- Chimera-users - RBVI Mailing Lists

substituting atoms
by simon chapman 03 Apr '18

03 Apr '18

Hello...for my Master's dissertation, I need to substitute a sulphur atom for an oxygen in a Molecular Dynamics simulation. The run works fine with my target molecule 1KF1.pdb uploaded into Chimera, but the substituted version sends quite a few error messages and won't run. It doesn't appear to recognise the novel S atom. Any help would be much appreciated...I've been stuck on this for nearly a week! Best wishes Simon

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intensity scaling of multiple cryo EM reconstructions
by Peter Doerschuk 03 Apr '18

03 Apr '18

Dear Chimera Community: We have several electron scattering intensity cubes from cryo EM. We would like to scale the intensity (not the size) of the particle so that we can fairly compare the intensity values in different cubes. We understand that some biophysical principle is required. Does Chimera contain tools related to such principles and the scaling calculations they imply? Thank you very much in advance for your help! Best regards, Peter

2 3

morph and surfaces
by Giorgio Luciano 02 Apr '18

02 Apr '18

Hello ! I was looking at the script for morphing among structures that can be found here http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html (*coordset #1 1,161). * I've tried to use the surfacecat command in the script in order to obtain a morph through volumes since my idea was to create the movie and then export all the surface perframe in order to use them in another 3d software. I've seen that surfcat can actually create volumes for all the surfaces included in the 1r7w but morph start does not seems to work among the surface created. I've seen also that it could be a solution to create density maps from the surface and them morph them using volume viewer but it seem quite an awkard solution (at least for me that I'm no expert :) I've tried to find the limitation of morph command but it does not report anything regarding surfaces. Any help is very appreciated. Sorry for the cross-posting

4 5

problem with ccp4 map fitting
by ela.nekardova＠gmail.com 29 Mar '18

29 Mar '18

Dears, I need to depict a map generated from CCP4/Sfall and a .pdb file corrected by Coot. I would like to create images by Chimera. Unfortunately, I cannot figure out how to make a correct view (in Coot, the map fits the molecule well), please, see the image/session in the attachment. I could not have found a guidance in the User's guide. Can you help me please? Thank you in advance for your help. Best regards, Michaela Nekardova Institute of Biotechnology CAS, v. v. i. Laboratory of Biomolecular Recognition Address: Průmyslová 595, 252 50 Vestec.

3 3

Reading and saving large files in chimera
by #TOFAYEL AHMED# 29 Mar '18

29 Mar '18

Hi Chimera developers and users, I have faced a problem with chain IDs and secondary structure while working on a large file. As I am refining my model in Phenix and visualizing in Chimera, I need to go back and forth between these two software and that creates a problem. To replicate my problem, here I have taken an example from PDB so that you get the idea. If I take model bearing PDB id 5IRE and apply "phenix.pdb.biomt_reconstruction" I can generate the complete virus icosahedral structure from the asymmetric unit. But when I open this complete virus structure in Chimera and save it back again the chain IDs get changed. Is there any work around to maintain the original chain IDs and therefore maintain the secondary structure definitions in the file header, after opening and thereafter saving using Chimera? Best regards, Tofayel NTU Singapore

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Chimera command to set the volume contour surface threshold
by Irene 29 Mar '18

29 Mar '18

Hi, I am new using Chimera and am writing a script to generate automatically some volume contour surfaces. I would like to know if there is command to set from the script the volume contour surface threshold? I came across a post from 2006 (https://www.cgl.ucsf.edu/pipermail/chimera-users/2006-November/001121.html) where it was mentioned that such command did not exist by that time. I hope there is one now! Thanks a lot, Irene

