users, Is there a way to extract the asymmetric unit from a volume which has been 'symmetrised’ from, say for instance, Relion? In this case what are the conventions used by chimera to define the bounds of the sub-volume to extract? Thanks for your help! Best wishes, Kyle

2 3

Request for support
by Mendoza Wilson, Ana Maria 03 Jun '16

03 Jun '16

Hello, How I can select an isodensity value in the Chimera software (1.11rc) for calculating molecular surface and molecular volume from one cube data file or fchk file previously generated in Gaussian 09? Thanks in advance -- Dra. Ana María Mendoza Wilson Investigador Titular Centro de Investigación en Alimentación y Desarrollo, A.C. Coordinación de Tecnología de Alimentos de Origen Vegetal Carretera a La Victoria Km. 0.6 Hermosillo, Sonora, México C.P. 83000 Tel +52 (662) 289 24 00 Ext. 354

2 3

FW: Chimera Log File
by Williams, Joanne 03 Jun '16

03 Jun '16

From: Erin Coppola <erincoppola8(a)gmail.com<mailto:erincoppola8@gmail.com>> Date: Friday, June 3, 2016 8:10 AM To: "chimera(a)cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>" <chimera(a)cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>> Subject: Chimera Log File Hi, When using Chimera, is there a way of tracking the script command versions of GUI actions performed?

2 1

Creating maps from models for map/model FSC calculations
by Ardan Patwardhan 03 Jun '16

03 Jun '16

Dear all We are using Chimera to align PDB models to maps, then creating maps from the models using the following command (as an example): molmap #0 5 gridSpacing 1.3 This should create a map with the voxel spacing of 1.3A and a gaussian atom spread function with the width related to 5A resolution (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html) Our problem is a) the map that is created can have an arbitrary size - we need it to be cubic and have the same (known) dimensions as the second map against which it will be compared b) we have tried padding it in other programs like bsoft but then we sometimes run into problems of centring the model. I was wondering if there was a way to get a centred map of a certain size from a model directly from Chimera? Perhaps there are certain parameters that can be used in molmap? You thoughts and advice on this issue are much appreciated! Many thanks and best wishes Ardan Patwardhan Coordinator - cellular structure & PDBe production Protein Data Bank in Europe (PDBe) European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD Tel: +44 1223 492649

3 7

mask
by Dougherty, Matthew T 02 Jun '16

02 Jun '16

I have a volume whose density values are -127 thru 127. Zero is a valid density & approximately the peak of the Guassian distribution. I would like to use the command mask. It sets the unmasked density values to zero. How can I set the unmasked density values to -128 using the mask command? Will I need to hack the code? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

2 1

finding residues with large effects on local electrostatic potential
by Elaine Meng 01 Jun '16

01 Jun '16

Hi Deniz, No need to apologize, that’s why we have an address for questions. :-) I am guessing you were coloring by electrostatic potential and want to figure out which residues are having large effects in some places. The question is not that simple because electrostatic interactions are long-range, meaning that the potential at a point is based on many atoms in many residues, including those farther away. However, the largest contributions at a surface point will generally be from the residues with net positive or negative charges that are not too far away. In other words, if you see a blue patch, you could then try to figure out positively charged residues are near it, or if a red patch, which negatively charged residues are near it. The problem in Chimera that you may be having is that when you put the mouse over the surface, the surface is blocking the atoms, so it does not tell you what residue is under that surface. One way to try to figure it out is to temporarily hide the surface (Favorites… Model Panel, uncheck the “Shown” button for the surface), then click back into the main window *without moving the structure* and put the mouse over the same area to see what residues are there, using the pop-up balloons with residue information. You would probably want to show all the sidechain atoms first (e.g. command: display protein), and maybe select residues that are known to be positive (or negative) to help guide yourself to the right place. Command: select :lys,arg,his (… the ones likely to contribute to positive patches…) Command: select :asp,glu (… the ones likely to contribute to negative patches…) You can keep turning the surface on and off with the checkbox in the Model panel. This is interactive guessing and may not be that easy. Just keep in mind that you can’t say that some patch is all from one or two residues, only that they have significant contributions. 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 1, 2016, at 3:44 PM, Deniz Simsek Buck <simsekd(a)stanford.edu> wrote: > Hi Elaine, > I am sorry for bothering you. But, I need urgent help. > If I tell chimera to find the surface charge, negative and positive, and if I want to know which residues are responsible for this charge, what do I do? > > thank you so much, > deniz

