On Apr 30, 2009, at 1:45 PM, #MAZIAR SOLEYMANI ARDEJANI# wrote:
Hi everybody,
I'm working with a pdb file (http://www.rcsb.org/pdb/files/2vxi.pdb1.gz ) made of two models. I need to merge this two models into one. How can I do that?
Thanks in advance,
Maziar S. Ardejani Lab 9, The Orner Lab Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences 21 Nanyang Link Nanyang Technological University Singapore 637371
Hi Maziar, In general, you can merge models with the "copy/combine" button on the right side of the Model Panel (Favorites... Model Panel) or with the "combine" command. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html
However, I opened 2vxi from the PDB and it is only one model, not two. Maybe you opened it two times by mistake? http://www.rcsb.org/pdb/explore/explore.do?structureId=2VXI
There are a few cases where structures have so many atoms or chains that the PDB has split them into multiple files (e.g. 3bz1 and 3bz2). If those parts collectively have more than 63 chains it won't work to merge them with Chimera because there are only 63 possible different chain ID symbols.
Please send Chimera questions to chimera-users@cgl.ucsf.edu and not to me directly, and if possible use an informative "subject" line - thanks!
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
Hi Maziar, Oh, now I see that your file is different than just getting entry 2vxi from the PDB, sorry I misunderstood.
To merge the models, it should work to use one of the methods described in my previous message. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Apr 30, 2009, at 2:49 PM, Elaine Meng wrote:
On Apr 30, 2009, at 1:45 PM, #MAZIAR SOLEYMANI ARDEJANI# wrote:
Hi everybody,
I'm working with a pdb file (http://www.rcsb.org/pdb/files/2vxi.pdb1.gz ) made of two models. I need to merge this two models into one. How can I do that?
Thanks in advance,
Maziar S. Ardejani Lab 9, The Orner Lab Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences 21 Nanyang Link Nanyang Technological University Singapore 637371
Hi Maziar, In general, you can merge models with the "copy/combine" button on the right side of the Model Panel (Favorites... Model Panel) or with the "combine" command. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html
However, I opened 2vxi from the PDB and it is only one model, not two. Maybe you opened it two times by mistake? http://www.rcsb.org/pdb/explore/explore.do?structureId=2VXI
There are a few cases where structures have so many atoms or chains that the PDB has split them into multiple files (e.g. 3bz1 and 3bz2). If those parts collectively have more than 63 chains it won't work to merge them with Chimera because there are only 63 possible different chain ID symbols.
Please send Chimera questions to chimera-users@cgl.ucsf.edu and not to me directly, and if possible use an informative "subject" line - thanks!
I hope this helps, Elaine
Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine and other friends,
Is there any way in Chimera to find the coordinates of a selected atom? without looking into pdb text file of course
Cheers,
Maziar S. Ardejani Lab 9, The Orner Lab Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences 21 Nanyang Link Nanyang Technological University Singapore 637371
Tel : (65) 6513 8205 Fax: (65) 67911961
Hi Maziar, See the "getcrd" command:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/getcrd.html
You could either select the atom(s) and then use "getcrd sel" or just specify the atom(s) directly without going through selection. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On May 3, 2009, at 1:07 PM, #MAZIAR SOLEYMANI ARDEJANI# wrote:
Hi Elaine and other friends,
Is there any way in Chimera to find the coordinates of a selected atom? without looking into pdb text file of course
Cheers,
Maziar S. Ardejani Lab 9, The Orner Lab Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences 21 Nanyang Link Nanyang Technological University Singapore 637371
Hi
I am using Chimera alpha 1.4 build 27395 in Ubuntu 9.04 Jaunty 32 bits version, in a laptop with Core2Duo@2.4GHz each core, 4 Gb RAM.
When I use Save Image, sometimes if I increase the size of the image or increase supersmple values, Chimera will crash with this terminal message:
X Error of failed request: GLXBadPbuffer Major opcode of failed request: 128 (GLX) Minor opcode of failed request: 28 (X_GLXDestroyPbuffer) Serial number of failed request: 107906 Current serial number in output stream: 107908
(The last 2 numbers will vary between crashes)
After restarting Chimera sometimes I can save the image using the same image specifications, other times it will keep crashing and only reducing the size or the Supersample numbers, I can save the image.
Is this laptop not powerful enough? Do you need more information? Should I try another build?
Thank you in advance
Victor Alves
PS: My first message to the BB, so congratulations to the developers for an excellent piece of software.
Hi Victor,
This appears to be a linux graphics driver problem that you see when using new Chimera 1.4 image saving code that uses off-screen OpenGL PBuffers to capture images. Chimera 1.3 saves images directly from your screen and will not have this problem. You can also make Chimera 1.4 use the older image saving technique by starting Chimera on linux with "chimera --debug-opengl", then turning off the Pbuffer switch in the opengl debug dialog that appears at startup. Greg Couch in our lab is working on the Pbuffer code and can provide more advice next week.
Tom
Victor Alves wrote:
Hi
I am using Chimera alpha 1.4 build 27395 in Ubuntu 9.04 Jaunty 32 bits version, in a laptop with Core2Duo@2.4GHz each core, 4 Gb RAM.
When I use Save Image, sometimes if I increase the size of the image or increase supersmple values, Chimera will crash with this terminal message:
X Error of failed request: GLXBadPbuffer Major opcode of failed request: 128 (GLX) Minor opcode of failed request: 28 (X_GLXDestroyPbuffer) Serial number of failed request: 107906 Current serial number in output stream: 107908
(The last 2 numbers will vary between crashes)
After restarting Chimera sometimes I can save the image using the same image specifications, other times it will keep crashing and only reducing the size or the Supersample numbers, I can save the image.
