Hi I am just calculating the Electrostatic Potential, and I wanted to know your opinion which force field is better for metallo proteins.And what is criteria to choose and not to choose the pKA... As I am doing the reaction at different pH and what I see in the PDB the proteins are crystallized at different pH then the reaction conditions. Structures are solved at low pH but the reactions are done at high pH. best Jiri
Hi Jiri, I guess you are using PDB2PQR to make input for APBS potential calculations. There is no choice for pKa, only for pH if you use PROPKA, and you just have to decide whether to use the crystallization or reaction pH. You could certainly use it multiple times for different pH values. Re force field, the short answer is I don’t know. Be aware that the pqr output may not even contain your metal ion, only the protein atoms. (Just close or hide the original model and look at the pqr model output by PDB2PQR to see what’s in it). As it says in the PDB2PQR help page, residues not in the force field will be omitted from the output. That is not necessarily bad, just be aware that the potential you get from APBS might be from the protein part only. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html> The long answer is that it isn’t really a Chimera question but more a general modeling question. You might read the papers cited for the force fields in the help page (linked above) and/or ask on some modeling forum like ccl.net. If you ask, you should say what program you are using (e.g. PDB2PQR), the purpose (e.g. electrostatic potential calculation and surface coloring) and what the choices for force field are, to increase your chances of getting any useful reply. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 20, 2017, at 10:16 AM, chemocev marker <jirivitali@gmail.com> wrote:
Hi I am just calculating the Electrostatic Potential, and I wanted to know your opinion which force field is better for metallo proteins.And what is criteria to choose and not to choose the pKA... As I am doing the reaction at different pH and what I see in the PDB the proteins are crystallized at different pH then the reaction conditions. Structures are solved at low pH but the reactions are done at high pH. best Jiri
Hello, For example, press a record button, do some things with Chimera-X, press a stop button, get a python script that allows to replay what was done inside Chimera. The goal is to quickly create a script when one wants to automate something using Chimera. Regards, F.
Hi Francois, We had discussed having a more complete record of actions in ChimeraX than in Chimera, but currently all you can do is save the log or command history. The advance so far is that clicking several of the ChimeraX icons to do something will put the corresponding command in the log (but not the command history). You can save the log as HTML, but the links do not execute the commands; instead they open the manual pages for the commands. We already have a ChimeraX ticket (request) #917 to allow saving the Log with the commands as executable instead of links to manual pages, but it has not been implemented. <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/917> We had discussed making more of the GUI buttons have equivalent commands, not just these icons. However, even if those distinct actions are also logged, things like moving structures by hand would not be logged. It is OK to ask here on the Chimera-users list, but just so you know, there is also a ChimeraX list chimerax-users@cgl.ucsf.edu you could use for ChimeraX-specific topics. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 20, 2017, at 4:29 PM, Francois BERENGER <berenger@bioreg.kyushu-u.ac.jp> wrote:
Hello, For example, press a record button, do some things with Chimera-X, press a stop button, get a python script that allows to replay what was done inside Chimera.
The goal is to quickly create a script when one wants to automate something using Chimera. Regards, F.
On 12/22/2017 02:02 AM, Elaine Meng wrote:
Hi Francois, We had discussed having a more complete record of actions in ChimeraX than in Chimera, but currently all you can do is save the log or command history. The advance so far is that clicking several of the ChimeraX icons to do something will put the corresponding command in the log (but not the command history).
Are the commands filled with their parameters or are they empty? As a software engineer, I know this is not trivial to implement and it would be super cool if the Chimera of the future can do it. This is not something you can add easily to an already existing software.
We already have a ChimeraX ticket (request) #917 to allow saving the Log with the commands as executable instead of links to manual pages, but it has not been implemented. <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/917>
We had discussed making more of the GUI buttons have equivalent commands, not just these icons. However, even if those distinct actions are also logged, things like moving structures by hand would not be logged.
Personally, I would use such functionality to easily create transformation scripts for structures to run chimera in batch mode (without any graphics). So, it would be OK if any structure moving (for example) is not captured. Regards, F.
It is OK to ask here on the Chimera-users list, but just so you know, there is also a ChimeraX list chimerax-users@cgl.ucsf.edu you could use for ChimeraX-specific topics. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 20, 2017, at 4:29 PM, Francois BERENGER <berenger@bioreg.kyushu-u.ac.jp> wrote:
Hello, For example, press a record button, do some things with Chimera-X, press a stop button, get a python script that allows to replay what was done inside Chimera.
The goal is to quickly create a script when one wants to automate something using Chimera. Regards, F.
On Dec 21, 2017, at 4:22 PM, Francois BERENGER <berenger@bioreg.kyushu-u.ac.jp> wrote:
Are the commands filled with their parameters or are they empty?
Hi Francois, The ChimeraX Log shows the whole command, with all the options and arguments. It also shows other messages from ChimeraX. See for example the screenshots in this page… all three righthand images include the Log window on the right side of the overall window. You can click each image to see it larger. <http://rbvi.ucsf.edu/chimerax/docs/user/advantages.html> We already have the capability of ChimeraX using its own internal browser to view HTML pages with click-to-execute-command links (for example, the Quick Start Guide opened from the ChimeraX Help menu). You can get ChimeraX now and try that. It’s just that the Log is not yet saved with that kind of link. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
participants (3)
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chemocev marker -
Elaine Meng -
Francois BERENGER