- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Chimera-users Digest, Vol 180, Issue 8
by Boaz Shaanan 10 Apr '18

10 Apr '18

1 0

ConSurf script on ChimeraX
by Fabian Glaser 10 Apr '18

10 Apr '18

Hi, I would like to use Chimera ConSurf scripts in ChimeraX, but I get the following error when I try to run the script on ChimeraX ModuleNotFoundError: No module named 'cPickle' File "consurf_final_zn.py", line 1, in See log for complete Python traceback. If you wish to report this error, send mail to chimerax-bugs(a)cgl.ucsf.edu <mailto:chimerax-bugs@cgl.ucsf.edu> and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created. Is this something that can be fixed or updated? More generally I would like to update ConSurf with a version of the script for ChimeraX, can you help me with that? Here is the beginning of the original chimera script import cPickle, base64 try: from SimpleSession.versions.v65 import beginRestore,\ registerAfterModelsCB, reportRestoreError, checkVersion except ImportError: from chimera import UserError raise UserError('Cannot open session that was saved in a' ' newer version of Chimera; update your version') checkVersion([1, 12, 41623]) import chimera from chimera import replyobj replyobj.status('Restoring session...', \ blankAfter=0) replyobj.status('Beginning session restore...', \ blankAfter=0, secondary=True) beginRestore() def restoreCoreModels(): from SimpleSession.versions.v65 import init, restoreViewer, \ restoreMolecules, restoreColors, restoreSurfaces, \ restoreVRML, restorePseudoBondGroups, restoreModelAssociations molInfo = Thanks a lot, Best, Fabian Fabian Glaser PhD Head of the Structural Bioinformatics section Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web http://bku.technion.ac.il/ <http://bku.technion.ac.il/> Tel +972 (0) 4 8293701

2 3

Dear team UCSF chimera, kindly help me I download and installed the UCSFf chimera but its showing short cut
by Maria Yousuf 09 Apr '18

09 Apr '18

Dear team UCSF chimera Hi I download and installed the UCSFf chimera followed the linkon windows 7 Microsoft Windows 64-bit chimera-1.12-win64.exe<https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=win64/c…> Size: 150984696 bytes MD5: b662f97cdacb8be458662aa638dd6694 Oct 24, 2017 Instructions<https://www.cgl.ucsf.edu/chimera/data/downloads/1.12/win64.html> Documentation<https://www.cgl.ucsf.edu/chimera/data/downloads/1.12/docs/> Runs on Windows 7 or later. Initially It worked well, but after 2 days a shortcut appeared in the file and some of its features are not functional, I cant able to open a docked file in .pdb format Kindly share the functional link to download chimera on 64bit windows 7 looking forward to hear from you soon regards Dr.Maria <http://aka.ms/weboutlook>

2 1

Chimera's hydrogen bond counting tool (FindHBond) from command-line?
by Gustavo Seabra 09 Apr '18

09 Apr '18

Hi all, Is there a way to run the Chimera's hydrogen bond counting tool (FindHBond) using the command line only? Could someone post me to the best way? -- Gustavo Seabra Professor Adjunto Universidade Federal de Pernambuco Recife - PE - Brasil +55-81-2126-7450 x5023 (goo.gl/ktsXSc)

2 3

chimeraX consurf
by Fabian Glaser 08 Apr '18

08 Apr '18

Hi, I would like to use Chimera ConSurf scripts in ChimeraX, but I get the following error when I try to run the script on ChimeraX ModuleNotFoundError: No module named 'cPickle' File "consurf_final_zn.py", line 1, in See log for complete Python traceback. If you wish to report this error, send mail to chimerax-bugs(a)cgl.ucsf.edu<mailto:chimerax-bugs@cgl.ucsf.edu> and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created. Is this something that can be fixed or updated? Thanks a lot, Best, Fabian Fabian Glaser PhD Head of the Structural Bioinformatics section Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web http://bku.technion.ac.il/ Tel +972 (0) 4 8293701

1 0

How to change 32bit map into 16bit map
by Jun Ha Song 05 Apr '18

05 Apr '18

Hello, I sometimes invert my map using Fiji, and I also convert my 32bit map into 16bit map using Fiji's "Image → Type → 16-bit" function, but the only way to retrieve the map from Fiji is to save the map as .tif stack, then use IMOD's "tif2mrc" to get it back as .mrc file. However, once I save my map as .tif, the pixel spacing information of the map is set to 1,1,1. Because of this, I always have to re-adjust the pixel spacing back to original using IMOD's "alterheader" once I use Fiji for any kind of image adjustment. I know I can invert a map in Chimera (without setting the pixel spacing to 1,1,1 like Fiji) by using "Volume Filter → Filter Type : Scale → Scale by -1", but I don't know how to turn my 32bit map into 16bit map. Although the "Value Type" of scale filter allows me to specify which bit I want the map to be in, when I filter my float32 map with value type set to either int16 or uint16, the filtered map shows histogram with only few lines. Can UCSF Chimera turn float32bit map into 16bit map? Best, Junha Song.

2 2

Hello I have a question
by Teddy Chen 05 Apr '18

05 Apr '18

Hi my name is Teddy, I used UCSF Chimera for my research, and it is a very good software! I appreciate you made it. I have a question about structure comparison, I usually use Matchmaker to overlap 2 similar protein fragment to compare the difference. I wonder if the structure is bent or twisted during the matching process, in order to fit the reference structure more? For example, the attachment is for demonstration. There is a protein A, and protein A have a short from that miss some amino acid (the green part is missed). So the result produced by the Matchmaker would be A or B? If the result is A, can I make result B by UCSF Chimera? Thank you!

2 2

Minimum system requirements for software
by Kerley, Jeremy L 04 Apr '18

04 Apr '18

I have a faculty member who uses the Chimera software. While using the software, his current computer continually freezes/locks-up and must be rebooted. Please email the minimum/recommended system requirements for the Chimera software. I’m in the process of building out a replacement system and need that information. Regards, —— Jeremy Kerley Computing Support Specialist II Emory University School of Medicine Dept of Pediatrics IT Ph: (404)727-4781 ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

2 1

Open density map
by Wolf, Nina Marie 04 Apr '18

04 Apr '18

Hi, I’ve searched the forums and continue to have issues opening a density map in Chimera. Can you help me figure out how to do this starting with an mtz file and using COOT/Phenix/CCP4 to convert the file and load into chimera? Thank you, Nina Wolf

2 1

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

3 14

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

4 7

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 *********************************************

2 5

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> >> >

1 0

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)

2 1

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> -----

2 1

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

2 1