Is there any one knows how to fit the density map to this red model?
[cid:71FF4B2F-87EA-443B-B280-CE3ABEA9B11B@its.yale.internal] On Dec 24, 2019, at 12:26 PM, chimera-users-request@cgl.ucsf.edumailto:chimera-users-request@cgl.ucsf.edu wrote:
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1. Re: Problem with DelPhi in chimera (labe boye) (Boaz Shaanan) - correction (Boaz Shaanan)
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Message: 1 Date: Tue, 24 Dec 2019 17:26:14 +0000 From: Boaz Shaanan bshaanan@bgu.ac.il To: "chimera-users@cgl.ucsf.edu" chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Problem with DelPhi in chimera (labe boye) (Boaz Shaanan) - correction Message-ID: 81ea8ecae3d04575b9c13ac2142612bf@bgu.ac.il Content-Type: text/plain; charset="windows-1255"
In my previous message I meant of course linux Delphi v.6. Sorry.
Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________ From: Chimera-users chimera-users-bounces@cgl.ucsf.edu on behalf of chimera-users-request@cgl.ucsf.edu chimera-users-request@cgl.ucsf.edu Sent: Tuesday, December 24, 2019 7:10 PM To: chimera-users@cgl.ucsf.edu Subject: Chimera-users Digest, Vol 200, Issue 20
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1. Re: Problem with DelPhi in chimera (labe boye) (Boaz Shaanan)
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Message: 1 Date: Tue, 24 Dec 2019 17:09:46 +0000 From: Boaz Shaanan bshaanan@bgu.ac.il To: "chimera-users@cgl.ucsf.edu" chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Problem with DelPhi in chimera (labe boye) Message-ID: a2abfa7a83394a56b27584878c181426@bgu.ac.il Content-Type: text/plain; charset="windows-1255"
Hi,
The Chimera v.6 that I used was the linux version NOT windows. The answer you got from the Delphi people sounds familiar to me which is why I switched to APBS interface on Chimera (works on both Windows and linux). The .dx file produced by APBS is read and contoured nicely by Chimera. If you need to ionize the structure, there is a Windows PDB2PQR executable as mentioned by Elaine (I understand that you're using Windows).
Cheers,
Boaz
Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________ From: Chimera-users chimera-users-bounces@cgl.ucsf.edu on behalf of chimera-users-request@cgl.ucsf.edu chimera-users-request@cgl.ucsf.edu Sent: Tuesday, December 24, 2019 6:34 PM To: chimera-users@cgl.ucsf.edu Subject: Chimera-users Digest, Vol 200, Issue 19
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1. Re: Problem with DelPhi in chimera (Elaine Meng) 2. Re: Chimera-users Digest, Vol 200, Issue 18 (Boaz Shaanan) 3. Re: Problem with DelPhi in chimera (Elaine Meng)
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Message: 1 Date: Mon, 23 Dec 2019 12:55:29 -0800 From: Elaine Meng meng@cgl.ucsf.edu To: "sintaspirulina@gmail.com" sintaspirulina@gmail.com Cc: Chimera BB chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Problem with DelPhi in chimera Message-ID: B59A5D0E-CA80-4151-9CD6-11B33435CA4A@cgl.ucsf.edu Content-Type: text/plain; charset=utf-8
We saw your Chimera bug report. However, the file you attached was not the ?.phi? file (electrostatic potential map) output from DelPhi. It was just the text output from the DelPhi program. If DelPhi runs successfully on your structure, it will create a separate file, with name ending in .phi, that is the electrostatic potential map.