2 1

Display channel as a filled body in Chimera
by Boaz Shaanan 27 Mar '18

27 Mar '18

Hi, Is there a way to display in Chimera a channel identified by CastP as a filled body rather than engulfed by a surface? Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Thursday, March 15, 2018 8:41 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 179, Issue 6 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: Surface picking (Tom Goddard) 2. Re: Surface picking (Priit Eek) 3. Re: Surface picking (Tom Goddard) 4. Re: Surface picking (Priit Eek) 5. Re: Surface picking (Tom Goddard) ---------------------------------------------------------------------- Message: 1 Date: Thu, 15 Mar 2018 10:34:40 -0700 From: Tom Goddard <goddard(a)sonic.net> To: Priit Eek <priit.eek(a)gmail.com> Cc: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Surface picking Message-ID: <EFAC0902-4CA7-4C28-8EB1-5166495B44C5(a)sonic.net> Content-Type: text/plain; charset=utf-8 Hi Prit, I can select the split surface pieces of an MSMS surface with ctrl-click using Chimera 1.12. Does ctrl-click work to select atoms, or the original unsplit surface? If not then it is probably a graphics driver problem, since some graphics capabilities are needed to know what object is under the mouse. Another possible graphics driver problem is the green outline is not shown ? but if you select something the magnifying glass icon in the lower right corner of the main Chimera window (select inspector) should turn green. Tom > On Mar 15, 2018, at 4:47 AM, Priit Eek <priit.eek(a)gmail.com> wrote: > > Hi, > > I am trying to visualize some specific inner cavities in a structure. I can display the MSMS surface and split it into pieces (accelerator Sc), but then I need to select the extra surfaces to hide/delete them (starting with the main outer surface). For some reason surface picking with mouse (Ctrl + left click) doesn?t work. I checked the surface attributes and ?selectable with mouse? was true. > > I recall that this used to work some years ago, but not anymore. I am using the latest daily build (v1.13 build 41684) on macOS v10.12.6. Is this a bug or have some settings changed? I couldn?t find anything referring to this in the docs. > > Best regards, > Priit > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > ------------------------------ Message: 2 Date: Thu, 15 Mar 2018 20:06:04 +0200 From: Priit Eek <priit.eek(a)gmail.com> To: Tom Goddard <goddard(a)sonic.net> Cc: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Surface picking Message-ID: <A1252D71-C057-4085-83B4-2DC06A198AC8(a)gmail.com> Content-Type: text/plain; charset=utf-8 Elaine and Tom, Thank you for your replies. Selecting atoms and ribbons works as it should, but ctrl-clicking on surfaces has no effect whatsoever, be it before or after splitting. I could use Sc only because I selected the whole model using the command line. Splitting does work and I get a bunch of pieces, but I have no obvious way to select the distinct surfaces. Also, I?m afraid that using visiblePatches or any other method that involves selecting all residues that define the blobs would be extremely cumbersome in my case. As I said, if I ctrl-click on an atom or a ribbon, it gets selected, is highlighted in green, and the magnifying glass icon turns green as well. However, if I then ctrl-click on a surface, the selection is cleared (status bar displays ?selection cleared?). The graphics driver incompatibility actually seems a likely culprit. I think the previous time I used this feature, I was still on my old laptop. I am currently running Chimera on a 13-inch Early 2015 MacBook Pro (MacBookPro12,1). It has a built-in Intel Iris Graphics 6100 chipset. Could there be an easy hack/workaround on my side or a software patch? If not, then I guess I?ll go and finish that particular figure on another computer :) Cheers, Priit > On 15 Mar 2018, at 19:34, Tom Goddard <goddard(a)sonic.net> wrote: > > Hi Prit, > > I can select the split surface pieces of an MSMS surface with ctrl-click using Chimera 1.12. Does ctrl-click work to select atoms, or the original unsplit surface? If not then it is probably a graphics driver problem, since some graphics capabilities are needed to know what object is under the mouse. Another possible graphics driver problem is the green outline is not shown ? but if you select something the magnifying glass icon in the lower right corner of the main Chimera window (select inspector) should