Problem with DelPhi in chimera
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 *
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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> 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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> 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,
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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp>
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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
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 *
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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp>
…specifically this is their academic website <http://compbio.clemson.edu/delphi> 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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp>
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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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 UniversityEthiopiaMobile: +251902432925Email: 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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp>
…specifically this is their academic website <http://compbio.clemson.edu/delphi> 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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp>
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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume> 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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp>
…specifically this is their academic website <http://compbio.clemson.edu/delphi>
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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp>
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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
labe boye -
sintaspirulina＠gmail.com