I finally figured out how to get flexes to work properly with my modified model without messing up the vertices I changed. Since all my flexes were in the head region, what I did was I deleted all the vertices in the original model except the ones in the head, and then exported the SMD. This created a new VTA file, and in the QC of my modified model I used that new VTA file.

I also figured out that the pointy vertices are somehow caused by the flexes, because when I commented them out from the QC file the model looked correct even when the $Model was set to the modified SMD.

Thanks, I changed the $Model to be the original SMD, and set the $Sequence to the modified SMD, and now the model correctly has their arms lowered in SFM with no weird glitches.

Thanks, I looked at the bones in the SMD referenced in the $Sequence and they were in the T-pose. I replaced the SMD used in the $Sequence to be the modified SMD, and now the model's arms are lowered correctly in SFM. However there is still something wrong with the arms where some of the vertices seem to be pointing out slightly and making sharp pyramids.

There is a .vta file that has the same name as the main SMD, and seems to contain all the vertices used in all the SMDs. When I view those vertices in Blender none of them have the arms lowered, so could that be causing the pointy vertices in the modified model?

The QC file does not contain $DefineBone anywhere, and I did not change the SMD of the first $Sequence line. There is actually only one $Sequence, and it is called "ragdoll". The model does in fact have lots of flexes, and several $BodyGroup entries.

Could the other $BodyGroup entries be a problem, since they are all in the original Jesus pose?

Yeah, I remember now that I also added back the Armature modifier before exporting. I think my issue has something to do with the QC file, because when I import the modified SMD back into blender it looks correct with the arms lowered, but when I import the QC file that uses the modified SMD the model's skeleton has the arms lowered, but the pose has the arms in the original position.

The QC file has other bodygroups that come from different SMD files, so maybe the other SMDs that I haven't modified are causing the main SMD to get reverted?

I'm trying to modify an existing SFM model so its default pose is not the Jesus pose, but has their arms at their sides. What I tried is:

1.) Decompiled the model with Crowbar.
2.) Imported the model into Blender.
3.) Rotated the model's arms into the position I want.
4.) Created a duplicate object of the model's vertices.
5.) Deleted all the Shape Keys from the duplicate. I did this because otherwise it wouldn't let me apply the Armature modifier.
6.) Applied the Armature modifier on the duplicate.
7.) Set the Pose as the Rest Pose.
8.) Exported the duplicate model.
9.) Modified the model's QC file to use the SMD file of the duplicate.
10.) Compiled the model.

What I'm seeing in SFM when I load the modified model is that the arms are still in the Jesus pose, but there seems to be some strange wrinkling at the shoulders. Are there any other steps I need to do to modify the model the way I want?

The $scale command works great, thanks.

I have a model I want to use in SFM and I need to rescale it in Blender because it has jigglebones, which don't behave nicely when rescaled in SFM. The model consists of one armature and one mesh.

Here are the steps I tried in Blender to rescale the model, but the exported model looks wrong, specifically it seems to not get scaled in the Y direction, even though it looks correctly scaled in Blender. Are there any problems with these steps?

1.) Import the model into Blender.
2.) Unparent the armature from the mesh.
3.) Remove the armature modifier from the mesh.
4.) Rescale the armature and mesh the same amount.
5.) With the armature and mesh selected, press CTRL+A and select "Scale".
6.) Verify that the "Scale" transform for both the mesh and armature are all (1, 1, 1) when in Object Mode.
7.) Set the parent of the mesh to be the armature.
8.) Re-add the armature modifier to the mesh.
9.) Export the model.

I figured out the problem. I was trying to use jiggle bones with the model, and didn't have a jiggle bone for the highest bone in the hierarchy that I rotated. This caused that bone to not appear rotated when viewed in the Source viewer, which might be a bug in itself but I can work around it. After I added a jiggle bone for that bone in my QC file the model looked correct in the Source viewer.

Thanks for your help guys.