CellBlender version compatibility

[bluescript1]

Hi, Although being new to MCell/CellBlender I have found it hugely useful however the current 815kb downloadable version 1.0.0, although it installs, can not run in my hands CellBlender models created using Cellblender version 1.0.0 installed from 5.9MB cellblender_v1.0_RC3.zip (results in exclamation mark red/yellow warning triangles in MCell Progress window, with no results generated even if the respective folders have been created). I am working in 64-bit Windows 7 with current MCell version 3.3 and Python 3.4.3. Any advice? Regards Armin

[cnlbob]

I believe the problem is likely with CellBlender and not Python or MCell. That might save you some experimentation / frustration.

We have been working on an upgrading system to handle older .blend files back to v1.0_RC3.

This upgrading system is still a work in progress, but you might try pulling the latest version from the repository and see if it will upgrade your RC3 file. Please write back if it works or not, and we can move forward from there.

[bluescript1]

Thanks for getting in touch. I have taken some screenshots in 64-bit Windows 7 if it is of any help. These are of the meshgeom.blend model both with the current and RC3 versions of Cellblender. Neither approach runs. When I try to open my own file created in Cellblender RC3 using the current version, it does not run either. It runs perfectly though in its original environment though.

Attached is my own file which runs well in RC3 version of it. What I have noticed is that the RC3 version was about 5.2MB in size, while the current one is 0.8 MB only.

Best wishes armin

Current meshgeom model in Blender 2.74 with CellBlender RC3 (downloaded 2-3 months ago) and MCell3.3. It ends with error message. [cid:image001.jpg@01D0AE9E.C63A4E00]

As above but with Cellblender downloaded today [cid:image002.jpg@01D0AE9E.C63A4E00]

Below is my own model (as attached) that was created in Cellblender RC3 but run in the current version Cellblender [cid:image003.jpg@01D0AE9E.C63A4E00]

The model attached runs perfectly well with Cellblender RC3.

From: cnlbob [mailto:notifications@github.com] Sent: 23 June 2015 01:27 To: mcellteam/cellblender Cc: Armin Sepp Subject: Re: [cellblender] CellBlender version compatibility (#89)

We have been working on an upgrading system to handle older .blend file back to v1.0_RC3.

This upgrading system is still a work in progress, but you might try pulling the latest version from the repository and see if it will upgrade your RC3 file. Please write back if it works or not, and we can move forward from there.

— Reply to this email directly or view it on GitHubhttps://github.com/mcellteam/cellblender/issues/89#issuecomment-114311659.

---

This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS.

[bluescript1]

Hi, Just to update, got the current version of CellBlender to work, it opens the models from the tutorials now. There appeared to be some settings upgrade notices that made the difference. As for the old CellBlender models, in my case they are so simple that I have no problem easily replicating them in the current version. Best wishes armin

From: cnlbob [mailto:notifications@github.com] Sent: 23 June 2015 01:27 To: mcellteam/cellblender Cc: Armin Sepp Subject: Re: [cellblender] CellBlender version compatibility (#89)

We have been working on an upgrading system to handle older .blend file back to v1.0_RC3.

This upgrading system is still a work in progress, but you might try pulling the latest version from the repository and see if it will upgrade your RC3 file. Please write back if it works or not, and we can move forward from there.

— Reply to this email directly or view it on GitHubhttps://github.com/mcellteam/cellblender/issues/89#issuecomment-114311659.

---

This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS.

[bluescript1]

Hi, Just a quick question, if somebody has time. MCell syntax can handle 2D reactions between surface molecules present on the same object. Is there a way to describe 2D reactions between surface molecules assigned to different objects, e.g. between TCR-MHC in the immune which can also be expected to follow 2D rules?

Best wishes Armin Sepp

Sr Scientific Investigator Biopharm Innovation RD Biopharm R&D

GSK Mailstop: BioPharm Innovation, Building 5S100, Glaxo Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK Email armin.z.sepp@gsk.commailto:armin.z.sepp@gsk.com Tel +44 1438 764618

From: cnlbob [mailto:notifications@github.com] Sent: 23 June 2015 01:27 To: mcellteam/cellblender Cc: Armin Sepp Subject: Re: [cellblender] CellBlender version compatibility (#89)

We have been working on an upgrading system to handle older .blend file back to v1.0_RC3.

This upgrading system is still a work in progress, but you might try pulling the latest version from the repository and see if it will upgrade your RC3 file. Please write back if it works or not, and we can move forward from there.

— Reply to this email directly or view it on GitHubhttps://github.com/mcellteam/cellblender/issues/89#issuecomment-114311659.

---

This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS.