Hi chimera team, Is there an easy way to control the transparency of a surface and its clipping cap separately? I managed to do this in one session where the caps are solid, but the rest of the surface is transparent (e.g. see this link: https://drive.google.com/file/d/1-WQtUdYWbITetPl2RgRtU96eXKUj3_v5/view?usp=s... ) [https://lh5.googleusercontent.com/QS16L041E4BqEh_EynLj2msR0gbNQVXbSZ7QexXke98uMB5CHksPVnpSMyM=w1200-h630-p]<https://drive.google.com/file/d/1-WQtUdYWbITetPl2RgRtU96eXKUj3_v5/view?usp=sharing> 3J9Q_wholetier_sliced_colcap.tif<https://drive.google.com/file/d/1-WQtUdYWbITetPl2RgRtU96eXKUj3_v5/view?usp=sharing> drive.google.com However in a different session I'm struggling to figure out how I achieved this. If I alter the surface colour in the Inspect dialog, it sets the surface and cap transparency to be the same. If I change the suface cap colour in the Effects > Side View dialogue, it gives the desired differential transparency, but colours ALL the surface endcaps identically which isn't what I want. Help me unpick what I did! Many thanks 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@warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (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
Hi Joe, There may be some bugginess/hysteresis going on, because at first I also had the same problem when I tried a simple example of two models, each with molecular surfaces. According to the documentation, if in Surface Capping, the “Use cap color” option is turned off, then each model will be capped with its own model color, as in your image. However, when I turned this option off when it had previously been on, both caps remained the color in that option instead of turning into the separate model colors, even when I moved the clipping plane or unclipped and reclipped. I was able to get the separate model-color caps by showing Model Panel, closing the surface models, making sure the “Use cap color” option was turned off, and re-creating the surfaces. (image attached below) I hope this helps (and sorry for the rigmarole), Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 9, 2018, at 4:39 AM, Healey, Joe <J.R.J.Healey@warwick.ac.uk> wrote:
Hi chimera team,
Is there an easy way to control the transparency of a surface and its clipping cap separately?
I managed to do this in one session where the caps are solid, but the rest of the surface is transparent (e.g. see this link: https://drive.google.com/file/d/1-WQtUdYWbITetPl2RgRtU96eXKUj3_v5/view?usp=s... )
3J9Q_wholetier_sliced_colcap.tif drive.google.com
However in a different session I'm struggling to figure out how I achieved this. If I alter the surface colour in the Inspect dialog, it sets the surface and cap transparency to be the same. If I change the suface cap colour in the Effects > Side View dialogue, it gives the desired differential transparency, but colours ALL the surface endcaps identically which isn't what I want.
Help me unpick what I did!
Many thanks
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@warwick.ac.uk
Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry)
Twitter: @JRJHealey | Website: MOAC Page | ORCID: orcid.org/0000-0002-9569-6738 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine, I thought it might be slightly buggy yeah, I encountered the same thing with the caps not responding to commands/toggled etc. There was also some strange clipping and disappearance of the caps as the models were moved (even with an offset). I’ll try redrawing the surfaces as you suggest - thanks! Joe M.Sc. B.Sc. (Hons) MSRB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620<tel:+44%207536%20042620> | Email: J.R.J.Healey@warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk> Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (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<http://orcid.org/0000-0002-9569-6738> On 9 Feb 2018, at 17:00, Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: Hi Joe, There may be some bugginess/hysteresis going on, because at first I also had the same problem when I tried a simple example of two models, each with molecular surfaces. According to the documentation, if in Surface Capping, the “Use cap color” option is turned off, then each model will be capped with its own model color, as in your image. However, when I turned this option off when it had previously been on, both caps remained the color in that option instead of turning into the separate model colors, even when I moved the clipping plane or unclipped and reclipped. I was able to get the separate model-color caps by showing Model Panel, closing the surface models, making sure the “Use cap color” option was turned off, and re-creating the surfaces. (image attached below) I hope this helps (and sorry for the rigmarole), Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco <caps.png> On Feb 9, 2018, at 4:39 AM, Healey, Joe <J.R.J.Healey@warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk>> wrote: Hi chimera team, Is there an easy way to control the transparency of a surface and its clipping cap separately? I managed to do this in one session where the caps are solid, but the rest of the surface is transparent (e.g. see this link: https://drive.google.com/file/d/1-WQtUdYWbITetPl2RgRtU96eXKUj3_v5/view?usp=s... ) 3J9Q_wholetier_sliced_colcap.tif drive.google.com<http://drive.google.com> However in a different session I'm struggling to figure out how I achieved this. If I alter the surface colour in the Inspect dialog, it sets the surface and cap transparency to be the same. If I change the suface cap colour in the Effects > Side View dialogue, it gives the desired differential transparency, but colours ALL the surface endcaps identically which isn't what I want. Help me unpick what I did! Many thanks 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@warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk> Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page | ORCID: orcid.org/0000-0002-9569-6738<http://orcid.org/0000-0002-9569-6738> _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi again Elaine, The process you described seems to work nicely - redrawing the surfaces looks to have worked and 'reset' the cap behaviour. Thanks! 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@warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (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 ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 09 February 2018 17:00:17 To: Healey, Joe Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Surface/Cap colouring Hi Joe, There may be some bugginess/hysteresis going on, because at first I also had the same problem when I tried a simple example of two models, each with molecular surfaces. According to the documentation, if in Surface Capping, the “Use cap color” option is turned off, then each model will be capped with its own model color, as in your image. However, when I turned this option off when it had previously been on, both caps remained the color in that option instead of turning into the separate model colors, even when I moved the clipping plane or unclipped and reclipped. I was able to get the separate model-color caps by showing Model Panel, closing the surface models, making sure the “Use cap color” option was turned off, and re-creating the surfaces. (image attached below) I hope this helps (and sorry for the rigmarole), Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco [cid:1B1E0633-82E7-438C-911B-57D70E7967E3@gateway.sonic.net] On Feb 9, 2018, at 4:39 AM, Healey, Joe <J.R.J.Healey@warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk>> wrote: Hi chimera team, Is there an easy way to control the transparency of a surface and its clipping cap separately? I managed to do this in one session where the caps are solid, but the rest of the surface is transparent (e.g. see this link: https://drive.google.com/file/d/1-WQtUdYWbITetPl2RgRtU96eXKUj3_v5/view?usp=s... ) 3J9Q_wholetier_sliced_colcap.tif drive.google.com However in a different session I'm struggling to figure out how I achieved this. If I alter the surface colour in the Inspect dialog, it sets the surface and cap transparency to be the same. If I change the suface cap colour in the Effects > Side View dialogue, it gives the desired differential transparency, but colours ALL the surface endcaps identically which isn't what I want. Help me unpick what I did! Many thanks 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@warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page | ORCID: orcid.org/0000-0002-9569-6738 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear UCSF-Chimera, Can Chimera calculate electron density maps from structure factor files (or link to an appropriate program)?. The tutorial (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/density.html) suggest fetching the density map from the Electron Density Server, but this server is no longer available. Thanks Hernando
Hi Hernando, The short answer is no, but we updated the EDS fetch to use PDBe, so I think you just need to get a newer Chimera (release 1.12 or newer). Just now I was able to fetch the data used in that tutorial, command open edsID:2fma Chimera 1.12 release notes <http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.12.html#1.12> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 9, 2018, at 9:32 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Dear UCSF-Chimera, Can Chimera calculate electron density maps from structure factor files (or link to an appropriate program)?. The tutorial (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/density.html) suggest fetching the density map from the Electron Density Server, but this server is no longer available. Thanks Hernando
This works, Thanks Elaine. Hernando Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.sosa@einstein.yu.edu -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Friday, February 09, 2018 1:34 PM To: Hernando J Sosa Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] crystal structure's electron density maps Hi Hernando, The short answer is no, but we updated the EDS fetch to use PDBe, so I think you just need to get a newer Chimera (release 1.12 or newer). Just now I was able to fetch the data used in that tutorial, command open edsID:2fma Chimera 1.12 release notes <http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.12.html#1.12> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 9, 2018, at 9:32 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Dear UCSF-Chimera, Can Chimera calculate electron density maps from structure factor files (or link to an appropriate program)?. The tutorial (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/density.html) suggest fetching the density map from the Electron Density Server, but this server is no longer available. Thanks Hernando
participants (3)
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Elaine Meng -
Healey, Joe -
Hernando J Sosa