This does help, thank you! Mrinalini Ramanan https://www.thehonestrational.com On Wed, Mar 18, 2026, 6:30 PM Guillaume Gaullier < guillaume.gaullier@kemi.uu.se> wrote:
Based on this structure, to me what you describe as the cap going clockwise or counter clockwise indeed describes opposite hands. So, you need to determine which one is correct. If your complex is sufficiently close to PDB 5GAQ, you can simply try to fit this model in your map and test both hands of the map: the correct one will give a much better fit that the other. This is another quick way to check for correct chirality (faster than waiting for ModelAngelo to produce nonsensical output).
I hope this helps,
Guillaume
On 18/03/2026 18.07, Mrinalini Ramanan wrote:
Dear Guillaume,
Understood, did reply-all this time :)
Right so the visual of a related protein is included here in the email, but in case it is not displaying correctly: PDB 5GAQ
if it helps to visualize the stem and cap. The stems are aligned but the cap is going in different directions, and the question is whether this qualifies as having the same chiral center with different directionalities.
Thanks for the feedback and best regards,
Mrinalini
Mrinalini Ramanan https://www.thehonestrational.com <https://www.thehonestrational.com/>
On Wed, Mar 18, 2026, 5:42 PM Guillaume Gaullier <guillaume.gaullier@kemi.uu.se <mailto:guillaume.gaullier@kemi.uu.se>> wrote:
Hi Mrinalini,
Let's try to keep the list in CC, so the messages get archived and can help others. :-)
It is difficult to understand your message without a visual. I don't know what you mean by "the stems of the proteins". But whatever it is that is going clockwise or counterclockwise, the fact that you are using these terms suggests to me that you are seeing different chiralities.
I have seen it once that ab initio reconstruction followed by heterogeneous refinement produced classes of opposite chirality. This is indeed surprising, but not impossible if the starting 3D references have very low resolution (or are heavily low-pass filtered at the first iteration of the job). If you look at both maps side by side and they are mirror images of each other, then only one is a correct representation of your molecule: the one with right-handed alpha helices.
(Unless you happen to work on mirror proteins made of D-amino acids, and decided to collect cryoEM data on a mixture of natural and mirror protein; but that would be a poor choice of experimental design, as it would make the image processing intractable to assign the particles to their true class.)
Good luck with your project!
Guillaume
------------------------------------------------------------------------
*From:* Mrinalini Ramanan <mrinalini.ramanan@gmail.com <mailto:mrinalini.ramanan@gmail.com>> *Sent:* Wednesday, March 18, 2026 5:27:46 PM *To:* Guillaume Gaullier *Subject:* Re: [chimerax-users] Easier way to reverse direction of PDB file? Dear Guillaume,
Thanks for this quick yet thorough reply. Is it also possible to get maps with the wrong handedness if I have the main map going in a counterclockwise direction, and then maps from 3dva or 3d classes from this main map being in a clockwise direction? Only one of the classes is in a counterclockwise direction that matches the main map, the others are in a clockwise direction.
I guess my question is regarding directionalities vs. chiral center: can two different directions result from the same chiral center? I've done vop flip on the maps and lined them up so that the stems of the proteins are aligned (with fit #1 in #2, and some with emailing), but the resulting cap directions are clockwise / counterclockwise.
Thanks in advance for your help,
Mrinalini
Mrinalini Ramanan https://www.thehonestrational.com <
https://www.thehonestrational.com/>
On Wed, Mar 18, 2026, 4:54 PM Guillaume Gaullier <guillaume.gaullier@kemi.uu.se <mailto:guillaume.gaullier@kemi.uu.se>> wrote:
Hello Mrinalini,
When reconstructing a 3D volume from 2D projections in cryoEM image processing, there is a 50% probability of getting either chirality. It is relatively easy to visualize why if you cast shadows of your hands: you can easily make the shadow look the same with both your right and left hand as the object casting it, despite your two hands not being the same in 3D due to chirality.
But natural proteins only have L-amino acids, their alpha helices are right-handed, etc. So the correct solution in your case is not to build a model into a map of the wrong chirality, because the only way it would work in terms of stereo- chemistry would be with D-amino acids. You simply need to mirror the map.
In ChimeraX, assuming your map is loaded as model #1, this command will mirror it: volume flip #1
(The resulting mirrored map will only live in your ChimeraX session, so if you want to keep it, you need to save it as an MRC file.)
There is also a job to mirror a map in CryoSPARC, if this is the program you are using to process your data: https:// guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/ utilities/job-volume-tools <https://guide.cryosparc.com/ processing-data/all-job-types-in-cryosparc/utilities/job-volume- tools> (this is the option "flip handedness" in this job).
To tell chirality only from a map, in general, you need sufficient resolution to trace the backbone, and a protein containing alpha helices: then you can determine whether they are right-handed (the correct chirality) and invert the map if they are not. Some particles have chiral features that can be identified at much lower resolution (for example the super-helical turn of DNA around nucleosomes). But it is not always easy to tell depending on particle and resolution. If auto-building programs like ModelAngelo fail or produce many short disconnected fragments when applied to a good-looking map, this is often a sign of wrong chirality.
I hope this helps,
Guillaume
------------------------------------------------------------------------
*From:* Mrinalini Ramanan via ChimeraX-users <chimerax- users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> *Sent:* Wednesday, March 18, 2026 3:23:48 PM *To:* chimerax-users@cgl.ucsf.edu <mailto:chimerax- users@cgl.ucsf.edu> *Subject:* [chimerax-users] Easier way to reverse direction of PDB file? Dear Chimerax community,
I have a molecule that has a clockwise directionality for some cryoem maps, and a counter-clockwise directionality for some maps. I see this difference in directions even after fitting each map with the fit #1 in #2 command, and am now trying to build in each map. In order to create a PDB file with both directionalities, I used PyMol to do alter_state 1, obj, y = -y, rebuild, and then exported the new molecule. Is there a command in Chimera or Chimerax to do the same operations? I tried using matrix invert to no avail.
Sincerely,
Mrinalini __
VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.
__
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/ dataskydd-personuppgifter/ <http://www.uu.se/om-uu/dataskydd- personuppgifter/>
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection- policy <http://www.uu.se/en/about-uu/data-protection-policy>
__
VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.
VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy