Hidden water molecules
Hi
I'm trying to visualise water molecules associated with the crystal structure of an enzyme (specifically PDB ID: 1C1D). They're listed when I open the pdb as a text file using WordPad, but I can't for the life of me get them to appear on the screen when I try to visualise the structure in Chimera (v. 1.10.2).
What am I missing?
Thanks in advance
Mike
--
Hi Mike,
If you haven’t messed around the PDB file in WordPad. i think doing “ disp: hoh “ in command line should show the water.
Hope this help, Dave
On Apr 6, 2016, at 7:38 AM, Michael Sharkey michael.sharkey@ucd.ie wrote:
Hi
I'm trying to visualise water molecules associated with the crystal structure of an enzyme (specifically PDB ID: 1C1D). They're listed when I open the pdb as a text file using WordPad, but I can't for the life of me get them to appear on the screen when I try to visualise the structure in Chimera (v. 1.10.2).
What am I missing?
Thanks in advance
Mike
--
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Michael, We try to present an initial view that is not too confusing, so it doesn’t automatically show all the atoms. However, you can show whichever atoms you want, and there are many ways. I’ll mention a few:
To show all atoms:
menu: Actions… Atoms/Bonds… show -OR- command: display -OR- menu: Presets…. Interactive 2 (all atoms)
In the all atom preset, however, the waters will be small dots and probably hard to see unless you change them into some representation other than wire. If you do either of the first two right after opening the structure, atoms will already be in stick representation, which for singletons is small balls and easier to see than the dots.
To show waters specifically:
menu: Select… Structure… solvent menu: Actions… Atoms/Bonds… show -OR- command: display solvent -OR- (if residue name is HOH) command: display :hoh
If you ALWAYS want to see alll the atoms when you open the structure instead of the simplified view, however, you can set that in the preferences. Menu: Favorites… Preferences, category: New Molecules, set “smart initial display” to “false”, click Save if you want this setting to apply to later uses of Chimera. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules
You may want to take a look at one of the getting-started tutorials to become familiar with how to specify sets of atoms, residues, etc. http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html http://www.rbvi.ucsf.edu/chimera/current/docs/UsersGuide/frametut.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 Apr 6, 2016, at 7:38 AM, Michael Sharkey michael.sharkey@ucd.ie wrote:
Hi I'm trying to visualise water molecules associated with the crystal structure of an enzyme (specifically PDB ID: 1C1D). They're listed when I open the pdb as a text file using WordPad, but I can't for the life of me get them to appear on the screen when I try to visualise the structure in Chimera (v. 1.10.2). What am I missing? Thanks in advance Mike
Hi Elaine
Thank you for your reply. I had manipulated the structure (opened in Swiss PDB Viewer and saved one chain of the asymmetric unit in a new file). I hadn't realised that the waters didn't save with the protein structure (although the heteroatoms did). So that's why I couldn't see them!
By-the-way, is there a way to select one chain (and associated molecules) and save it as a new PDB file through Chimera? I haven't been able to find a way - hence the use of Swiss PDB Viewer.
Kind regards
Mike
On 6 April 2016 at 17:48, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Michael, We try to present an initial view that is not too confusing, so it doesn’t automatically show all the atoms. However, you can show whichever atoms you want, and there are many ways. I’ll mention a few:
To show all atoms:
menu: Actions… Atoms/Bonds… show -OR- command: display -OR- menu: Presets…. Interactive 2 (all atoms)
In the all atom preset, however, the waters will be small dots and probably hard to see unless you change them into some representation other than wire. If you do either of the first two right after opening the structure, atoms will already be in stick representation, which for singletons is small balls and easier to see than the dots.
To show waters specifically:
menu: Select… Structure… solvent menu: Actions… Atoms/Bonds… show -OR- command: display solvent -OR- (if residue name is HOH) command: display :hoh
If you ALWAYS want to see alll the atoms when you open the structure instead of the simplified view, however, you can set that in the preferences. Menu: Favorites… Preferences, category: New Molecules, set “smart initial display” to “false”, click Save if you want this setting to apply to later uses of Chimera. < http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Mole...
You may want to take a look at one of the getting-started tutorials to become familiar with how to specify sets of atoms, residues, etc. http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html http://www.rbvi.ucsf.edu/chimera/current/docs/UsersGuide/frametut.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 Apr 6, 2016, at 7:38 AM, Michael Sharkey michael.sharkey@ucd.ie wrote:
Hi I'm trying to visualise water molecules associated with the crystal
structure of an enzyme (specifically PDB ID: 1C1D). They're listed when I open the pdb as a text file using WordPad, but I can't for the life of me get them to appear on the screen when I try to visualise the structure in Chimera (v. 1.10.2).
What am I missing? Thanks in advance Mike
Hi Mike, Yes, definitely! You can select any set of atoms that you like and then use an option to save selected atoms only. Or, you could delete all the other atoms and then save all the remaining atoms.