If by ?cube? you mean Gaussian cube grid, Chimera does read that format. https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ffiletypes.html%23volume&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937326851&sdata=syWyZ7IUR20yv8QyPCDnWM%2BocXEvOGDM8NoPg1Y2Q0I%3D&reserved=0 However, this format is handled simply as a map that is not necessarily electrostatic potential, so it would require more steps in Chimera to get the coloring you want. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 23, 2019, at 10:01 AM, sintaspirulina@gmail.com wrote:
OK, I tried all the three academic versions of DelPhi for windows; and none is working for me. I contacted the DelPhi supporters and SUGGESTED to use CUBE output format which isn't possible in Chimera. In the mean time, the two Chimera versions I installed read 3eeb.phi file from the tutorial. I will report the problem. regards,
Sintayehu M. Shenkutie, Dr. rer. nat. Assistant Professor of Biochemistry. Department of Chemistry Hawassa University Ethiopia Mobile: +251902432925 Email: dr.sintayehu@hu.edu.et Sintayehu.M.Shenkutie@bot3.bio.uni-giessen.de
On Monday, December 23, 2019, 08:30:26 PM GMT+3, Elaine Meng meng@cgl.ucsf.edu wrote:
It should be any DelPhi version that you get from the academic website, which was a link in this page I sent earlier:
The DelPhi files that Chimera can read are from the academic version of DelPhi, as mentioned here: https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ffiletypes.html%23esp&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937326851&sdata=qpjwIjue%2BnkBte46u6VICybT3puZdN3LiRCFMoODMwQ%3D&reserved=0
?specifically this is their academic website https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcompbio.clemson.edu%2Fdelphi&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937326851&sdata=tKP9y%2FfkiyRazSZfDWRm18PzmEyT6UYhtoAW8n6fwss%3D&reserved=0
I don?t remember what version I used several years ago to make 3eebB.phi, but as far as I know the format didn?t change. It is possible it changed and we didn?t know about it, but we would need example(s) of the files.
If you believe you used the academic version of DelPhi but you get the error opening the phi file, you could try using Chimera menu Help? Report a Bug and attach your phi file so we could take a look at it. However, that does not guarantee it will be possible to fix.
I hope this helps, Elaine
On Dec 22, 2019, at 4:23 AM, labe boye sintaspirulina@gmail.com wrote:
Hi Thank you for your reply. Could you please let me know which version of DelPhi academic version is compatible with Chimera? Which DelPhi version was used to generate the 3eeb.phi file in the tutorial? kindest regards,
On Fri, Dec 20, 2019 at 11:16 PM Elaine Meng meng@cgl.ucsf.edu wrote: Hi, Chimera is saying that your phi file output from Delphi contains inconsistent information, like maybe it got truncated. I do not know if it is possible to fix the phi file, sorry.
The DelPhi files that Chimera can read are from the academic version of DelPhi, as mentioned here: https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ffiletypes.html%23esp&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937326851&sdata=qpjwIjue%2BnkBte46u6VICybT3puZdN3LiRCFMoODMwQ%3D&reserved=0
If you have some other version of DelPhi associated with a commercial package, maybe the format is different and Chimera does not know how to read it.
Linked to the last section of this tutorial, there is an example DelPhi phi file (3eebB.phi) that Chimera can read: https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ftutorials%2Fsurfprop.html&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937326851&sdata=ddqLEJ%2BfrRaTzDU3FgYmvLAQRKUnxdYjQE2kqLyMpAw%3D&reserved=0
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 20, 2019, at 10:33 AM, labe boye sintaspirulina@gmail.com wrote:
Hi, I use windows, UCSF Chimera 1.14 and tried all versions of DelPhi for windows but I get the following error Error reading file default.phi, format delphi Record size > file size What is the solution? regards,
-- Sintayehu M. Shenkutie, Dr. rer. nat. Assistant Professor of Biochemistry. Department of Chemistry Hawassa University Ethiopia Mobile: +251902432925 Email: dr.sintayehu@hu.edu.et Sintayehu.M.Shenkutie@bot3.bio.uni-giessen.de
The bamboo that bends is stronger than the oak that resists
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Message: 2 Date: Mon, 23 Dec 2019 21:21:35 +0000 From: Boaz Shaanan bshaanan@bgu.ac.il To: "chimera-users@cgl.ucsf.edu" chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Chimera-users Digest, Vol 200, Issue 18 Message-ID: d539fbf953d74b6783b5dc0a632313d3@bgu.ac.il Content-Type: text/plain; charset="windows-1255"
Hi,
I ran into this Chimera/Delphi problem a few months ago (and discussed it with the Chimera/Delphi people). The latest Delphi version that I tried (8.4) produced a cube format file which formally can be read and contoured in the Chimera volume viewer. I hated the way the electrostatic surface produced that way looked and abandoned it. Delphi v. 6 which I have (and which I think Elaine used 3 years ago) produced the good old .phi which is file properly displayed in Chimera . I think one can still get hold of V.6 from the Delphi distribution site.
To avoid this mess I used the APBS interface of Chimera which worked fine and produced a nice, familiar style, looking electrostatic surface (see for example Fig. S10 in the supplementary of doi: 10.1093/nar/gkz604).
Regards,
Boaz
Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________ From: Chimera-users chimera-users-bounces@cgl.ucsf.edu on behalf of chimera-users-request@cgl.ucsf.edu chimera-users-request@cgl.ucsf.edu Sent: Monday, December 23, 2019 10:48 PM To: chimera-users@cgl.ucsf.edu Subject: Chimera-users Digest, Vol 200, Issue 18
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Today's Topics:
1. Re: Problem with DelPhi in chimera (Elaine Meng) 2. need your assistance (Asmi Mahmood) 3. Re: Problem with DelPhi in chimera (labe boye) 4. Re: Problem with DelPhi in chimera (Elaine Meng) 5. dock prep for many ligands (Elaine Meng) 6. Re: Problem with DelPhi in chimera (sintaspirulina@gmail.com)
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Message: 1 Date: Fri, 20 Dec 2019 12:16:20 -0800 From: Elaine Meng meng@cgl.ucsf.edu To: labe boye sintaspirulina@gmail.com Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Problem with DelPhi in chimera Message-ID: 1158BCF0-F94F-4B55-98DA-27166E19CEDC@cgl.ucsf.edu Content-Type: text/plain; charset=us-ascii
Hi, Chimera is saying that your phi file output from Delphi contains inconsistent information, like maybe it got truncated. I do not know if it is possible to fix the phi file, sorry.
The DelPhi files that Chimera can read are from the academic version of DelPhi, as mentioned here: https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ffiletypes.html%23esp&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937326851&sdata=qpjwIjue%2BnkBte46u6VICybT3puZdN3LiRCFMoODMwQ%3D&reserved=0
If you have some other version of DelPhi associated with a commercial package, maybe the format is different and Chimera does not know how to read it.
Linked to the last section of this tutorial, there is an example DelPhi phi file (3eebB.phi) that Chimera can read: https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ftutorials%2Fsurfprop.html&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937326851&sdata=ddqLEJ%2BfrRaTzDU3FgYmvLAQRKUnxdYjQE2kqLyMpAw%3D&reserved=0
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 20, 2019, at 10:33 AM, labe boye sintaspirulina@gmail.com wrote:
Hi, I use windows, UCSF Chimera 1.14 and tried all versions of DelPhi for windows but I get the following error Error reading file default.phi, format delphi Record size > file size What is the solution? regards,
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Message: 2 Date: Sat, 21 Dec 2019 15:10:00 +0000 (UTC) From: Asmi Mahmood asmi_mahmood@yahoo.com To: "chimera-users@cgl.ucsf.edu" chimera-users@cgl.ucsf.edu, "chimera-bugs@cgl.ucsf.edu" chimera-bugs@cgl.ucsf.edu Subject: [Chimera-users] need your assistance Message-ID: 844676351.2239559.1576941000519@mail.yahoo.com Content-Type: text/plain; charset="utf-8"
Hi Hope you are doing good. I need your assistance regarding chimera. I'm working on virtual docking and need to prepare more than 10k ligands (in a single file as SDF) for docking process. I need to know that if chimera desktop latest version can fulfill my need. If yes please give me a tutorial pdf or video.
Regards Waiting for a quick response Asma Tariq
Hi Wangbiao, I don’t know what that red thing is. Is it just a surface, or is it another map that happens to have an isosurface displayed? (What kind of file did it come from?) You can fit a map to another map, http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html but there isn’t a tool to fit a map to a surface… it’s just an empty shell. Maybe you could somehow first make a new map based on that surface (e.g. 1 inside 0 outside) and then try to fit to that, but I don’t know if that really makes sense or would even work. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 24, 2019, at 1:49 PM, Guo, Wangbiao wangbiao.guo@yale.edu wrote:
Is there any one knows how to fit the density map to this red model?
Dear Elaine: Thank you very much. The red model is the Amira segmentation file, I changed it to mrc file. I want to fit the model with density map. I don’t know why I cannot save the model as map.
