- Chimera-users - RBVI Mailing Lists

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

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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>

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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

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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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