I was looking into building a computer and I had a couple of questions. When plugging in fans for my case what do I plug them into the motherboard or the power supply. Secondly I am a little confused on 3 and 4 pin connectors. What is more common and what do I have to watch for when buying. Lastly I find that both my motherboard and power supply say nothing about having connectors for 3-4 pins unless they are called something different. BTW- this is my first build and I have not yet bought any of the things I need, I am just trying to know everything that might cause a problem to try to avoid it.
The 3 pin connectors on the fan go to the motherboards fan header, they give you the ability to control the speed of the fan. If the fan has a speed control built into it or you just want it to run at full speed you use a 4 pin(Molex) connector from the power supply, the same type that you use for IDE optical drives and hard drives. Use one or the other not both.
Actually, what you have is 3 and 4 pin fan headers and molex connectors:
3 pin fan: pins 1 -3 - Ground, 12 volt , and sense
4 pin fan: pins 1 - 4 - Ground, 12 volt ,sense, and control.
Molex connectors, by themselves, give you the possibility of two speeds:
full speed, default, 12 volts between black and yellow wires.
half speed by moving the black wire on the fan connector to mate up with the red wire on the power supply connector (puts 7 volts across the fan).
You probably have a 3 pin fan header plugged into the 4 pin CPU fan connector on the motherboard.
You can use either motherboard headers or molex for the fans.
Motherboard headers allow you to monitor the fans, while molex do not.
On the motherboard header the 4-pin is for PWM (Pulse Width Modulated).
4 pin connector enables fan speed control.
You can still use voltage control with the 3-pin motherboard connector to regulate the fan.
Both 3-pin and 4-pin systems allow two things involving the mobo: monitor the fan's speed (and also alarm if speed drops to zero), and control the fan's speed (done by BIOS, with options you set about how control is done). The difference between the two is in how power is fed to the fan for control purposes.
In a practical sense, boards with 4-pin connectors allow either type of fan to be connected and controlled. The connectors are made so that you cannot put them together wrong. In fact, I believe that the other way could be done - that is, plug a 4-pin fan connector into a 3-pin board connector - and still work OK. So you should have not problem there.
Many boards have up to 4 fan connection points. One always is the CPU cooler, and this MUST be used for that purpose - no other fan. The speed control function for this one is based on a temperature sensed within the CPU chip case. One MAY be labeled "PSU_FAN" or "Power Fan". Some power supplies have a special lead coming out with a fan connector on the end, and it goes to this mobo point. It does not involve control, but it allows the mobo to monitor the speed of the fan inside the PSU, and send out alarms if necessary if it fails. (Any control of the PSU fan is done within the PSU itself.) If your PSU does not have such a lead, simply don't use it. The mobo also will have one or two "SYS_FAN_" connectors that are used for case ventilation fans. Speed for these is based on temperature sensors built into the mobo.
Within the BIOS Setup screens there usually are places to customize how each fan is handled. Usually there's a place to set the option to ignore this fan's speed entirely (use if there is no fan attached) or display it. There's another place to set how control is done, with options like run full-speed (or some other reduced speed) all the time, or control the fan speed according to the temp sensor. If you are using temp-based control, sometimes there are settings for the details of how that is done. Some boards may allow you to customize the temperature at which it sets off an alarm, or takes protective action like slowing down the system or shutting down entirely. After assembly as you build, you should go into the BIOS Setup and check all these, changing settings as necessary. If you don't have a fan on a port, set it to Ignore. For example, I built a system recently with a PSU that had no fan speed monitor connection leads. When first booted, it sent out a piercing tone because the PSU Fan Monitor was set by default to send an alarm if the PSU fan was not turning, and the mobo had no signal on its connector to confirm fan operation there. I had to set that to Ignore.
If you have more than 2 case fans you have to power them from some source other than the mobo ports. This usually is done using one of the large 4-pin Molex connectors originally used for disk drives, etc. - your PSU usually has a few extra hanging around, or you can buy 2-from-1 splitters. Plug in directly and the fan will run full speed always. Some fans come with (or you can buy) simple speed controllers that allow you to set a fan to run slower that full speed at all times until you physically go into the case and change this control device. Although it might be possible to connect more than one fan to one of the mobo's SYS_FAN_ ports, it would take some skill and may risk damaging the mobo's fan controller system, so I don't recommend it.