Re: ChimeraX-users Digest, Vol 99, Issue 28
Hi friends, On a related issue: I'd like to explore the effect of replacing Val by Asp on the electrostatic potential 'seen' by a cofactor which is completely surrounded by the protein (this is relevant for understanding the change in reaction rate following such replacement). I thought of the following steps: 1. Omit the cofactor from the pdb2pqr and APBS. 2. Read into chimerax the complete pdb (i.e. including the cofactor). 3. Generate the surfaces (protein and cofactor). 4. Render the electrostatic potential on both surfaces (i.e. Cofactor and protein surrounding it) and probe the potential on the cofactor. 5. Does it make sense? Does APBS generate potential values in the void where the cofactor resides even though it wasn't present in the input pdb2pqr (i.e. in the void where the cofactor resides). I'd appreciate your input. 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 ________________________________ From: chimerax-users-request@cgl.ucsf.edu <chimerax-users-request@cgl.ucsf.edu> Sent: Friday, 14 March 2025 21:00 To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: ChimeraX-users Digest, Vol 99, Issue 28 Send ChimeraX-users mailing list submissions to chimerax-users@cgl.ucsf.edu To subscribe or unsubscribe via email, send a message with subject or body 'help' to chimerax-users-request@cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..." Today's Topics: 1. sybyl vs amber atom types in ChimeraX (laurene.jacquot) 2. Re: sybyl vs amber atom types in ChimeraX (David A Case) ---------------------------------------------------------------------- Message: 1 Date: Fri, 14 Mar 2025 09:47:39 +0000 From: "laurene.jacquot" <laurene.jacquot@etu.chimieparistech.psl.eu> Subject: [chimerax-users] sybyl vs amber atom types in ChimeraX To: "chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu> Message-ID: <MR1P264MB2612AFE1D7D6BEF80D0B069A92D22@MR1P264MB2612.FRA P264.PROD.OUTLOOK.COM> Content-Type: multipart/alternative; boundary="_000_MR1P264MB2612AF E1D7D6BEF80D0B069A92D22MR1P264MB2612FRAP_" Dear ChimeraX community, I hope this message finds you well. I am a master student currently working on a project where I need to generate a mol2 file with amber atom types for a protein. Chimera does not manage to parametrize my protein at all, which is why I switched to ChimeraX. ChimeraX does manage to generate a mol2 file, but it writes sybyl atom types. Despite looking on forums, I have not found a feature like in Chimera to write amber atom types instead. I was wondering if such a feature exists in ChimeraX ? Thanks in advance, Best, Laurène Jacquot PSL University, ChimieParisTech -------------- next part -------------- A message part incompatible with plain text digests has been removed ... Name: not available Type: text/html Size: 3823 bytes Desc: not available ------------------------------ Message: 2 Date: Fri, 14 Mar 2025 09:08:36 -0600 From: David A Case <dacase1@gmail.com> Subject: [chimerax-users] Re: sybyl vs amber atom types in ChimeraX To: "laurene.jacquot" <laurene.jacquot@etu.chimieparistech.psl.eu>, chimerax-users@cgl.ucsf.edu Message-ID: <20250314150836.x2iskz4ufcygpsqt@pop-os.localdomain> Content-Type: text/plain; charset=us-ascii; format=flowed On Fri, Mar 14, 2025, laurene.jacquot via ChimeraX-users wrote:
I am a master student currently working on a project where I need to generate a mol2 file with amber atom types for a protein.
I don't have a ChimeraX answer here, but rather a question: why do you need a protein mol2 file with Amber atom types? Amber workflows would not create a mol2 file for an entire protein; but of course, you may need such a file for some other purpose. If so, we may be able to find some Amber tools that does this (or avoids needing it), if the ChimeraX folks themselves don't have a solution. ....dave case ------------------------------ Subject: Digest Footer _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://protect.checkpoint.com/v2/r02/___https://mail.cgl.ucsf.edu/mailman/a... ------------------------------ End of ChimeraX-users Digest, Vol 99, Issue 28 **********************************************
Hi Boaz, I changed the subject line to try to describe this topic. We aren't the APBS experts but my understanding is that yes, it will generate potential at all points in the rectangular grid, based on the input atoms charges and locations. There will of course be potential values even at grid points where there are no atoms, since electrostatics are fairly long-range interactions. However, the magnitude will depend on what dielectric parameters you have given the calculation. Whether it makes sense: that is somewhat up to your scientific judgement. In my opinion, yes, it makes sense, but you have to think carefully about the "offset" you use to color the cofactor surface. Normally when the surface is on the same atoms that produced the charge, you use a positive offset (default 1.4) to color by values projected that distance outward from the surface, to represent what other outside atoms might "see". If you are coloring a surface of the cofactor atoms to try to understand the potential from the protein that the cofactor "sees," you should consider instead using a negative (say -1.4) or zero offset. The offset is adjustable in the Surface Color dialog options and the "color electrostatic" command: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map> Note that an analogous procedure could be done in ChimeraX with the Coulombic electrostatic potential. For example, see the MOLE channels tutorial where we calculate the Coulombic potential from the protein but then show a surface on pseudoatoms representing a channel calculated by MOLEonline, and then color that channel surface by the protein potential. <https://www.rbvi.ucsf.edu/chimerax/data/mole-channel/mole-channel.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 15, 2025, at 10:30 AM, Boaz Shaanan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi friends, On a related issue: I'd like to explore the effect of replacing Val by Asp on the electrostatic potential 'seen' by a cofactor which is completely surrounded by the protein (this is relevant for understanding the change in reaction rate following such replacement). I thought of the following steps:
• Omit the cofactor from the pdb2pqr and APBS. • Read into chimerax the complete pdb (i.e. including the cofactor). • Generate the surfaces (protein and cofactor). • Render the electrostatic potential on both surfaces (i.e. Cofactor and protein surrounding it) and probe the potential on the cofactor. • Does it make sense? Does APBS generate potential values in the void where the cofactor resides even though it wasn't present in the input pdb2pqr (i.e. in the void where the cofactor resides). I'd appreciate your input. Boaz
participants (2)
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Boaz Shaanan -
Elaine Meng