Dear All, I am using chimera 1.41 and 1.4 on a 3 GB Core 2 duo machine. When i draw surface for any ligand or residue then suddenly it get closed. This problem occurs in both versions 1.4 and 1.4.1. Kindly suggest me to fix this problem. Regards Kshatresh Dutta Dubey
Hi Kshatresh, Although we are aware of problems calculating some surfaces, this sounds like a different problem because the others would not stop Chimera, and they only happen for some fraction of structures, not all the time as you suggest. Your problem is more likely with the graphics driver on your machine. It is better to use "Help... Report a Bug" in the Chimera menu to report these problems (not sending mail to chimera- users@cgl.ucsf.edu), because that would send us details about your machine. However, some things you could try are - updating your graphics driver - in Chimera, set Preferences (under Favorites), General category, "Debug OpenGL on startup" to "true", click Save. Exit Chimera and restart, and then in the debug dialog, turn off "VertexBufferObject" Although it doesn't sound like you are having the other surface problems I mentioned, they and some workarounds are discussed here: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-January/004713.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 31, 2010, at 4:18 AM, Kshatresh Dutta Dubey wrote:
Dear All, I am using chimera 1.41 and 1.4 on a 3 GB Core 2 duo machine. When i draw surface for any ligand or residue then suddenly it get closed. This problem occurs in both versions 1.4 and 1.4.1. Kindly suggest me to fix this problem. Regards Kshatresh Dutta Dubey
This is error report when I try to run this program. Thanks. Yongjun You are now running Chimera version 1.4.1 (build 30333). Your previous version was 1.4.1 (build 30226). Check the release notes for new features and other info. (To access the release notes, use the Help menu to bring up the User's Guide. Then click the 'Documentation index' link and you will then see a link for the release notes.) /Applications/Chimera.app/Contents/Resources/bin/mscalc 1.400000 2.000000 1 MSMSLIB 1.3 started on wirelessjhmi144-10-237-144-73.ebalto.jhmi.edu Copyright M.F. Sanner (March 2000) Compilation flags Surface 2otl, category ligand, probe radius 1.4, vertex density 2 1 connected surface components Total solvent excluded surface area = 171.512 Total solvent accessible surface area = 345.462 /Applications/Chimera.app/Contents/Resources/bin/mscalc 1.400000 2.000000 1 MSMSLIB 1.3 started on wirelessjhmi144-10-237-144-73.ebalto.jhmi.edu Copyright M.F. Sanner (March 2000) Compilation flags ERROR: add_rs_component: Too many RS components Calculation of some surface components failed. Falling back to single-component calculation. /Applications/Chimera.app/Contents/Resources/bin/mscalc 1.400000 2.000000 0 MSMSLIB 1.3 started on wirelessjhmi144-10-237-144-73.ebalto.jhmi.edu Copyright M.F. Sanner (March 2000) Compilation flags Surface calculation failed, mscalc returned code -11 On 3/31/10 12:04 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi Kshatresh, Although we are aware of problems calculating some surfaces, this sounds like a different problem because the others would not stop Chimera, and they only happen for some fraction of structures, not all the time as you suggest.
Your problem is more likely with the graphics driver on your machine. It is better to use "Help... Report a Bug" in the Chimera menu to report these problems (not sending mail to chimera- users@cgl.ucsf.edu), because that would send us details about your machine.
However, some things you could try are - updating your graphics driver - in Chimera, set Preferences (under Favorites), General category, "Debug OpenGL on startup" to "true", click Save. Exit Chimera and restart, and then in the debug dialog, turn off "VertexBufferObject"
Although it doesn't sound like you are having the other surface problems I mentioned, they and some workarounds are discussed here: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-January/004713.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 31, 2010, at 4:18 AM, Kshatresh Dutta Dubey wrote:
Dear All, I am using chimera 1.41 and 1.4 on a 3 GB Core 2 duo machine. When i draw surface for any ligand or residue then suddenly it get closed. This problem occurs in both versions 1.4 and 1.4.1. Kindly suggest me to fix this problem. Regards Kshatresh Dutta Dubey
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Yongjun, Again, we do not recommend sending bug reports to chimera-users@cgl.ucsf.edu -- instead you should use "Help... Report a Bug" in the Chimera menu. However, there is no need to do that in this case, it is the common problem previously discussed in many messages. Please see this previous post for possible workarounds: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-January/004713.html
Elaine On Mar 31, 2010, at 9:40 AM, Yongjun Dang wrote:
This is error report when I try to run this program. Thanks. Yongjun
You are now running Chimera version 1.4.1 (build 30333). Your previous version was 1.4.1 (build 30226). Check the release notes for new features and other info. (To access the release notes, use the Help menu to bring up the User's Guide. Then click the 'Documentation index' link and you will then see a link for the release notes.) /Applications/Chimera.app/Contents/Resources/bin/mscalc 1.400000 2.000000 1 MSMSLIB 1.3 started on wirelessjhmi144-10-237-144-73.ebalto.jhmi.edu Copyright M.F. Sanner (March 2000) Compilation flags
Surface 2otl, category ligand, probe radius 1.4, vertex density 2 1 connected surface components Total solvent excluded surface area = 171.512 Total solvent accessible surface area = 345.462 /Applications/Chimera.app/Contents/Resources/bin/mscalc 1.400000 2.000000 1 MSMSLIB 1.3 started on wirelessjhmi144-10-237-144-73.ebalto.jhmi.edu Copyright M.F. Sanner (March 2000) Compilation flags ERROR: add_rs_component: Too many RS components Calculation of some surface components failed. Falling back to single-component calculation. /Applications/Chimera.app/Contents/Resources/bin/mscalc 1.400000 2.000000 0 MSMSLIB 1.3 started on wirelessjhmi144-10-237-144-73.ebalto.jhmi.edu Copyright M.F. Sanner (March 2000) Compilation flags Surface calculation failed, mscalc returned code -11
On 3/31/10 12:04 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi Kshatresh, Although we are aware of problems calculating some surfaces, this sounds like a different problem because the others would not stop Chimera, and they only happen for some fraction of structures, not all the time as you suggest.
Your problem is more likely with the graphics driver on your machine. It is better to use "Help... Report a Bug" in the Chimera menu to report these problems (not sending mail to chimera- users@cgl.ucsf.edu), because that would send us details about your machine.
However, some things you could try are - updating your graphics driver - in Chimera, set Preferences (under Favorites), General category, "Debug OpenGL on startup" to "true", click Save. Exit Chimera and restart, and then in the debug dialog, turn off "VertexBufferObject"
Although it doesn't sound like you are having the other surface problems I mentioned, they and some workarounds are discussed here: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-January/004713.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 31, 2010, at 4:18 AM, Kshatresh Dutta Dubey wrote:
Dear All, I am using chimera 1.41 and 1.4 on a 3 GB Core 2 duo machine. When i draw surface for any ligand or residue then suddenly it get closed. This problem occurs in both versions 1.4 and 1.4.1. Kindly suggest me to fix this problem. Regards Kshatresh Dutta Dubey
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Kshatresh Dutta Dubey -
Yongjun Dang