turn green. > > Tom > > >> On Mar 15, 2018, at 4:47 AM, Priit Eek <priit.eek(a)gmail.com> wrote: >> >> Hi, >> >> I am trying to visualize some specific inner cavities in a structure. I can display the MSMS surface and split it into pieces (accelerator Sc), but then I need to select the extra surfaces to hide/delete them (starting with the main outer surface). For some reason surface picking with mouse (Ctrl + left click) doesn?t work. I checked the surface attributes and ?selectable with mouse? was true. >> >> I recall that this used to work some years ago, but not anymore. I am using the latest daily build (v1.13 build 41684) on macOS v10.12.6. Is this a bug or have some settings changed? I couldn?t find anything referring to this in the docs. >> >> Best regards, >> Priit >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > ------------------------------ Message: 3 Date: Thu, 15 Mar 2018 11:13:14 -0700 From: Tom Goddard <goddard(a)sonic.net> To: Priit Eek <priit.eek(a)gmail.com> Cc: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Surface picking Message-ID: <AB507F91-8402-4939-8962-B91D8D457836(a)sonic.net> Content-Type: text/plain; charset=utf-8 Hi Prit, It seems like a graphics driver bug, but I haven?t seen this before where only surfaces cannot be selected. Did you try drag select ? that draws a rectangle and uses a different code path and maybe it would select the surface. If you use "molmap #0 5? to make a density map surface from molecule #0 can you select the resulting surface with ctrl-click? Are you showing your surface in mesh or some other unusual style? Tom > On Mar 15, 2018, at 11:06 AM, Priit Eek <priit.eek(a)gmail.com> wrote: > > Elaine and Tom, > > Thank you for your replies. Selecting atoms and ribbons works as it should, but ctrl-clicking on surfaces has no effect whatsoever, be it before or after splitting. I could use Sc only because I selected the whole model using the command line. Splitting does work and I get a bunch of pieces, but I have no obvious way to select the distinct surfaces. Also, I?m afraid that using visiblePatches or any other method that involves selecting all residues that define the blobs would be extremely cumbersome in my case. As I said, if I ctrl-click on an atom or a ribbon, it gets selected, is highlighted in green, and the magnifying glass icon turns green as well. However, if I then ctrl-click on a surface, the selection is cleared (status bar displays ?selection cleared?). > > The graphics driver incompatibility actually seems a likely culprit. I think the previous time I used this feature, I was still on my old laptop. I am currently running Chimera on a 13-inch Early 2015 MacBook Pro (MacBookPro12,1). It has a built-in Intel Iris Graphics 6100 chipset. Could there be an easy hack/workaround on my side or a software patch? If not, then I guess I?ll go and finish that particular figure on another computer :) > > Cheers, > Priit > > >> On 15 Mar 2018, at 19:34, Tom Goddard <goddard(a)sonic.net> wrote: >> >> Hi Prit, >> >> I can select the split surface pieces of an MSMS surface with ctrl-click using Chimera 1.12. Does ctrl-click work to select atoms, or the original unsplit surface? If not then it is probably a graphics driver problem, since some graphics capabilities are needed to know what object is under the mouse. Another possible graphics driver problem is the green outline is not shown ? but if you select something the magnifying glass icon in the lower right corner of the main Chimera window (select inspector) should turn green. >> >> Tom >> >> >>> On Mar 15, 2018, at 4:47 AM, Priit Eek <priit.eek(a)gmail.com> wrote: >>> >>> Hi, >>> >>> I am trying to visualize some specific inner cavities in a structure. I can display the MSMS surface and split it into pieces (accelerator Sc), but then I need to select the extra surfaces to hide/delete them (starting with the main outer surface). For some reason surface picking with mouse (Ctrl + left click) doesn?t work. I checked the surface attributes and ?selectable with mouse? was true. >>> >>> I recall that this used to work some years ago, but not anymore. I am using the latest daily build (v1.13 build 41684) on macOS v10.12.6. Is this a bug or have some settings changed? I couldn?t find anything referring to this in the docs. >>> >>> Best regards, >>> Priit >>> _______________________________________________ >>> 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 > ------------------------------ Message: 4 Date: Thu, 15 Mar 2018 20:27:15 +0200 From: Priit Eek <priit.eek(a)gmail.com> To: Tom Goddard <goddard(a)sonic.net> Cc: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Surface picking Message-ID: <D8228774-0335-4697-A2B5-4CDF453AF5B6(a)gmail.com> Content-Type: text/plain; charset=utf-8 Tom, Drag-selecting selects the atoms and ribbons, but not the MSMS surface, even if the atoms are behind the surface. However, I can select the molmap surface with both clicking and dragging. The MSMS surface is a solid. I haven?t done anything to surface display settings to my knowledge, so I should be using the default style. Priit > On 15 Mar 2018, at 20:13, Tom Goddard <goddard(a)sonic.net> wrote: > > Hi Prit, > > It seems like a graphics driver bug, but I haven?t seen this before where only surfaces cannot be selected. Did you try drag select ? that draws a rectangle and uses a different code path and maybe it would select the surface. If you use "molmap #0 5? to make a density map surface from molecule #0 can you select the resulting surface with ctrl-click? Are you showing your surface in mesh or some other unusual style? > > Tom > > >> On Mar 15, 2018, at 11:06 AM, Priit Eek <priit.eek(a)gmail.com> wrote: >> >> Elaine and Tom, >> >> Thank you for your replies. Selecting atoms and ribbons works as it should, but ctrl-clicking on surfaces has no effect whatsoever, be it before or after splitting. I could use Sc only because I selected the whole model using the command line. Splitting does work and I get a bunch of pieces, but I have no obvious way to select the distinct surfaces. Also, I?m afraid that using visiblePatches or any other method that involves selecting all residues that define the blobs would be extremely cumbersome in my case. As I said, if I ctrl-click on an atom or a ribbon, it gets selected, is highlighted in green, and the magnifying glass icon turns green as well. However, if I then ctrl-click on a surface, the selection is cleared (status bar displays ?selection cleared?). >> >> The graphics driver incompatibility actually seems a likely culprit. I think the previous time I used this feature, I was still on my old laptop. I am currently running Chimera on a 13-inch Early 2015 MacBook Pro (MacBookPro12,1). It has a built-in Intel Iris Graphics 6100 chipset. Could there be an easy hack/workaround on my side or a software patch? If not, then I guess I?ll go and finish that particular figure on another computer :) >> >> Cheers, >> Priit >> >> >>> On 15 Mar 2018, at 19:34, Tom Goddard <goddard(a)sonic.net> wrote: >>> >>> Hi Prit, >>> >>> I can select the split surface pieces of an MSMS surface with ctrl-click using Chimera 1.12. Does ctrl-click work to select atoms, or the original unsplit surface? If not then it is probably a graphics driver problem, since some graphics capabilities are needed to know what object is under the mouse. Another possible graphics driver problem is the green outline is not shown ? but if you select something the magnifying glass icon in the lower right corner of the main Chimera window (select inspector) should turn green. >>> >>> Tom >>> >>> >>>> On Mar 15, 2018, at 4:47 AM, Priit Eek <priit.eek(a)gmail.com> wrote: >>>> >>>> Hi, >>>> >>>> I am trying to visualize some specific inner cavities in a structure. I can display the MSMS surface and split it into pieces (accelerator Sc), but then I need to select the extra surfaces to hide/delete them (starting with the main outer surface). For some reason surface picking with mouse (Ctrl + left click) doesn?t work. I checked the surface attributes and ?selectable with mouse? was true. >>>> >>>> I recall that this used to work some years ago, but not anymore. I am using the latest daily build (v1.13 build 41684) on macOS v10.12.6. Is this a bug or have some settings changed? I couldn?t find anything referring to this in the docs. >>>> >>>> Best regards, >>>> Priit >>>> _______________________________________________ >>>> 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 >> > ------------------------------ Message: 5 Date: Thu, 15 Mar 2018 11:41:04 -0700 From: Tom Goddard <goddard(a)sonic.net> To: Priit Eek <priit.eek(a)gmail.com> Cc: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Surface picking Message-ID: <5AB9B1A1-5920-4EF9-B2FD-EC66931D9670(a)sonic.net> Content-Type: text/plain; charset=utf-8 Hi Priit, That is especially weird that MSMS surfaces cannot be selected by ctrl-click while the molmap