It puckers ASN and ASP (and probably other amino acids). (I run it to relieve steric conflicts only)
How do you fix this?
And can you run it with the whole protein selected?
Hi Jacqueline, I haven’t seen this, at least when the sidechains have room to relax freely. Maybe in your case, they are smashed up against some other atoms in such a way that prevents relaxation to the preferred planar state. Minimization will only find a nearby local minimum, not cross energy barriers to find a lower minimum. Although there is no reasonable way for users to edit the force field, I don’t expect this to be a problem of the force field (which is well established).
Things you could try include:
(1) run more steps of minimization
(2) try to resolve the steric conflict somehow, which could be by manually rotating bonds or even running some molecular dynamics. However, keep in mind that such interventions could make your structure worse and/or less realistic. See “Adjust Torsions” in the Build Structure tool, and the “Molecular Dynamics Simulation” tool (in Chimera 1.11 and newer). http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html
For minimization, you can specify as many atoms as “fixed” (frozen) as you want, and whether they are the selected atoms or the unselected atoms. If you wanted all atoms to move, don’t bother selecting, just set “fixed atoms: none”. Still, if you are only minimizing, things generally won’t move that much. 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 Oct 17, 2016, at 1:00 PM, Jacqueline Vitali jackie.vitali@gmail.com wrote:
It puckers ASN and ASP (and probably other amino acids). (I run it to relieve steric conflicts only)
How do you fix this?
And can you run it with the whole protein selected?
Hi All,
Is there a way to usefully (and conveniently) view ribosomes recognizing that Chimera does not support large structure formats like mmcif?
-John
Hi John, That is one of the major issues addressed in our next-generation program, ChimeraX.
ChimeraX is not yet publicly available, but we plan to make development daily builds available very soon (this month). However, it is in an early stage and lacks many features. It will take some time to become as functionally rich as Chimera, so how useful it will be for you depends on what types of structural analysis you wished to perform. If primarily viewing, it may already fill the bill. We envision people using both packages for a while, depending on their needs. You can get a feel for what ChimeraX can do now from the website and documentation linked below.
ChimeraX homepage http://www.rbvi.ucsf.edu/chimerax/index.html
Advantages shortlist http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html
User Guide http://www.rbvi.ucsf.edu/chimerax/docs/user/index.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 Dec 7, 2016, at 8:09 AM, John Mercer, Ph.D. jmercer@duke.edu wrote:
Hi All, Is there a way to usefully (and conveniently) view ribosomes recognizing that Chimera does not support large structure formats like mmcif? -John
Hi John,
The Chimera mmCIF reader is incredibly slow, taking minutes to read a ribosome structure. This code was developed outside our lab and is all in Python. So practically, you would need to download use the multiple PDB format files for structures over 100,000 atoms. The PDB has made this more difficult for new entries because they get a single ID code and only the mmCIF is easily available if the entry has more than 100,000 atoms. For fewer atoms Chimera simply fetches the PDB format if you use fetch or command "open 1xyz”, but it fetches the mmCIF for new entries where the PDB format is not readily available. For those (e.g. 5LZS) you can go to the RCSB web site and use the web page Download menu to get the *.tar.gz file containing several PDB format files representing the model.
As Elaine said our new ChimeraX is much faster and uses mmCIF by default. For instance 200,000 atoms of 5LZS opens in 1.5 seconds in ChimeraX.
Tom
On Dec 7, 2016, at 11:39 AM, Elaine Meng wrote:
Hi John, That is one of the major issues addressed in our next-generation program, ChimeraX.
ChimeraX is not yet publicly available, but we plan to make development daily builds available very soon (this month). However, it is in an early stage and lacks many features. It will take some time to become as functionally rich as Chimera, so how useful it will be for you depends on what types of structural analysis you wished to perform. If primarily viewing, it may already fill the bill. We envision people using both packages for a while, depending on their needs. You can get a feel for what ChimeraX can do now from the website and documentation linked below.
ChimeraX homepage http://www.rbvi.ucsf.edu/chimerax/index.html
Advantages shortlist http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html
User Guide http://www.rbvi.ucsf.edu/chimerax/docs/user/index.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 Dec 7, 2016, at 8:09 AM, John Mercer, Ph.D. jmercer@duke.edu wrote:
Hi All, Is there a way to usefully (and conveniently) view ribosomes recognizing that Chimera does not support large structure formats like mmcif? -John
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you Elaine. Look forward to trying it. Best, -John
On Dec 7, 2016, at 2:39 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi John, That is one of the major issues addressed in our next-generation program, ChimeraX.
ChimeraX is not yet publicly available, but we plan to make development daily builds available very soon (this month). However, it is in an early stage and lacks many features. It will take some time to become as functionally rich as Chimera, so how useful it will be for you depends on what types of structural analysis you wished to perform. If primarily viewing, it may already fill the bill. We envision people using both packages for a while, depending on their needs. You can get a feel for what ChimeraX can do now from the website and documentation linked below.
ChimeraX homepage <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimer... >
Advantages shortlist <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimer... >
User Guide <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimer... >
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 Dec 7, 2016, at 8:09 AM, John Mercer, Ph.D. jmercer@duke.edu wrote:
Hi All, Is there a way to usefully (and conveniently) view ribosomes recognizing that Chimera does not support large structure formats like mmcif? -John
participants (4)
-
Elaine Meng -
Jacqueline Vitali -
John Mercer, Ph.D. -
Tom Goddard