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I've scanned several ore deposits, and Thumped one or two, but I can never seem to get the scan percentage above ~50%. I gather that finding a deposit means I should attempt to find a more precise location with a higher percentage, but no matter how much I hammer the area, the highest I can get still seems to be ~50%.

How do I properly use the Scan Hammer to find a good place to Thump?

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After a few days of experimentation, this question should actually be split into two parts:

How do I properly use the Scan Hammer?

When you strike the ground with the Scan Hammer, it detects the mineral types directly under the point of impact. A box will pop up with the results of the scan, telling you what minerals a Thumper will extract from this point.

The Scan Hammer also sends seismic waves through the ground ahead of you, color-coded to the type of resource, with a height equivalent to the concentration.

There are certain regions which tend to hold one type of resource over another, but the best way to find out what's under your feet is to hop along, hammering as you go.

Why won't the percentage go much higher than 50%?

The maximum concentration of a resource deposit varies from vein to vein. Veins change at a regular interval, but it is very likely that the vein you're currently attempting to scan tops out at 50%.

If you put down a Thumper on an "only traces" area, the only thing it will pull up is Sifted Earth (which can be refined at the molecular printer). If the Thumper is on top of a resource deposit, a percentage of the haul will consist of the given resource. For example, calling down a Stock Personal Thumper on a spot with 50% Aluminum will return 125 Sifted Earth and 125 Aluminum on a full load. A full load also grants you a double resource bonus, so that topped off Stock Personal Thumper would actually net you 250 Sifted Earth and 250 Aluminum.

Since Thumpers attract a significant number of enemies, you can also collect lots of other resources, DNA, and parts as well.

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    It's worth nothing that the height of the (green) waveforms indicates resource concentration.
    – Ingmar
    Commented Mar 16, 2013 at 17:33
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Besides what's already been mentioned, the scan hammer will draw waves on the ground in front of you in roughly a 60 degree arc.

After scanning, you can scan and turn again, then repeat until you've done a complete circle.

This will not help you if you're very far away from the max for a given vein, but if you are, and the max isn't in some un-thumpable place (accord restricted zone, rock, etc), a peak will be obvious in the wave pattern.

This is also useful for seeing what areas are thump-able when you're near rocky areas, hills, others people thumping, etc.

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When you're not near the max, you generally just scan, move a bit in one direction, scan again and see if it's gone up ... if it has, then keep moving in that direction, scanning every so often until it goes down. Once you find the max in that axis, try going 90 degrees off of it, and see which direction it continues increasing.

Although there are occurances of 80+%, and I've seen a 100%, it's rare to get that high ... you're much more likely to top out in the 50-80% range. (note that this may change with the patch expected this week, as they change around resource distributions)

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You can download add-ons like peakseek triage and surveyor which helps with resource scan tracking.

I haven't used them myself but have seen videos of them and they look to be quite effective.

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