Hi Elaine, Following on the recent exchange of messages: I've actually been wondering for quite some time why there isn't an APBS plugin for Chimera. Is it because of no interest on the APBS side? Should we ask them to develop one? I'm sure we can collect enough votes to promote that. For example, I find the Consurf and Castp plugins (maybe interfaces, whatever they should be called) very nice and useful, so why not APBS too? Happy New Year to you all (still not too late). 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 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: chimera-users-bounces@cgl.ucsf.edu [chimera-users-bounces@cgl.ucsf.edu] on behalf of chimera-users-request@cgl.ucsf.edu [chimera-users-request@cgl.ucsf.edu] Sent: Friday, January 06, 2012 2:22 AM To: chimera-users@cgl.ucsf.edu Subject: Chimera-users Digest, Vol 105, Issue 5 Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: APBS (Elaine Meng) 2. Re: APBS (Elaine Meng) 3. Re: APBS (Anjana Ramnath) 4. Re: How to place a metal ion in protein model (Suneel N.A.) 5. Re: How to place a metal ion in protein model (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Thu, 5 Jan 2012 12:04:22 -0800 From: Elaine Meng <meng@cgl.ucsf.edu> To: Anjana Ramnath <anjanaram1@gmail.com> Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] APBS Message-ID: <4CE9538A-80A1-4A3B-B99D-D4F401A73A6E@cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Hello Anjana, Are you sure you're using Chimera? As far as I know there is no APBS plugin for Chimera, only for Pymol. In Chimera, (A) there are several ways to show distances, including selecting two atoms (Ctrl-click on one atom, Shift-Ctrl-click on the second atom) and using command: distance sel (B) there is no tool especially for aromatic interactions, but you can use the tool Find Clashes/Contacts or command findclash to identify contacts between two sets of aromatic residues. For example, to identify contacts between aromatic amino acids in chain A and aromatic amino acids in chain B, command: findclash :.a&aromatic test :.b&aromatic overlap -1 hb 0 (You would probably also want to display all atoms so you can see where the contacts are.) The same thing could be done using the Find Clashes/Contacts graphical interface, in the menu under Tools... Structure Analysis. GUI documentation: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash...> Command documentation: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.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 Jan 4, 2012, at 9:02 PM, Anjana Ramnath wrote:
Hello all, My question is simple: im trying to install the APBS plugin but have so far been unsuccessful. I am also trying to show the interactions between aromatic residues on a PDB molecule. how do i do this? im also having trouble with showing the distance between 2 residues. im using Fedora 12 and also WindowsXP. please do let me know. thank you very much! sincerely, Anjana.
------------------------------ Message: 2 Date: Thu, 5 Jan 2012 12:23:49 -0800 From: Elaine Meng <meng@cgl.ucsf.edu> To: Anjana Ramnath <anjanaram1@gmail.com> Cc: Chimera BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] APBS Message-ID: <5BAFC2C8-8868-4D58-A577-C2EE7DD1C6CE@cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Hi Anjana, After showing a surface, you can either (A) open an electrostatic potential (ESP) map previously calculated with some other program (DelPhi, Grasp, UHBD, APBS) in Chimera and then use it to color the surface with "Electrostatic Surface Coloring" (in menu under Tools... Surface/Binding Analysis) or command "scolor" <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor...> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html> or (B) use the "Coulombic Surface Coloring" tool (in same menu as above) or command "coulombic" to calculate Coulombic ESP and color the surface based on those values <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic...> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html> ... for example, as in this tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> Best, 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 Jan 5, 2012, at 12:14 PM, Anjana Ramnath wrote:
thanks so much for your prompt response! well actually, i was wondering if there was a way to show the electrostatic surface in chimera?
------------------------------ Message: 3 Date: Fri, 6 Jan 2012 01:56:19 +0530 From: Anjana Ramnath <anjanaram1@gmail.com> To: Chimera BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] APBS Message-ID: <CAAwO1H_Lt3ZRSnjqTNx+qXDpYa7jhF3=-hf+F5TMM1QRjGnj8w@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" thanks so much Elaine! let me just say that Chimera user support is waayy better than any other popular graphics program ive come across! youve got a chimera fan here now. :) On Fri, Jan 6, 2012 at 1:53 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Anjana, After showing a surface, you can either
(A) open an electrostatic potential (ESP) map previously calculated with some other program (DelPhi, Grasp, UHBD, APBS) in Chimera and then use it to color the surface with "Electrostatic Surface Coloring" (in menu under Tools... Surface/Binding Analysis) or command "scolor" <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor...
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html>
or (B) use the "Coulombic Surface Coloring" tool (in same menu as above) or command "coulombic" to calculate Coulombic ESP and color the surface based on those values < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic...
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html>
... for example, as in this tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
Best, 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 Jan 5, 2012, at 12:14 PM, Anjana Ramnath wrote:
thanks so much for your prompt response! well actually, i was wondering if there was a way to show the electrostatic surface in chimera?
Hi Boaz, Happy New Year to you too! Although I'm sure people would like to have an APBS-Chimera interface, I imagine it is not trivial to develop considering the large number of parameters. As far as our team, the ratio of potential things to do (no pun intended) vs. people to do them is very high. As far as the rest of the world, I lack the information to answer! 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 Jan 6, 2012, at 7:25 AM, Boaz Shaanan wrote:
Hi Elaine,
Following on the recent exchange of messages: I've actually been wondering for quite some time why there isn't an APBS plugin for Chimera. Is it because of no interest on the APBS side? Should we ask them to develop one? I'm sure we can collect enough votes to promote that. For example, I find the Consurf and Castp plugins (maybe interfaces, whatever they should be called) very nice and useful, so why not APBS too?