1 0

How to build symmetry in Chimera
by Ana Ramos 01 Jun '16

01 Jun '16

To whom it may concern, I am working with a protein with P61 symmetry, and I would like to build symmetry mates; however in the pdb, the symmetry is not stated. How can I build in chimera symmetry mates with a P61 symmetry? Best, Ana

3 2

Chimera 1.11 - Combining Transparancies of Ribbon and Surface
by Falko Jähnert 01 Jun '16

01 Jun '16

To whom it may concern, since I'm using Chimera a lot lately I enjoy the usage of this program and can't await the release of Chimera X. Now I like to ask if it is possible to combine the transparency of the ribbon and the surface representation using Chimera so that you can visualize both parts in varying transparency levels. My problem with this is if I use "transparency 80,r [Tag]" the part of my protein gets transparent (as requested) whilst activating the transparency function of the surface results in complete hiding of the previously chosen amino acids. Is there a workaround available? Thanks in advance for your help. Best regards, Falko Jähnert. _____ Martin-Luther-University Halle-Wittenberg Institute for Biochemistry and Biotechnology Departement for Naturstoffbiochemie Kurt-Mothes-Str. 3 D-06110 Halle/Saale _____ Tel. +49 (0)345 - 55 24812 Mail. <mailto:falko.jaehnert@biochemtech.uni-halle.de> falko.jaehnert(a)biochemtech.uni-halle.de

2 1

Re: [Chimera-users] Analysis of the contact maps from the MARTINI MD trajectory
by James Starlight 01 Jun '16