surface can be selected. The problem is either your machine?s graphics driver or one other idea it could somehow be some setting in your preferences file. You might try quiting Chimera, renaming your Chimera preferences file ~/.chimera/preferences so Chimera does not find it, and restarting and see if that helps. Tom > On Mar 15, 2018, at 11:27 AM, Priit Eek <priit.eek(a)gmail.com> wrote: > > Tom, > > Drag-selecting selects the atoms and ribbons, but not the MSMS surface, even if the atoms are behind the surface. However, I can select the molmap surface with both clicking and dragging. The MSMS surface is a solid. I haven?t done anything to surface display settings to my knowledge, so I should be using the default style. > > Priit > > >> On 15 Mar 2018, at 20:13, Tom Goddard <goddard(a)sonic.net> wrote: >> >> Hi Prit, >> >> It seems like a graphics driver bug, but I haven?t seen this before where only surfaces cannot be selected. Did you try drag select ? that draws a rectangle and uses a different code path and maybe it would select the surface. If you use "molmap #0 5? to make a density map surface from molecule #0 can you select the resulting surface with ctrl-click? Are you showing your surface in mesh or some other unusual style? >> >> Tom >> >> >>> On Mar 15, 2018, at 11:06 AM, Priit Eek <priit.eek(a)gmail.com> wrote: >>> >>> Elaine and Tom, >>> >>> Thank you for your replies. Selecting atoms and ribbons works as it should, but ctrl-clicking on surfaces has no effect whatsoever, be it before or after splitting. I could use Sc only because I selected the whole model using the command line. Splitting does work and I get a bunch of pieces, but I have no obvious way to select the distinct surfaces. Also, I?m afraid that using visiblePatches or any other method that involves selecting all residues that define the blobs would be extremely cumbersome in my case. As I said, if I ctrl-click on an atom or a ribbon, it gets selected, is highlighted in green, and the magnifying glass icon turns green as well. However, if I then ctrl-click on a surface, the selection is cleared (status bar displays ?selection cleared?). >>> >>> The graphics driver incompatibility actually seems a likely culprit. I think the previous time I used this feature, I was still on my old laptop. I am currently running Chimera on a 13-inch Early 2015 MacBook Pro (MacBookPro12,1). It has a built-in Intel Iris Graphics 6100 chipset. Could there be an easy hack/workaround on my side or a software patch? If not, then I guess I?ll go and finish that particular figure on another computer :) >>> >>> Cheers, >>> Priit >>> >>> >>>> On 15 Mar 2018, at 19:34, Tom Goddard <goddard(a)sonic.net> wrote: >>>> >>>> Hi Prit, >>>> >>>> I can select the split surface pieces of an MSMS surface with ctrl-click using Chimera 1.12. Does ctrl-click work to select atoms, or the original unsplit surface? If not then it is probably a graphics driver problem, since some graphics capabilities are needed to know what object is under the mouse. Another possible graphics driver problem is the green outline is not shown ? but if you select something the magnifying glass icon in the lower right corner of the main Chimera window (select inspector) should turn green. >>>> >>>> Tom >>>> >>>> >>>>> On Mar 15, 2018, at 4:47 AM, Priit Eek <priit.eek(a)gmail.com> wrote: >>>>> >>>>> Hi, >>>>> >>>>> I am trying to visualize some specific inner cavities in a structure. I can display the MSMS surface and split it into pieces (accelerator Sc), but then I need to select the extra surfaces to hide/delete them (starting with the main outer surface). For some reason surface picking with mouse (Ctrl + left click) doesn?t work. I checked the surface attributes and ?selectable with mouse? was true. >>>>> >>>>> I recall that this used to work some years ago, but not anymore. I am using the latest daily build (v1.13 build 41684) on macOS v10.12.6. Is this a bug or have some settings changed? I couldn?t find anything referring to this in the docs. >>>>> >>>>> Best regards, >>>>> Priit >>>>> _______________________________________________ >>>>> 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 >>> >> > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > ------------------------------ Subject: Digest Footer _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ------------------------------ End of Chimera-users Digest, Vol 179, Issue 6 *********************************************

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defining attribute from python
by Wood Ortiz, Francisca (NIH/NEI) [F] 27 Mar '18

27 Mar '18

Hello, I am a post-bac fellow at the NEI/NIH working with protein modeling. We are hoping to automate a procedure which requires the protein structure to be colored using an attribute file and exported as an .html and .py session. We would like this to be completed from the command line without the need to open the Chimera graphics window. Could this be done? Thank you for your help. Best, Francisca Wood Ortiz Postbaccalaureate Fellow, Ophthalmic Genetics and Visual Function Branch, NIH/NEI

2 1

Chimera Help Desk: Missing Output file
by Arturo Estolano Cobián 26 Mar '18

26 Mar '18

Dear Chimera Help Desk, I have a problem while running molecular docking on Chimera. After running Tools --> Surface/Binding Analysis --> AutoDock Vina, I do not get the results from the docking analysis. I get the regular *name*.receptor.pdb , *name*.receptor.pdbqt , *name*.ligand.pdb , *name*.ligand.pdbqt and *name*.conf files, but the *name* file (the docking results) does not generate. In the Reply Log I found this, which I assume is involved in the problem: standard error ----- Unable to initialize environment because of error: cannot register event client. Only 99 event clients are allowed in the system Exiting. ----- Traceback (most recent call last): File "C:\Program Files (x86)\Chimera 1.11.2\share\chimera\tasks.py", line 179, in runStatusCB task.statusCBList[0]() File "C:\Program Files (x86)\Chimera 1.11.2\share\WebServices\appWebService.py", line 171, in statusCB self.finishCB(self.backend, fileMap) File "C:\Program Files (x86)\Chimera 1.11.2\share\vina\ws.py", line 179, in _wsFinish raise NonChimeraError("No data file returned from " NonChimeraError: No data file returned from AutoDock Vina web service And I can't find how to solve this and get the results from the docking experiments I'm doing. Can you please help me solve this problem? Thank you in advance for your attention. Arturo Estolano Cobián <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Libre de virus. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

2 2

vina error
by Sofia Vasilakaki 25 Mar '18

25 Mar '18

Dear Chimera developers, I am trying to run vina 1.1.2 on opal server and I am getting the following error: Unable to initialize environment because of error: cannot register event client. Only 99 event clients are allowed in the system Exiting Any suggestions? Thank you, Sofia

1 0

Custom Preset Folder not detecting any scripts
by Eiros Zamora, Juan 22 Mar '18

22 Mar '18

Hello everyone, >From what I’ve gathered, I can save custom presets in a text file with Chimera commands, directly as I would type them in the Command console. So for example my custom preset file is simple, for testing purposes: ribbon protein color white protein repr sphere :CAL disp :CAL I’ve saved the file with a .com extension (as specified here http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Presets) and then indicated the directory it’s in by Clicking on Presets > Add Custom Presets … (after selecting it, I press the Save button). >From here, I’m a bit lost. I think the file is not detected as I get no new options under the Presets tab, nor does the command `preset list c` give any output in the Reply log. Also closing and opening Chimera again does not help (although the custom preset folder is remembered if I try the previous steps). What am I doing wrong? Best regards, Juan

2 2

FW: Question about 3D visualization by chimera
by Williams, Joanne 21 Mar '18

21 Mar '18

From: "Ahmet Cenk ANDAC, ISU" <acandac(a)istinye.edu.tr> Date: Monday, March 19, 2018 at 5:28 PM To: "chimera(a)cgl.ucsf.edu" <chimera(a)cgl.ucsf.edu> Subject: Question about 3D visualization by chimera Hi! I was wondering if it would be possible to view 3D projections of molecules in chimera using polarized glasses? If not, would the Chimera team consider adding such feature in the next release of chimera? Thanks,, Cenk Andac, M.S., M.S., Ph.D., Head, Chair Asst. Professor of Medicinal Chemistry Head of Pharmaceutical Sciences Division Chair of Medicinal Chemistry Department School of Pharmacy, Istinye University, Zeytinburnu-Istanbul, TURKIYE http://eczacilik.istinye.edu.tr/akademik-kadro/ahmet-cenk-andac.shtml Cell: +90-(536)-4813012 E-Mail: cenk_andac(a)yahoo.com

4 4

Autodock Vina outputs
by Elaine Meng 20 Mar '18

20 Mar '18

Hi Simon, The various output files are described in Chimera’s Autodock Vina documentation. As also mentioned in that page, when the docking results are returned they get opened up automatically: i.e. you do not have to explicitly open any files. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> That link is the copy on our website, but you should see basically the same page if you just click the Help button on the Autodock Vina dialog. If no results appeared automatically, the possibilities include: - job is still running - job failed for some reason, check Reply Log - job finished but zero results possible given the input structures/parameters I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco >> >> From: simon chapman <rowanlodge19(a)gmail.com> >> Subject: Re: [Chimera-users] substituting atoms >> Date: March 20, 2018 at 4:31:04 AM PDT >> To: Eric Pettersen <pett(a)cgl.ucsf.edu> >> >> Many thanks Elaine and Eric, much obliged. Sorry if I got the protocol wrong! >> >> 5 files appear on my desktop after a docking run. One is the conf fie, the others are PDB or PDBQT files for ligand and receptor. >> >> I'll keep battling, but perhaps cc.ing your colleagues will help. I'llet you know if the puzzle is resolved. >> >> Simon >> >> On 19 March 2018 at 17:26, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: >> Hi Simon, >> You should initially send these types of questions to the chimera-users list. I’m one member of a programming team and therefore not the expert on all aspects of Chimera — AutoDock Vina being one of the ones I’m not an expert on. I have cc’ed the team members who are the AutoDock Vina experts on this mail and one of them should be able to help out… >> >> —Eric >> >>> On Mar 19, 2018, at 8:17 AM, simon chapman <rowanlodge19(a)gmail.com> wrote: >>> >>> OK, me again....the Irish troublemaker. >>> >>> I've been tinkering with the AutoDock Vina facility in Chimera Tools. All goes well until a pop-up asks me to specify a file type to open the resulting configuration file. >>> >>> I have no idea what those abbreviations mean. I tried a few, but error messages appear every time. >>> >>> Any thoughts? More beers if you can help. >>> >>> Best wishes Simon >> >> <vina 1.PNG> >> <vina 2.PNG> >> >