Happy New Year to you all (still not too late). Boaz
Yeah, there were some tentative feelers about such a plugin a couple of years back, but it fizzled out. If you made a request on the APBS- users list (SourceForge.net: Mailing Lists for APBS) they might consider it. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jan 6, 2012, at 7:25 AM, Boaz Shaanan wrote:
Hi Elaine,
Following on the recent exchange of messages: I've actually been wondering for quite some time why there isn't an APBS plugin for Chimera. Is it because of no interest on the APBS side? Should we ask them to develop one? I'm sure we can collect enough votes to promote that. For example, I find the Consurf and Castp plugins (maybe interfaces, whatever they should be called) very nice and useful, so why not APBS too?
Happy New Year to you all (still not too late).
Boaz
Some of the difficulties in putting APBS into Chimera are: 1) There are a lot of parameters in an APBS calculation, 2) It can take a lot of memory when running (I recall 1 Gbyte for a few thousand atom protein), 3) It can take a long time to compute. None of these prevent it from going in to Chimera but to make it work well requires significant work. Someone would have to decide which are the most important parameters to allow the user to change. It might be very helpful to estimate the peak memory usage for instance when choosing grid spacing since once it exceeds the physical memory of the machine it will be extremely slow and could make the machine unusable while it runs. It also should not freeze Chimera when running since even a modest computation takes minutes I think. Tom
Yeah, there were some tentative feelers about such a plugin a couple of years back, but it fizzled out. If you made a request on the APBS-users list (SourceForge.net: Mailing Lists for APBS <http://sourceforge.net/mail/?group_id=148472>) they might consider it.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jan 6, 2012, at 7:25 AM, Boaz Shaanan wrote:
Hi Elaine,
Following on the recent exchange of messages: I've actually been wondering for quite some time why there isn't an APBS plugin for Chimera. Is it because of no interest on the APBS side? Should we ask them to develop one? I'm sure we can collect enough votes to promote that. For example, I find the Consurf and Castp plugins (maybe interfaces, whatever they should be called) very nice and useful, so why not APBS too?
Happy New Year to you all (still not too late).
Boaz
Hi, in which way we could help? Multiple requests to the APBS mailing list is sufficient ? Marco Tom Goddard <goddard@sonic.net> ha scritto:
Some of the difficulties in putting APBS into Chimera are: 1) There are a lot of parameters in an APBS calculation, 2) It can take a lot of memory when running (I recall 1 Gbyte for a few thousand atom protein), 3) It can take a long time to compute.
None of these prevent it from going in to Chimera but to make it work well requires significant work. Someone would have to decide which are the most important parameters to allow the user to change. It might be very helpful to estimate the peak memory usage for instance when choosing grid spacing since once it exceeds the physical memory of the machine it will be extremely slow and could make the machine unusable while it runs. It also should not freeze Chimera when running since even a modest computation takes minutes I think.
Tom
Yeah, there were some tentative feelers about such a plugin a couple of years back, but it fizzled out. If you made a request on the APBS-users list (SourceForge.net: Mailing Lists for APBS <http://sourceforge.net/mail/?group_id=148472>) they might consider it.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jan 6, 2012, at 7:25 AM, Boaz Shaanan wrote:
Hi Elaine,
Following on the recent exchange of messages: I've actually been wondering for quite some time why there isn't an APBS plugin for Chimera. Is it because of no interest on the APBS side? Should we ask them to develop one? I'm sure we can collect enough votes to promote that. For example, I find the Consurf and Castp plugins (maybe interfaces, whatever they should be called) very nice and useful, so why not APBS too?
Happy New Year to you all (still not too late).
Boaz
Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 www.rete29aprile.it ---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it
My feeling is that a request to the APBS users list would be the most likely way to get a plugin sooner rather than much, much later. ;-) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jan 9, 2012, at 11:54 AM, sette@uniroma2.it wrote:
Hi,
in which way we could help? Multiple requests to the APBS mailing list is sufficient ?
Marco
Tom Goddard <goddard@sonic.net> ha scritto:
Some of the difficulties in putting APBS into Chimera are: 1) There are a lot of parameters in an APBS calculation, 2) It can take a lot of memory when running (I recall 1 Gbyte for a few thousand atom protein), 3) It can take a long time to compute.
None of these prevent it from going in to Chimera but to make it work well requires significant work. Someone would have to decide which are the most important parameters to allow the user to change. It might be very helpful to estimate the peak memory usage for instance when choosing grid spacing since once it exceeds the physical memory of the machine it will be extremely slow and could make the machine unusable while it runs. It also should not freeze Chimera when running since even a modest computation takes minutes I think.
Tom
Yeah, there were some tentative feelers about such a plugin a couple of years back, but it fizzled out. If you made a request on the APBS-users list (SourceForge.net: Mailing Lists for APBS <http://sourceforge.net/mail/?group_id=148472
) they might consider it.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jan 6, 2012, at 7:25 AM, Boaz Shaanan wrote:
Hi Elaine,
Following on the recent exchange of messages: I've actually been wondering for quite some time why there isn't an APBS plugin for Chimera. Is it because of no interest on the APBS side? Should we ask them to develop one? I'm sure we can collect enough votes to promote that. For example, I find the Consurf and Castp plugins (maybe interfaces, whatever they should be called) very nice and useful, so why not APBS too?
Happy New Year to you all (still not too late).
Boaz
Dr.Marco Sette, Ph.D.
Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328
www.rete29aprile.it
---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it
participants (5)
-
Boaz Shaanan -
Elaine Meng -
Eric Pettersen -
sette＠uniroma2.it -
Tom Goddard