01 Jun '16

Yep thanks so much Eric! In my case the contacts have been started to be recognized both from only after choosing the vdw cutoff > -4.0 A and decreasing statistical (weight discard edge threshold) factor to 0.3 (here I am analyzing big trajectory consisted of 7 independent MD trajectories for the same system merged together where both proteins are present both in bound and unbound states during the progression of simulation). Eventually I obtained LYS 25.A vdw SER 712.C 0.39322 CYS 14.A vdw TRP 1586.I 0.427119 HIS 33.A vdw ions 0.335593 HIS 33.A vdw LYS 1577.I 0.444068 LYS 27.A vdw TRP 1586.I 0.369492 GLU 838.C vdw PHE 46.A 0.444068 GLN 12.A vdw TRP 1586.I 0.501695 ASP 1580.I vdw LYS 7.A 0.318644 PHE 46.A vdw TRP 1586.I 0.491525 GLU 732.C vdw LYS 79.A 0.372881 PHE 46.A vdw solvent 0.501695 CYS 1584.I vdw HIS 26.A 0.616949 HIS 26.A vdw SER 712.C 0.423729 ASP 1580.I vdw LYS 8.A 0.305085 TYR 1542.I vdw VAL 11.A 0.311864 LYS 27.A vdw solvent 0.40678 THR 28.A vdw TYR 731.C 0.379661 PHE 46.A vdw TYR 1587.I 0.484746 Also may I ask within this output the first column should correspond to first selection, right? here the contacts was defined as between atoms from chain A which is the smaller protein and the rest of the system consisted of atoms of receptor. Thanks again! Gleb 2016-05-17 22:37 GMT+02:00 Eric Pettersen <pett(a)cgl.ucsf.edu>: > Well, if I were you I would go to a trajectory frame that I think should have contacts, and then bring up the Find Clashes/Contacts tool (in the Structure Analysis category of Tools) and play around with the criteria to see what yields contacts. You might also change the atoms to sphere mode (Actions->Atoms/Bonds->sphere) to see if they have any VDW overlap or are close. You might also measure some distances (control-click an atom, then control-shift-double-click a second atom and then pick “Show Distance” from the popup menu). Without actual access to your data, I can’t offer any more specific suggestions. > > —Eric > >> On May 17, 2016, at 2:08 AM, James Starlight <jmsstarlight(a)gmail.com> wrote: >> >> Thanks Eric! >> >> it quite strange that no interactions are found- because in my >> trajectory the complex between both proteins are emerged very soon >> after beginning of the simulation and is quite stable until ed of it. >> Seems like the Chimera does not recognize martini's CG atoms properly. >> Are there any suggestions to fix it e.g by the variations using any of >> options - e.g vdw settings etc? >> >> Gleb >> >> 2016-05-17 1:32 GMT+02:00 Eric Pettersen <pett(a)cgl.ucsf.edu>: >>> The clustering is based on least-squares-fit RMSDs between corresponding atoms, and therefore global translations and rotations are irrelevant. >>> >>> —Eric >>> >>>> On May 16, 2016, at 9:08 AM, James Starlight <jmsstarlight(a)gmail.com> wrote: >>>> >>>> update :-) >>>> >>>> in addition to the previous question which is still actual I am >>>> interesting in the clusterization of binding interfaces established >>>> during MD e.g based on the position of one protein regarding another. >>>> >>>> For my case I have performed such clusterization from MD movie plugin >>>> (which was based on current selection which was the atoms of smaller >>>> protein) obtaining alot of overlapped clusters in case of smallest >>>> step size and afew clusters increasing step size twisly. Is it >>>> possible here to increase accuracy of the clusterization and to remove >>>> some degrees of freedom which are not important for my case ? E.g to >>>> pre-process trajectory using PCA before clusterization to discard >>>> rotation translation of the system will be good option? >>>> >>>> >>>> >>>> James >>>> >>>> 2016-05-16 15:20 GMT+02:00 James Starlight <jmsstarlight(a)gmail.com>: >>>>> update : >>>>> >>>>> already playing with the plugin MD movie and "residue iteration >>>>> network within the trajectory" tool >>>>> just selecting atoms from the chain A as 1st selection >>>>> and other atoms from other chains as 2nd selection >>>>> >>>>> running calculation (trying to varry cut-off corresponded to vdw overlap radii) >>>>> >>>>> obtained error >>>>> AttributeError: 'ResInteractionDialog' object has no attribute 'markers' >>>>> >>>>> File "/opt/UCSF/Chimera64-1.10.2/share/Movie/ResInteraction.py", >>>>> line 535, in Apply >>>>> markerSettings = [(m['xy'], m['rgba']) for m in self.markers] >>>>> >>>>> See reply log for Python traceback. >>>>> >>>>> Does it means that somethig special should be specified for the >>>>> MARTINI CG atoms? >>>>> >>>>> Thanks ! >>>>> >>>>> Gleb >>>>> >>>>> 2016-05-16 12:13 GMT+02:00 James Starlight <jmsstarlight(a)gmail.com>: >>>>>> something relevant in my model: >>>>>> >>>>>> this is martini CG model consisted of big membrane protein and small >>>>>> water soluble protein. In my particular trajectory I have only atoms >>>>>> of both proteins recognized by chimera as individual chains (e.g small >>>>>> protein is chain A and the biggest is consisted of chains B-N). >>>>>> >>>>>> Gleb >>>>>> >>>>>> 2016-05-16 11:58 GMT+02:00 James Starlight <jmsstarlight(a)gmail.com>: >>>>>>> update: >>>>>>> >>>>>>> with the up-to-date chimera Trajectory is loaded fine >>>>>>> now the question is related to the analysis of the binding interface. >>>>>>> is it possible to make contact maps plots based on the 2 selections >>>>>>> from the input trajectory assuming that I am using martini CG model? >>>>>>> >>>>>>> Gleb >>>>>>> >>>>>>> 2016-05-16 10:39 GMT+02:00 James Starlight <jmsstarlight(a)gmail.com>: >>>>>>>> OK will try to update Chimera today ! >>>>>>>> >>>>>>>> What chimera's tools could be useful for the contact map based >>>>>>>> analysis of md trajectories related to my case ? E.g to determine >>>>>>>> binding interface between 2 proteins from long md simulation. >>>>>>>> >>>>>>>> Gleb >>>>>>>> >>>>>>>> 2016-05-13 19:52 GMT+02:00 Eric Pettersen <pett(a)cgl.ucsf.edu>: >>>>>>>>> Hi Gleb, >>>>>>>>> If you are using Gromacs 5 trajectories, you have to be using at least >>>>>>>>> version 1.10.2 of Chimera. If you are using that version (or later), please >>>>>>>>> use “Report a Bug” in Chimera’s Help menu to file a bug report and attach >>>>>>>>> your topology file to the bug report. Thanks! >>>>>>>>> >>>>>>>>> —Eric >>>>>>>>> >>>>>>>>> Eric Pettersen >>>>>>>>> UCSF Computer Graphics Lab >>>>>>>>> >>>>>>>>> >>>>>>>>> On May 13, 2016, at 1:46 AM, James Starlight <jmsstarlight(a)gmail.com> wrote: >>>>>>>>> >>>>>>>>> Dear Chimera users! >>>>>>>>> >>>>>>>>> >>>>>>>>> I am in charge with the analysis of protein-protein association during >>>>>>>>> long molecular dynamic simulation where my system was parametrized >>>>>>>>> using MARTINI CG force field. In particularly I am interesting to >>>>>>>>> find residues on one of the protein which are crustal for the binding >>>>>>>>> interface established during this MD. >>>>>>>>> For that purpose I am trying to use Chimera to load trajectory and >>>>>>>>> corresponded tpr file using MD movie plugin and than to >>>>>>>>> map contact maps produced by Gromacs onto the 3D structure using Chimera. >>>>>>>>> The problem that Chimera does not recognize properly the trajectory >>>>>>>>> and topology. Briefly I have removed all solvent from both files >>>>>>>>> before loading them to the Chimera using editconf and gmx convert-tpr >>>>>>>>> obtaining eventually trajectory and topology with the same number of >>>>>>>>> atoms. >>>>>>>>> >>>>>>>>> >>>>>>>>> Than when I load it to Chimera that is the error which MD movie sent me: >>>>>>>>> >>>>>>>>> VERSION 5.0.2 >>>>>>>>> using floats >>>>>>>>> version 100, generation 26 >>>>>>>>> 8 atoms >>>>>>>>> Traceback (most recent call last): >>>>>>>>> File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", >>>>>>>>> line 1747, in __call__ >>>>>>>>> File "CHIMERA/share/chimera/baseDialog.py", line 328, in command >>>>>>>>> File "CHIMERA/share/chimera/baseDialog.py", line 543, in OK >>>>>>>>> File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 92, in Apply >>>>>>>>> File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line >>>>>>>>> 56, in loadEnsemble >>>>>>>>> File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line >>>>>>>>> 67, in loadEnsemble >>>>>>>>> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 25, >>>>>>>>> in __init__ >>>>>>>>> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 86, >>>>>>>>> in __init__ >>>>>>>>> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line >>>>>>>>> 345, in _readTopology >>>>>>>>> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line >>>>>>>>> 338, in _readString >>>>>>>>> File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring >>>>>>>>> raise EOFError >>>>>>>>> EOFError >>>>>>>>> EOFError >>>>>>>>> >>>>>>>>> File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring >>>>>>>>> raise EOFError >>>>>>>>> >>>>>>>>> See reply log for Python traceback. >>>>>>>>> >>>>>>>>> Will be thankful for any suggestions! >>>>>>>>> >>>>>>>>> Gleb >>>>>>>>> _______________________________________________ >>>>>>>>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>>>>>>>> Manage subscription: >>>>>>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>>>>>>> >>>>>>>>> >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>> >>> >> >