Is this laptop not powerful enough? Do you need more information? Should I try another build?
Thank you in advance
Victor Alves
PS: My first message to the BB, so congratulations to the developers for an excellent piece of software.
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Tom
Your advice worked perfectly. I updated to build 27479 from 2009-05-03 and 2D Labels are now visible in saved images and disabling Pbuffer as suggested in your other mail allowed me to save really huge images with no problems at all.
Since I decided to use daily builds, I am aware that this bugs are normal and part of the development cycle, but I happily trade some stability for cutting edge developments :-)
So my question is: is the general Chimera mailing list the proper channel for discussing these software quirks from these alpha or beta versions?
Thank you so much
Victor Alves
-----Original Message----- From: Tom Goddard [mailto:goddard@cgl.ucsf.edu] Sent: sábado, 2 de Maio de 2009 1:09 To: Victor Alves Cc: 'Chimera BB' Subject: Re: [Chimera-users] Chimera crashes when saving image
Hi Victor,
This appears to be a linux graphics driver problem that you see when using new Chimera 1.4 image saving code that uses off-screen OpenGL PBuffers to capture images. Chimera 1.3 saves images directly from your screen and will not have this problem. You can also make Chimera 1.4 use the older image saving technique by starting Chimera on linux with "chimera --debug-opengl", then turning off the Pbuffer switch in the opengl debug dialog that appears at startup. Greg Couch in our lab is working on the Pbuffer code and can provide more advice next week.
Tom
Victor Alves wrote:
Hi
I am using Chimera alpha 1.4 build 27395 in Ubuntu 9.04 Jaunty 32 bits version, in a laptop with Core2Duo@2.4GHz each core, 4 Gb RAM.
When I use Save Image, sometimes if I increase the size of the image or increase supersmple values, Chimera will crash with this terminal message:
X Error of failed request: GLXBadPbuffer Major opcode of failed request: 128 (GLX) Minor opcode of failed request: 28 (X_GLXDestroyPbuffer) Serial number of failed request: 107906 Current serial number in output stream: 107908
(The last 2 numbers will vary between crashes)
After restarting Chimera sometimes I can save the image using the same
image
specifications, other times it will keep crashing and only reducing the
size
or the Supersample numbers, I can save the image.
Is this laptop not powerful enough? Do you need more information? Should I try another build?
Thank you in advance
Victor Alves
PS: My first message to the BB, so congratulations to the developers for
an
excellent piece of software.
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Victor,
If you get an error traceback in Chimera it is best to press the "Report Bug" button. That sends the traceback, Chimera version, platform and graphics driver version to us for debugging. That is usually much more efficient than discussing it on chimera-users.
If you are unsure if some behavior is a bug then chimera-users is the place to discuss that.
If Chimera crashes then restart it and use Help / Report a Bug and briefly describe what led to the crash. That will send along your system and Chimera configuration info.
Tom
Victor Alves wrote:
Dear Tom
Your advice worked perfectly. I updated to build 27479 from 2009-05-03 and 2D Labels are now visible in saved images and disabling Pbuffer as suggested in your other mail allowed me to save really huge images with no problems at all.
Since I decided to use daily builds, I am aware that this bugs are normal and part of the development cycle, but I happily trade some stability for cutting edge developments :-)
So my question is: is the general Chimera mailing list the proper channel for discussing these software quirks from these alpha or beta versions?
Thank you so much
Victor Alves
-----Original Message----- From: Tom Goddard [mailto:goddard@cgl.ucsf.edu] Sent: sábado, 2 de Maio de 2009 1:09 To: Victor Alves Cc: 'Chimera BB' Subject: Re: [Chimera-users] Chimera crashes when saving image
Hi Victor,
This appears to be a linux graphics driver problem that you see when using new Chimera 1.4 image saving code that uses off-screen OpenGL PBuffers to capture images. Chimera 1.3 saves images directly from your screen and will not have this problem. You can also make Chimera 1.4 use the older image saving technique by starting Chimera on linux with "chimera --debug-opengl", then turning off the Pbuffer switch in the opengl debug dialog that appears at startup. Greg Couch in our lab is working on the Pbuffer code and can provide more advice next week.
TomVictor Alves wrote:
Hi
I am using Chimera alpha 1.4 build 27395 in Ubuntu 9.04 Jaunty 32 bits version, in a laptop with Core2Duo@2.4GHz each core, 4 Gb RAM.
When I use Save Image, sometimes if I increase the size of the image or increase supersmple values, Chimera will crash with this terminal message:
X Error of failed request: GLXBadPbuffer Major opcode of failed request: 128 (GLX) Minor opcode of failed request: 28 (X_GLXDestroyPbuffer) Serial number of failed request: 107906 Current serial number in output stream: 107908
(The last 2 numbers will vary between crashes)
After restarting Chimera sometimes I can save the image using the same
image
specifications, other times it will keep crashing and only reducing the
size
or the Supersample numbers, I can save the image.
Is this laptop not powerful enough? Do you need more information? Should I try another build?
Thank you in advance
Victor Alves
PS: My first message to the BB, so congratulations to the developers for
an
excellent piece of software.
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 (5)
-
#MAZIAR SOLEYMANI ARDEJANI# -
Elaine Meng -
Thomas Goddard -
Tom Goddard
-
Victor Alves