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Save Image problem
by James Boyd 19 Mar '18

19 Mar '18

Hi, I am a new Chimera user although I have used other molecular graphics programs from time to time. I like the CHimera feel and the menus are pretty easy to navigate. I am trying to save on screen images as .jpg files. I keep getting an error message that says that the file doesn't exist ( e.g. C:\Users\james\desktop\protein\protein.jpg does not exist.) When I look in the folder an image file by that name has been created but it has no image in it. (see NADPH2 for an example). I was able to get an image saved correctly one time (NADPH.jpg) but not again so things appear to be working, it's just that I am doing something wrong. Any suggestions? Thanks, Jim James G Boyd, PhD HealthTell, Inc. 145 S 79th St Chandler, AZ 85226 james.boyd(a)healthtell.com (cell) 860-941-9566 (off) 925-215-5615 (x1001)

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Metal Geometry
by Pascal Auffinger 16 Mar '18

16 Mar '18

Dear All, Metal Geometry is a great tool. However, it can be tedious to use it when the list of metals is long like in some ribosomes where sometimes over 200 of them are found. Is there a quick way to move from a given metal to the next one without using the pulldown menu ? Thanks a lot, Pascal ----- Pascal Auffinger IBMC/CNRS 15 rue René Descartes 67084 Strasbourg Cedex p.auffinger(a)ibmc-cnrs.unistra.fr <mailto:p.auffinger@ibmc-cnrs.unistra.fr> -----

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Topology file creation
by Sankaran SV . 16 Mar '18

16 Mar '18

Hi users, Currently Iam working on protein glycosylation. Can anyone could give me a reference for topology file creation for running the simulation of glycosylated protein. -- Sankaran.s.v bbin

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Permission to use Chimera for non-academic purposes
by Helander, Jon 16 Mar '18

16 Mar '18

Hello, I'm a computational biologist at Wash U. in Saint Louis and have been using Chimera for some years now. I also do some stock market research in biotech and write informative articles about some companies that do small-molecule research. To aid in this, I would like to include some Chimera-generated images. Would this be alright and can I obtain some written confirmation if so? Thanks Jon Helander

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Surface picking
by Priit Eek 15 Mar '18

15 Mar '18

Hi, I am trying to visualize some specific inner cavities in a structure. I can display the MSMS surface and split it into pieces (accelerator Sc), but then I need to select the extra surfaces to hide/delete them (starting with the main outer surface). For some reason surface picking with mouse (Ctrl + left click) doesn’t work. I checked the surface attributes and ‘selectable with mouse’ was true. I recall that this used to work some years ago, but not anymore. I am using the latest daily build (v1.13 build 41684) on macOS v10.12.6. Is this a bug or have some settings changed? I couldn’t find anything referring to this in the docs. Best regards, Priit

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Animation
by David Bhella 14 Mar '18

14 Mar '18

Dear All, I have noticed that the animation tool appears to begin encoding movies before the final frame settings are set, consequently all my movies are missing the last frame. I can see a way to fix this but, it would be better if it didn’t happen. Has anyone else noticed this? D. Dr David Bhella Director - Scottish Centre for Macromolecular Imaging MRC-University of Glasgow Centre for Virus Research Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch [University of Glasgow: The Times Scottish University of the Year 2018]

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Re: [Chimera-users] ellipsoids
by Tom Goddard 12 Mar '18