For example, you could select everything with chain ID C with a command (sel :.c) or the menu (Select… Chain… C) and then save with
(A) GUI: menu: File… Save PDB, with checkbox option “save selected atoms only” http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb - or - (B) command “write” with “selected” option http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html
With the other approach, you could first delete all the non-chain-C atoms. It could be done with the menu by selecting chain C, inverting selection, and deleting the resulting selection, or with one command: delete ~ :.c (delete NOT chain C)
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 Apr 15, 2016, at 1:22 AM, Michael Sharkey michael.sharkey@ucd.ie wrote:
Hi Elaine Thank you for your reply. I had manipulated the structure (opened in Swiss PDB Viewer and saved one chain of the asymmetric unit in a new file). I hadn't realised that the waters didn't save with the protein structure (although the heteroatoms did). So that's why I couldn't see them!
By-the-way, is there a way to select one chain (and associated molecules) and save it as a new PDB file through Chimera? I haven't been able to find a way - hence the use of Swiss PDB Viewer. Kind regards Mike
Dear UCSF-Chimera,
What would be the best approach to draw vectors between equivalent atoms of two alternative conformations of a protein. Is there a script available to do this?
Thanks
Hernando
Hi Hernando, “Best” depends on personal preferences, but there are two main approaches.
(1) draw pseudobonds between the two structures. This could be done by listing specifications of the pairs of atoms in a text file (pseudobond file) and reading it in with Pseudobond Reader, http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.html
...or by writing a command script with distance measurements between all the pairs of atoms. You could hide the distance labels afterward, for example with the Distances tool. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances
You can control pseudobond line style, line width, color, or change them to sticks in the Selection Inspector or with the “setattr” command. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html
(2) create a simple text file in BILD format describing cylinders or 3D arrows between the pairs of points. Then opening the file (name ending in .bld) shows the objects. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.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 Apr 11, 2019, at 8:42 AM, Hernando J Sosa hernando.sosa@einstein.yu.edu wrote:
Dear UCSF-Chimera, What would be the best approach to draw vectors between equivalent atoms of two alternative conformations of a protein. Is there a script available to do this? Thanks Hernando
Thanks Elaine
I tried with a BILD file (option 2) and that works well.
Best
Hernando
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Thursday, April 11, 2019 12:21 PM To: Hernando J Sosa Cc: chimera-users@cgl.ucsf.edu Mailing List Subject: Re: [Chimera-users] Drawing vectors
Hi Hernando, “Best” depends on personal preferences, but there are two main approaches.
(1) draw pseudobonds between the two structures. This could be done by listing specifications of the pairs of atoms in a text file (pseudobond file) and reading it in with Pseudobond Reader, https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fpbreader%2Fpbreader.html&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7Cfdf84225579a4adc615908d6be99c03f%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636905964898957264&sdata=0ei2Lh28LCMLyHyyNUaZaUCHHa7rhXzbyBK6tkvkd30%3D&reserved=0
...or by writing a command script with distance measurements between all the pairs of atoms. You could hide the distance labels afterward, for example with the Distances tool. https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fdistance.html&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7Cfdf84225579a4adc615908d6be99c03f%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636905964898957264&sdata=6R39jMPzaQnf5Lo%2BaFOSv0wAoGIInF6OzyiaOI86dDk%3D&reserved=0 https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fstructuremeas%2Fstructuremeas.html%23distances&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7Cfdf84225579a4adc615908d6be99c03f%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636905964898957264&sdata=YvC65xCvjF7Vma9D01xC3fyqVIvPWenIPK8SorXDmuk%3D&reserved=0
You can control pseudobond line style, line width, color, or change them to sticks in the Selection Inspector or with the “setattr” command. https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Finspection.html&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7Cfdf84225579a4adc615908d6be99c03f%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636905964898957264&sdata=kbcKBqYSRsH9SBwtp7WVq0YDGeCxxjUcaScUFSjca%2Bw%3D&reserved=0 https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fsetattr.html&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7Cfdf84225579a4adc615908d6be99c03f%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636905964898957264&sdata=R3aPq5QjWm%2FLBnn%2BeXq95fyH0RQa3%2BAsh3iMtq2ujno%3D&reserved=0
(2) create a simple text file in BILD format describing cylinders or 3D arrows between the pairs of points. Then opening the file (name ending in .bld) shows the objects. https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fbild.html&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7Cfdf84225579a4adc615908d6be99c03f%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636905964898957264&sdata=bJCew1z3HjRgLim8XTDMqqf1ra1RDe0zmzuWbEpN15M%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 Apr 11, 2019, at 8:42 AM, Hernando J Sosa hernando.sosa@einstein.yu.edu wrote:
Dear UCSF-Chimera, What would be the best approach to draw vectors between equivalent atoms of two alternative conformations of a protein. Is there a script available to do this? Thanks Hernando
participants (4)
-
Elaine Meng -
Gae, David Hyon -
Hernando J Sosa -
Michael Sharkey