3 14

suggest improvements/group viz
by Dougherty, Matthew T 31 May '16

31 May '16

1) in a group viz it would be desirable to have two cursors. A regular cursor that would operate as expected under the OS, and a second cursor that would be restricted to the view window overlay. The first cursor would be controlled by the viz operator used to adjust parameters. The second cursor would be controlled by the group through a gamepad etc, that could be used as a pointer. Possibly the volume eraser might be a quick work around. 2) volume eraser when erasing sets the density to zero. Need to be able to set the value. Zero is a valid density value, usually in the middle of the density histogram, which causes problems for volume rendering. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

1 0

Rotamers in Chimera
by Lew Jacobson 31 May '16

31 May '16

I am using Chmiera 1.10 build 40304 on a Mac. (I am a leftover Midas user!) So far as I can tell, this version is still using the Dunbrack 2002 rotamer library. Is any subsequent version using the improved 2011 Dunbrack library? If not, can you instruct me how to incorporate that newer library into Chimera? thanks, Lew Jacobson -- Dr. Lewis Jacobson Professor of Biological Sciences Univ. of Pittsburgh Pittsburgh PA 15260 412-624-4647 Fax 412-624-4759 LJAC(a)pitt.edu

2 1

Can I use wait command over Rest service?
by Mungo Carstairs (Staff) 31 May '16

31 May '16

Hi, I am trying to devise a way to highlight locations on a structure in Chimera while mousing over the sequence in Jalview. My latest attempt tries to 'flash' the side-chain display at the residue position i.e. - hide then show atoms (if currently displayed e.g. display is in atom mode) - or show then hide atoms (if currently not displayed e.g. display is in ribbon mode) I'm sending a command like display #0:30.A;wait 20;~display #0:30.A to the Rest service. However while this seems to do what I want when used at the Chimera command line, via the Rest service it ignores the wait command, with the result that the action is too quick to see. Any suggestions please for how to get this to work, or a better alternative? Thanks, Mungo Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School 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

3 8