On Dec 24, 2019, at 9:57 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Wangbiao, I don’t know what that red thing is. Is it just a surface, or is it another map that happens to have an isosurface displayed? (What kind of file did it come from?) You can fit a map to another map, https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Ffitmaps%2Ffitmaps.html&data=02%7C01%7Cwangbiao.guo%40yale.edu%7C6275cd9bc9384e8c922508d788e6212b%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128394297998014&sdata=W0Nw0%2Bwu2pdGYvP2WF29ZGrlUlMDUZs5%2BYZSfKm3ZZE%3D&reserved=0 but there isn’t a tool to fit a map to a surface… it’s just an empty shell. Maybe you could somehow first make a new map based on that surface (e.g. 1 inside 0 outside) and then try to fit to that, but I don’t know if that really makes sense or would even work. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 24, 2019, at 1:49 PM, Guo, Wangbiao wangbiao.guo@yale.edu wrote:
Is there any one knows how to fit the density map to this red model?
Hi Wangbiao, I’m guessing that an Amira mesh file may just describe a surface or surfaces, rather than a map (3D grid with values at every point).
I see that Amira mesh is listed together with map formats (e.g. with the Chimera “listfiletypes” startup option) and in this table http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume …but it may be because they are generally used together. If my guess is correct, it may not be interchangeable with or equivalent to those data types.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 26, 2019, at 10:00 AM, Guo, Wangbiao wangbiao.guo@yale.edu wrote:
Dear Elaine: Thank you very much. The red model is the Amira segmentation file, I changed it to mrc file. I want to fit the model with density map. I don’t know why I cannot save the model as map.
On Dec 24, 2019, at 9:57 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Wangbiao, I don’t know what that red thing is. Is it just a surface, or is it another map that happens to have an isosurface displayed? (What kind of file did it come from?) You can fit a map to another map, https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Ffitmaps%2Ffitmaps.html&data=02%7C01%7Cwangbiao.guo%40yale.edu%7C6275cd9bc9384e8c922508d788e6212b%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128394297998014&sdata=W0Nw0%2Bwu2pdGYvP2WF29ZGrlUlMDUZs5%2BYZSfKm3ZZE%3D&reserved=0 but there isn’t a tool to fit a map to a surface… it’s just an empty shell. Maybe you could somehow first make a new map based on that surface (e.g. 1 inside 0 outside) and then try to fit to that, but I don’t know if that really makes sense or would even work. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 24, 2019, at 1:49 PM, Guo, Wangbiao wangbiao.guo@yale.edu wrote:
Is there any one knows how to fit the density map to this red model?
The segmented Amira file when converted to mrc should be similar to a binary. E.g. every voxel not highlighted would have the value 0, the the first label field will have the value 1, the second label field 2 etc.
Multiple the segmented mrc file with the original map and then use the output file to fit the pdb to.
On Thu, Dec 26, 2019, 10:40 AM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Wangbiao, I’m guessing that an Amira mesh file may just describe a surface or surfaces, rather than a map (3D grid with values at every point).
I see that Amira mesh is listed together with map formats (e.g. with the Chimera “listfiletypes” startup option) and in this table http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume …but it may be because they are generally used together. If my guess is correct, it may not be interchangeable with or equivalent to those data types.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 26, 2019, at 10:00 AM, Guo, Wangbiao wangbiao.guo@yale.edu
wrote:
Dear Elaine: Thank you very much. The red model is the Amira segmentation
file, I changed it to mrc file. I want to fit the model with density map. I don’t know why I cannot save the model as map.
On Dec 24, 2019, at 9:57 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Wangbiao, I don’t know what that red thing is. Is it just a surface, or is it
another map that happens to have an isosurface displayed? (What kind of file did it come from?) You can fit a map to another map,
<
https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.uc...
but there isn’t a tool to fit a map to a surface… it’s just an empty
shell. Maybe you could somehow first make a new map based on that surface (e.g. 1 inside 0 outside) and then try to fit to that, but I don’t know if that really makes sense or would even work.
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 24, 2019, at 1:49 PM, Guo, Wangbiao wangbiao.guo@yale.edu
wrote:
Is there any one knows how to fit the density map to this red model?
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you very much, Elaine, may be I should try again.
On Dec 26, 2019, at 1:31 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Wangbiao, I’m guessing that an Amira mesh file may just describe a surface or surfaces, rather than a map (3D grid with values at every point).