12 Mar '18

Hi Carlos, The fix is in tonight’s daily build, the one that will be compiled in about 14 hours (2 AM Pacific time). It is not available yet. Chimera does not handle small molecule crystals. It is for protein and nucleic acid structures. So it does not handle the small molecule cif format which has extra symmetries that occur only in small-molecule crystals — you will need other software for that. Tom > On Mar 12, 2018, at 12:04 PM, Carlos Romero wrote: > > Hello Tom, > > thank you for your quick answer. I just installed the daily build however the problem persist. Any suggestion? > Moreover i have a new problem, a cif file that contain totally symmetric molcule, Chimera only represent half! while other softwares confirm that the cif file is correct. An expert in crystallography said that it might because a special inversion center and that " the program should apply the symmetry to complete the molecule" could you help me with this too? i thank you very much for your valuable help > > Carlos > > On Mon, Mar 12, 2018 at 7:06 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Carlos, > > The Chimera unit cell tool was not copying the anisotropic b-factor information. I fixed that in tonight’s daily build. > > Tom > > > > On Mar 12, 2018, at 6:16 AM, Carlos Romero wrote: > > > > First of all congratulations for the your software Chimera, it renders really beautiful images and helps attracting the interest of students for science! > > > > I have a question. I am representing an X-ray structure from cif file. I am able to build up the unit cell, but i would like all the atoms to be represented with the thermal ellipsoids. However, i can only apply the ellipsoids to one molecule of the unit cell. Would it be possible to display all molecules with the ellipsoids and not only one? i was unable to find a solution. > > > > Thanks a lot in advance for any help > > > > kind regards > > > > Carlos > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> > >

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ellipsoids
by Carlos Romero 12 Mar '18

12 Mar '18

First of all congratulations for the your software Chimera, it renders really beautiful images and helps attracting the interest of students for science! I have a question. I am representing an X-ray structure from cif file. I am able to build up the unit cell, but i would like all the atoms to be represented with the thermal ellipsoids. However, i can only apply the ellipsoids to one molecule of the unit cell. Would it be possible to display all molecules with the ellipsoids and not only one? i was unable to find a solution. Thanks a lot in advance for any help kind regards Carlos

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Looking for help on starting of Chimera 1.11 on win32
by 杨超 09 Mar '18

09 Mar '18

Hi Chimera users, I am Ph.D. student who foucing on genetic study of skin disease from Anhui Medical University, Hefei, China. Recently, I want to used Chimera to draw a protein structure. But after I installed Chimera 1.11 on my win 7(win32 system), I can't open it. It showed such error when I started the --debug command. Could anyone give me a hand? Thank you so much. Chao Yang Anhui Medical University Hefei, China

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Cannot save PDB as multiple chains of a single model.
by Matthews-Palmer, Teige Rowan Seal 09 Mar '18

09 Mar '18

Dear Chimera-users, I have a PDB file containing a single chain, that I have copied and applied turns about a symmetry axis. So now I have several models with transformed positions. When I save PDB>save multiple models in a single file, my output PDB does not seem to handle CHAINID properly. If my input PDB has CHAINID A and ends with TER, then my output PDB has everything as CHAINID A, no TER, and instead separates the models by MODEL 1 […] ENDMDL MODEL 2 [...etcetera] I would like to save a PDB with these symmetrical copies as different chains A,B,C… (and not different models). Can anyone suggest a way to do this? Help greatly appreciated. Teige

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Density map segments and segment associated sequence extraction
by Ahmad Abdelzaher 26 Feb '18

26 Feb '18

Hello, I have a density map that i'm trying to segment. I want to fit in my structure in the segmented map, and save each segment of the map as an independent mrc map, and each corresponding segment of the sequence as a fasta file. How can I do that? Kind regards

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'Automatically' annotate multiple structures
by Healey, Joe 26 Feb '18

26 Feb '18

Hi again Chimera team, I'm looking for a fairly quick and dirty way to apply some annotations using 2D labels to a bunch of open structures. Basically, I have ~16 structures open on screen, which I then tile to compare. I'd like the model name to be displayed just below each model so that its easy to track. I've found this thread (http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-July/004081.html) which appears to be attempting a similar thing (though I'd like to use the model.name not serial number), but the approach doesn't seem to work (no labels appear and there is no information in the reply log or IDLE to give me any clues). Any suggestions/alternatives appreciated! Joe Joe Healey M.Sc. B.Sc. (Hons) MSRB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738

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