I see that Amira mesh is listed together with map formats (e.g. with the Chimera “listfiletypes” startup option) and in this table https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ffiletypes.html%23volume&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cf586d0b0398e445f5c2108d78a31e047%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637129819141381522&sdata=Ykbx%2B3U8UTeqctsAxRzUjuWWsTmu1QzQp2ufpfmFrX4%3D&reserved=0 …but it may be because they are generally used together. If my guess is correct, it may not be interchangeable with or equivalent to those data types.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 26, 2019, at 10:00 AM, Guo, Wangbiao wangbiao.guo@yale.edu wrote:
Dear Elaine: Thank you very much. The red model is the Amira segmentation file, I changed it to mrc file. I want to fit the model with density map. I don’t know why I cannot save the model as map.
On Dec 24, 2019, at 9:57 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Wangbiao, I don’t know what that red thing is. Is it just a surface, or is it another map that happens to have an isosurface displayed? (What kind of file did it come from?) You can fit a map to another map, https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Ffitmaps%2Ffitmaps.html&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cf586d0b0398e445f5c2108d78a31e047%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637129819141381522&sdata=4cEg0SRnXSv6OFqZSp0Tn34PiSd%2FwemOvB3p2Nqlu0w%3D&reserved=0 but there isn’t a tool to fit a map to a surface… it’s just an empty shell. Maybe you could somehow first make a new map based on that surface (e.g. 1 inside 0 outside) and then try to fit to that, but I don’t know if that really makes sense or would even work. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 24, 2019, at 1:49 PM, Guo, Wangbiao wangbiao.guo@yale.edu wrote:
Is there any one knows how to fit the density map to this red model?
Yes, the Amira mesh is just a surface (a set of triangles), not a density map. Chimera has no way to fit a surface to a density map. You could convert the surface to a density map with all ones inside the surface and all zeros outside using the Chimera mask command
https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/mask.html
for example
mask ones #1
where the Amira mesh is model #1. If you are trying to fit a PDB to the density within this surface you could instead use the mask command on the original EM density
mask #0 #1
where #0 is the original density and #1 is the Amira mesh to get just the density within the surface, then fit the PDB in the resulting masked density as Karen suggested.
Tom
On Dec 27, 2019, at 7:44 AM, Guo, Wangbiao wangbiao.guo@yale.edu wrote:
Thank you very much, Elaine, may be I should try again.
On Dec 26, 2019, at 1:31 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Wangbiao, I’m guessing that an Amira mesh file may just describe a surface or surfaces, rather than a map (3D grid with values at every point).
I see that Amira mesh is listed together with map formats (e.g. with the Chimera “listfiletypes” startup option) and in this table https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ffiletypes.html%23volume&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cf586d0b0398e445f5c2108d78a31e047%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637129819141381522&sdata=Ykbx%2B3U8UTeqctsAxRzUjuWWsTmu1QzQp2ufpfmFrX4%3D&reserved=0 …but it may be because they are generally used together. If my guess is correct, it may not be interchangeable with or equivalent to those data types.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 26, 2019, at 10:00 AM, Guo, Wangbiao wangbiao.guo@yale.edu wrote:
Dear Elaine: Thank you very much. The red model is the Amira segmentation file, I changed it to mrc file. I want to fit the model with density map. I don’t know why I cannot save the model as map.
On Dec 24, 2019, at 9:57 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Wangbiao, I don’t know what that red thing is. Is it just a surface, or is it another map that happens to have an isosurface displayed? (What kind of file did it come from?) You can fit a map to another map, https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Ffitmaps%2Ffitmaps.html&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cf586d0b0398e445f5c2108d78a31e047%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637129819141381522&sdata=4cEg0SRnXSv6OFqZSp0Tn34PiSd%2FwemOvB3p2Nqlu0w%3D&reserved=0 but there isn’t a tool to fit a map to a surface… it’s just an empty shell. Maybe you could somehow first make a new map based on that surface (e.g. 1 inside 0 outside) and then try to fit to that, but I don’t know if that really makes sense or would even work. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 24, 2019, at 1:49 PM, Guo, Wangbiao wangbiao.guo@yale.edu wrote:
Is there any one knows how to fit the density map to this red model?
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participants (4)
-
Elaine Meng -
Guo, Wangbiao -
Karen Davies -
Tom Goddard